From 31cdefe420fe84d3c6264eebdf65e4aaa9100dc2 Mon Sep 17 00:00:00 2001 From: Julian Mueller Date: Thu, 16 Jul 2020 13:57:19 +0200 Subject: [PATCH 1/8] Implement parsing of MGF files that contain ion names --- pyteomics/auxiliary/__init__.py | 2 +- pyteomics/auxiliary/file_helpers.py | 4 +- pyteomics/auxiliary/structures.py | 14 +++++ pyteomics/mgf.py | 88 ++++++++++++++++++++++------- 4 files changed, 84 insertions(+), 24 deletions(-) diff --git a/pyteomics/auxiliary/__init__.py b/pyteomics/auxiliary/__init__.py index c2d03ef3..67931f72 100644 --- a/pyteomics/auxiliary/__init__.py +++ b/pyteomics/auxiliary/__init__.py @@ -7,7 +7,7 @@ from .structures import ( PyteomicsError, Charge, ChargeList, - _parse_charge, BasicComposition, + _parse_charge, _parse_ion, BasicComposition, unitfloat, unitint, unitstr, cvstr, cvquery) diff --git a/pyteomics/auxiliary/file_helpers.py b/pyteomics/auxiliary/file_helpers.py index bafcc181..b2103b1a 100644 --- a/pyteomics/auxiliary/file_helpers.py +++ b/pyteomics/auxiliary/file_helpers.py @@ -244,11 +244,11 @@ def get_by_id(self, elem_id): index = self.default_index if index is None: raise PyteomicsError('Access by ID requires building an offset index.') - offsets = index[elem_id] + offsets = index[str(elem_id)] return self._item_from_offsets(offsets) def get_by_ids(self, ids): - return [self.get_by_id(key) for key in ids] + return [self.get_by_id(str(key)) for key in ids] def get_by_index(self, i): try: diff --git a/pyteomics/auxiliary/structures.py b/pyteomics/auxiliary/structures.py index fe20567d..c6f801f5 100644 --- a/pyteomics/auxiliary/structures.py +++ b/pyteomics/auxiliary/structures.py @@ -82,6 +82,15 @@ def __new__(cls, *args, **kwargs): def __str__(self): return str(abs(self)) + '+-'[self < 0] +class Ion(str): + """Represents an Ion, right now just a subclass of String. + """ + def __init__(self, *args, **kwargs): + if args and isinstance(args[0], basestring): + try: + self.ion_type, self.neutral_loss, self.charge = re.match(r'([abcxyz]\d+(\-H2O|\-NH3)?)([\+|-]\d+)', args[0]).groups() #"y2-H2O+1" + except Exception as e: + raise PyteomicsError("Malformed ion string, must match the regex r'([abcxyz]\d+(\-H2O|\-NH3)?)([\+|-]\d+)'") class ChargeList(list): """Just a list of :py:class:`Charge`s. When printed, looks like an @@ -117,6 +126,11 @@ def _parse_charge(s, list_only=False): pass return ChargeList(s) +def _parse_ion(ion_text): + try: + return Ion(ion_text) + except Exception as e: + print(e) class BasicComposition(defaultdict, Counter): """A generic dictionary for compositions. diff --git a/pyteomics/mgf.py b/pyteomics/mgf.py index 9339cedd..585217df 100644 --- a/pyteomics/mgf.py +++ b/pyteomics/mgf.py @@ -84,10 +84,11 @@ class MGFBase(object): _array_converters = { 'm/z array': [_identity, _array, _array], 'intensity array': [_identity, _array, _array], - 'charge array': [_identity, _array, _ma] + 'charge array': [_identity, _array, _ma], + 'ion array': [_identity, _array, _array] } - _array_keys = ['m/z array', 'intensity array', 'charge array'] - _array_keys_unicode = [u'm/z array', u'intensity array', u'charge array'] + _array_keys = ['m/z array', 'intensity array', 'charge array', 'ion array'] + _array_keys_unicode = [u'm/z array', u'intensity array', u'charge array', u'ion array'] encoding = None @@ -107,7 +108,7 @@ def __init__(self, source=None, **kwargs): Default is :py:const:`True`. convert_arrays : one of {0, 1, 2}, optional, keyword only - If `0`, m/z, intensities and (possibly) charges will be returned as regular lists. + If `0`, m/z, intensities and (possibly) charges or (possibly) ions will be returned as regular lists If `1`, they will be converted to regular :py:class:`numpy.ndarray`'s. If `2`, charges will be reported as a masked array (default). The default option is the slowest. `1` and `2` require :py:mod:`numpy`. @@ -115,9 +116,13 @@ def __init__(self, source=None, **kwargs): read_charges : bool, optional, keyword only If `True` (default), fragment charges are reported. Disabling it improves performance. + read_ions : bool, optional + If `True` (default: False), fragment ions are reported. Disabling it improves performance. + Note that right now, only one of (read_charges, read_ions) may be True. + dtype : type or str or dict, optional, keyword only dtype argument to :py:mod:`numpy` array constructor, one for all arrays or one for each key. - Keys should be 'm/z array', 'intensity array' and/or 'charge array'. + Keys should be 'm/z array', 'intensity array', 'charge array' and/or 'ion array'. encoding : str, optional, keyword only File encoding. @@ -129,6 +134,10 @@ def __init__(self, source=None, **kwargs): if self._convert_arrays and np is None: raise aux.PyteomicsError('numpy is required for array conversion') self._read_charges = kwargs.pop('read_charges', True) + self._read_ions = kwargs.pop('read_ions', False) + #Make sure no charges are read if ions are read + if self._read_ions: + self._read_charges = False dtype = kwargs.pop('dtype', None) self._dtype_dict = dtype if isinstance(dtype, dict) else {k: dtype for k in self._array_keys} if self._use_header: @@ -136,12 +145,16 @@ def __init__(self, source=None, **kwargs): else: self._header = None + def parse_precursor_charge(self, charge_text, list_only=False): return aux._parse_charge(charge_text, list_only=list_only) def parse_peak_charge(self, charge_text, list_only=False): return aux._parse_charge(charge_text, list_only=False) + def parse_peak_ion(self, ion_text): + return aux._parse_ion(ion_text) + @property def header(self): if self._header is None: @@ -173,6 +186,7 @@ def _read_spectrum_lines(self, lines): masses = [] intensities = [] charges = [] + ions = [] params = self.header.copy() if self._use_header else {} @@ -202,6 +216,8 @@ def _read_spectrum_lines(self, lines): data = {'m/z array': masses, 'intensity array': intensities} if self._read_charges: data['charge array'] = charges + if self._read_ions: + data['ion array'] = ions for key, values in data.items(): out[key] = self._array_converters[key][self._convert_arrays](values, dtype=self._dtype_dict.get(key)) if self.encoding and sys.version_info.major == 2: @@ -221,6 +237,8 @@ def _read_spectrum_lines(self, lines): intensities.append(float(l[1])) if self._read_charges: charges.append(self.parse_peak_charge(l[2]) if len(l) > 2 else 0) + if self._read_ions: + ions.append(self.parse_peak_ion(l[2]) if len(l) > 2 else "") except ValueError: raise aux.PyteomicsError( 'Error when parsing %s. Line:\n%s' % (getattr(self._source, 'name', 'MGF file'), line)) @@ -238,10 +256,11 @@ class IndexedMGF(MGFBase, aux.TaskMappingMixin, aux.TimeOrderedIndexedReaderMixi If created using a file object, it needs to be opened in binary mode. When iterated, :py:class:`IndexedMGF` object yields spectra one by one. - Each 'spectrum' is a :py:class:`dict` with four keys: 'm/z array', - 'intensity array', 'charge array' and 'params'. 'm/z array' and + Each 'spectrum' is a :py:class:`dict` with five keys: 'm/z array', + 'intensity array', 'charge array', 'ion array' and 'params'. 'm/z array' and 'intensity array' store :py:class:`numpy.ndarray`'s of floats, 'charge array' is a masked array (:py:class:`numpy.ma.MaskedArray`) of ints, + 'ion_array' is an array of Ions (str) and 'params' stores a :py:class:`dict` of parameters (keys and values are :py:class:`str`, keys corresponding to MGF, lowercased). @@ -254,20 +273,21 @@ class IndexedMGF(MGFBase, aux.TaskMappingMixin, aux.TimeOrderedIndexedReaderMixi time : RTLocator A property used for accessing spectra by retention time. """ - delimiter = 'BEGIN IONS' - label = r'TITLE=([^\n]*\S)\s*' + + - def __init__(self, source=None, use_header=True, convert_arrays=2, read_charges=True, - dtype=None, encoding='utf-8', _skip_index=False, **kwargs): + def __init__(self, source=None, use_header=True, convert_arrays=2, read_charges=True, + read_ions=False, dtype=None, encoding='utf-8', index_by_scans=False, _skip_index=False, **kwargs): + self.label = r'SCANS=(\d+)\s*' if index_by_scans else r'TITLE=([^\n]*\S)\s*' super(IndexedMGF, self).__init__(source, parser_func=self._read, pass_file=False, args=(), kwargs={}, use_header=use_header, convert_arrays=convert_arrays, read_charges=read_charges, - dtype=dtype, encoding=encoding, _skip_index=_skip_index, **kwargs) + read_ions=read_ions, dtype=dtype, encoding=encoding, _skip_index=_skip_index, **kwargs) def __reduce_ex__(self, protocol): return (self.__class__, (self._source_init, False, self._convert_arrays, self._read_charges, - self._dtype_dict, self.encoding, True), + self._read_ions, self._dtype_dict, self.encoding, True), self.__getstate__()) def __getstate__(self): @@ -301,7 +321,7 @@ def _read(self, **kwargs): yield spectrum def get_spectrum(self, key): - return self.get_by_id(key) + return self.get_by_id(str(key)) def _get_time(self, spectrum): try: @@ -318,10 +338,11 @@ class MGF(MGFBase, aux.FileReader): constant-time access to spectra. :py:class:`MGF` object behaves as an iterator, **yielding** spectra one by one. - Each 'spectrum' is a :py:class:`dict` with four keys: 'm/z array', - 'intensity array', 'charge array' and 'params'. 'm/z array' and + Each 'spectrum' is a :py:class:`dict` with five keys: 'm/z array', + 'intensity array', 'charge array', 'ion array' and 'params'. 'm/z array' and 'intensity array' store :py:class:`numpy.ndarray`'s of floats, 'charge array' is a masked array (:py:class:`numpy.ma.MaskedArray`) of ints, + 'ion_array' is a masked array of Ions (str) and 'params' stores a :py:class:`dict` of parameters (keys and values are :py:class:`str`, keys corresponding to MGF, lowercased). @@ -334,9 +355,10 @@ class MGF(MGFBase, aux.FileReader): """ def __init__(self, source=None, use_header=True, convert_arrays=2, read_charges=True, - dtype=None, encoding=None): + read_ions=False, dtype=None, encoding=None): super(MGF, self).__init__(source, mode='r', parser_func=self._read, pass_file=False, args=(), kwargs={}, - encoding=encoding, use_header=use_header, convert_arrays=convert_arrays, read_charges=read_charges, dtype=dtype) + encoding=encoding, use_header=use_header, convert_arrays=convert_arrays, read_charges=read_charges, + read_ions=read_ions, dtype=dtype) # self.encoding = encoding @aux._keepstate_method @@ -360,6 +382,16 @@ def get_spectrum(self, title): spectrum['params']['title'] = title return spectrum +#TODO DELETE BEFORE COMMIT + # @aux._keepstate_method + # def get_spectrum_by_scan(self, scan): + # for line in self._source: + # sline = line.strip() + # if sline[:5] == 'SCANS' and sline.split('=', 1)[1].strip() == str(scan): + # spectrum = self._read_spectrum() + # #spectrum['params']['scans'] = scan + # return spectrum + def __getitem__(self, key): return self.get_spectrum(key) @@ -391,9 +423,13 @@ def read(*args, **kwargs): read_charges : bool, optional If `True` (default), fragment charges are reported. Disabling it improves performance. + read_ions : bool, optional + If `True` (default: False), fragment charges are reported. Disabling it improves performance. + Note that right now, only one of (read_charges, read_ions) may be True. + dtype : type or str or dict, optional dtype argument to :py:mod:`numpy` array constructor, one for all arrays or one for each key. - Keys should be 'm/z array', 'intensity array' and/or 'charge array'. + Keys should be 'm/z array', 'intensity array', 'charge array' and/or 'ion array'. encoding : str, optional File encoding. @@ -510,7 +546,7 @@ def _default_repr(key, val): @aux._file_writer() def write(spectra, output=None, header='', key_order=_default_key_order, - fragment_format=None, write_charges=True, use_numpy=None, + fragment_format=None, write_charges=True, write_ions=False, use_numpy=None, param_formatters=_default_value_formatters): """ Create a file in MGF format. @@ -547,6 +583,10 @@ def write(spectra, output=None, header='', key_order=_default_key_order, If :py:const:`False`, fragment charges from 'charge array' will not be written. Default is :py:const:`True`. + write_ions : bool, optional + If :py:const:`False`, fragment ions from 'ion array' will not be written. + Default is :py:const:`False`. + fragment_format : str, optional Format string for m/z, intensity and charge of a fragment. Useful to set the number of decimal places, e.g.: @@ -649,7 +689,7 @@ def key_value_line(key, val): try: success = True if np is not None and use_numpy: - if not write_charges or 'charge array' not in spectrum: + if (not write_charges or 'charge array' not in spectrum) and (not write_ions or 'ion array' not in spectrum): X = np.empty((len(spectrum['m/z array']), 2)) X[:, 0] = spectrum['m/z array'] X[:, 1] = spectrum['intensity array'] @@ -660,6 +700,12 @@ def key_value_line(key, val): X[:, 1] = spectrum['intensity array'] X[:, 2] = spectrum['charge array'] np.savetxt(output, X, fmt=np_format_3) + elif isinstance(spectrum.get('ion array'), np.ndarray): + X = np.empty((len(spectrum['m/z array']), 3), dtype=object) + X[:, 0] = spectrum['m/z array'] + X[:, 1] = spectrum['intensity array'] + X[:, 2] = spectrum['ion array'] + np.savetxt(output, X, fmt=np_format_3) else: success = False else: From a056a57ea779046016601fea41aa35ebed598f6d Mon Sep 17 00:00:00 2001 From: Julian Mueller Date: Thu, 8 Oct 2020 09:15:10 +0200 Subject: [PATCH 2/8] Delete deprecated code --- pyteomics/mgf.py | 10 ---------- 1 file changed, 10 deletions(-) mode change 100644 => 100755 pyteomics/mgf.py diff --git a/pyteomics/mgf.py b/pyteomics/mgf.py old mode 100644 new mode 100755 index 585217df..bb8268d8 --- a/pyteomics/mgf.py +++ b/pyteomics/mgf.py @@ -382,16 +382,6 @@ def get_spectrum(self, title): spectrum['params']['title'] = title return spectrum -#TODO DELETE BEFORE COMMIT - # @aux._keepstate_method - # def get_spectrum_by_scan(self, scan): - # for line in self._source: - # sline = line.strip() - # if sline[:5] == 'SCANS' and sline.split('=', 1)[1].strip() == str(scan): - # spectrum = self._read_spectrum() - # #spectrum['params']['scans'] = scan - # return spectrum - def __getitem__(self, key): return self.get_spectrum(key) From 0e1699e62db8c709060d9590127912c7488e48c4 Mon Sep 17 00:00:00 2001 From: Julian Mueller Date: Fri, 9 Oct 2020 10:20:59 +0200 Subject: [PATCH 3/8] Add tests for annotated mgf --- tests/data.py | 5292 +++++++++++++++++++++----------------- tests/test_annotated.mgf | 31 + tests/test_mgf.py | 31 +- 3 files changed, 2954 insertions(+), 2400 deletions(-) mode change 100644 => 100755 tests/data.py create mode 100644 tests/test_annotated.mgf mode change 100644 => 100755 tests/test_mgf.py diff --git a/tests/data.py b/tests/data.py old mode 100644 new mode 100755 index 956b2376..90450444 --- a/tests/data.py +++ b/tests/data.py @@ -24,1306 +24,1389 @@ def makeCA(arr): pepxml_results = [ - {'spectrum': 'pps_sl20060731_18mix_25ul_r1_1154456409.0100.0100.1', - 'end_scan': 100, - 'start_scan': 100, - 'index': 1, - 'assumed_charge': 1, - 'precursor_neutral_mass': 860.392, - 'search_hit': [{ - 'num_missed_cleavages': 0, - 'tot_num_ions': 12, - 'is_rejected': False, - 'search_score': { - 'deltacn': 0.081, - 'sprank': 1.0, - 'deltacnstar': 0.0, - 'spscore': 894.0, - 'xcorr': 1.553}, - 'hit_rank': 1, - 'num_matched_ions': 11, - 'num_tot_proteins': 1, - 'peptide': 'SLNGEWR', - 'massdiff': -0.5, - 'analysis_result': [{'analysis': 'peptideprophet', - 'peptideprophet_result': - {'all_ntt_prob': [0.0422, 0.509, 0.96], - 'parameter': - {'fval': 1.4723, 'massd': -0.5, 'nmc': 0.0, 'ntt': 2.0}, - 'probability': 0.96}}], - 'modifications': [], - 'modified_peptide': 'SLNGEWR', - 'proteins': [{'num_tol_term': 2, - 'protein': 'sp|P00722|BGAL_ECOLI', - 'peptide_prev_aa': 'R', - 'protein_descr': 'BETA-GALACTOSIDASE (EC 3.2.1.23) ' - '(LACTASE) - Escherichia coli.', - 'peptide_next_aa': 'F'}], - 'calc_neutral_pep_mass': 860.892}]}, - {'precursor_neutral_mass': 677.392, - 'spectrum': 'pps_sl20060731_18mix_25ul_r1_1154456409.0040.0040.1', - 'start_scan': 40, - 'assumed_charge': 1, - 'index': 2, - 'end_scan': 40, - 'search_hit': [{'tot_num_ions': 10, - 'num_missed_cleavages': 1, - 'is_rejected': False, - 'hit_rank': 1, - 'num_matched_ions': 8, - 'search_score': { - 'sprank': 1.0, - 'deltacn': 0.165, - 'deltacnstar': 0.0, - 'spscore': 427.0, - 'xcorr': 1.644}, - 'num_tot_proteins': 1, - 'peptide': 'GKKFAK', - 'massdiff': -0.5, - 'analysis_result': [{'analysis': 'peptideprophet', - 'peptideprophet_result': { - 'all_ntt_prob': [0.0491, 0.548, 0.9656], - 'parameter': { - 'fval': 2.0779, 'massd': -0.5, 'nmc': 1.0, 'ntt': 1.0}, - 'probability': 0.548}}], - 'modifications': [], - 'modified_peptide': 'GKKFAK', - 'proteins': [{'num_tol_term': 1, - 'protein': 'gi|3212198|gb|AAC22319.1|', - 'peptide_prev_aa': 'N', - 'protein_descr': 'hemoglobin-binding protein ' - '[Haemophilus influenzae Rd]', - 'peptide_next_aa': 'I'}], - 'calc_neutral_pep_mass': 677.892}]}, - {'assumed_charge': 2, - 'end_scan': 1366, - 'index': 29, - 'precursor_neutral_mass': 718.4136, - 'retention_time_sec': 38.426123, - 'search_hit': [{'calc_neutral_pep_mass': 718.4126, - 'search_score': { - 'expect': 0.0, - 'homologyscore': 46.61, - 'identityscore': 25.38, - 'star': 0.0, - 'ionscore': 36.45}, - 'hit_rank': 1, - 'is_rejected': False, - 'massdiff': 0.0011, - 'modifications': [], - 'modified_peptide': 'VGQFIR', - 'num_matched_ions': 5, - 'num_missed_cleavages': 0, - 'num_tot_proteins': 1, - 'peptide': 'VGQFIR', - 'analysis_result': [{'analysis': 'peptideprophet', - 'peptideprophet_result': - {'all_ntt_prob': [0., 0.5741, 0.7264], - 'parameter': { - 'fval': 0.6052, 'massd': 0.001, 'nmc': 0.0, 'ntt': 2.0}, - 'probability': 0.7264}}], - 'proteins': [{'num_tol_term': 2, - 'peptide_next_aa': 'L', - 'peptide_prev_aa': 'K', - 'protein': 'IPI00200898', - 'protein_descr': None}], - 'tot_num_ions': 10}], - 'spectrum': 'MASCOT', - 'start_scan': 1366}, - {'assumed_charge': 2, - 'end_scan': 6862, - 'index': 49, - 'precursor_neutral_mass': 1404.7476, - 'search_hit': [{'search_score': { - 'bscore': 2.0, - 'expect': 0.012, - 'nextscore': 14.6, - 'hyperscore': 23.5, - 'yscore': 8.7}, - 'calc_neutral_pep_mass': 1404.7435, - 'hit_rank': 1, - 'is_rejected': False, - 'massdiff': 0.004, - 'modifications': [{'mass': 1.0079, 'position': 0}, - {'mass': 147.0354, 'position': 10}, - {'mass': 17.0031, 'position': 13}], - 'modified_peptide': 'EVPLNTIIFM[147]GR', - 'num_matched_ions': 8, - 'num_missed_cleavages': 0, - 'num_tot_proteins': 2, - 'peptide': 'EVPLNTIIFMGR', - 'proteins': [{'num_tol_term': 2, - 'peptide_next_aa': 'V', - 'peptide_prev_aa': 'R', - 'protein': 'sp|P01008|ANT3_HUMAN', - 'protein_descr': 'Antithrombin-III OS=Homo sapiens GN=SERPINC1 PE=1 SV=1'}, - {'num_tol_term': 2, 'protein': 'tr|Q8TCE1|Q8TCE1_HUMAN', 'protein_descr': 'SERPINC1 protein OS=Homo sapiens GN=SERPINC1 PE=2 SV=1'}], - 'tot_num_ions': 22}], - 'spectrum': 'X!Tandem', - 'start_scan': 6862}, - {'assumed_charge': 3, - 'end_scan': 23, - 'index': 3, - 'precursor_neutral_mass': 3254.044921875, - 'search_hit': [{'calc_neutral_pep_mass': 3254.04711914062, - 'search_score': { - 'expect': 13690.946579388728, - 'pvalue': 59.52585469299447}, - 'hit_rank': 1, - 'is_rejected': False, - 'massdiff': -0.002197265625, - 'modifications': [{'mass': 166.99803, 'position': 6}, - {'mass': 166.99803, 'position': 7}, - {'mass': 166.99803, 'position': 9}, - {'mass': 160.03019, 'position': 15}, - {'mass': 160.03019, 'position': 21}], - 'modified_peptide': 'DQQFDS[166]S[166]SS[166]MALEDCGEETNCQSDFK', - 'num_matched_ions': 3, - 'num_tot_proteins': 1, - 'peptide': 'DQQFDSSSSMALEDCGEETNCQSDFK', - 'proteins': [{'num_tol_term': 0, - 'peptide_next_aa': 'I', - 'peptide_prev_aa': 'R', - 'protein': 'BL_ORD_ID:125453', - 'protein_descr': 'sp|O43149|ZZEF1_HUMAN Zinc finger ZZ-type and EF-hand domain-containing protein 1 OS=Homo sapiens GN=ZZEF1 PE=1 SV=6:reversed'}], - 'tot_num_ions': 50}, - {'calc_neutral_pep_mass': 3254.04711914062, - 'search_score': {'expect': 14837.682803311733, - 'pvalue': 64.51166436222492}, - 'hit_rank': 2, - 'is_rejected': False, - 'massdiff': -0.002197265625, - 'modifications': [{'mass': 243.02933, 'position': 6}, - {'mass': 170.10596, 'position': 8}, - {'mass': 181.01368, 'position': 11}, - {'mass': 181.01368, 'position': 13}, - {'mass': 181.01368, 'position': 18}, - {'mass': 181.01368, 'position': 21}, - {'mass': 160.03019, 'position': 1}, - {'mass': 160.03019, 'position': 4}], - 'modified_peptide': 'CENCNY[243]PK[170]EGT[181]HT[181]NQHET[181]LHT[181]SR', - 'num_matched_ions': 6, - 'num_tot_proteins': 2, - 'peptide': 'CENCNYPKEGTHTNQHETLHTSR', - 'proteins': [{'num_tol_term': 0, - 'peptide_next_aa': 'S', - 'peptide_prev_aa': 'R', - 'protein': 'BL_ORD_ID:144314', - 'protein_descr': 'tr|Q6ZND3|Q6ZND3_HUMAN Zinc finger protein 184 OS=Homo sapiens GN=ZNF184 PE=2 SV=1:reversed'}, - {'protein': 'BL_ORD_ID:154629', 'protein_descr': 'sp|Q99676|ZN184_HUMAN Zinc finger protein 184 OS=Homo sapiens GN=ZNF184 PE=1 SV=4:reversed'}], - 'tot_num_ions': 44}], - 'spectrum': ' Cmpd 24, +MSn(1085.6886), 1.2 min.23.23.3', - 'start_scan': 23}] + {'spectrum': 'pps_sl20060731_18mix_25ul_r1_1154456409.0100.0100.1', + 'end_scan': 100, + 'start_scan': 100, + 'index': 1, + 'assumed_charge': 1, + 'precursor_neutral_mass': 860.392, + 'search_hit': [{ + 'num_missed_cleavages': 0, + 'tot_num_ions': 12, + 'is_rejected': False, + 'search_score': { + 'deltacn': 0.081, + 'sprank': 1.0, + 'deltacnstar': 0.0, + 'spscore': 894.0, + 'xcorr': 1.553}, + 'hit_rank': 1, + 'num_matched_ions': 11, + 'num_tot_proteins': 1, + 'peptide': 'SLNGEWR', + 'massdiff': -0.5, + 'analysis_result': [{'analysis': 'peptideprophet', + 'peptideprophet_result': + {'all_ntt_prob': [0.0422, 0.509, 0.96], + 'parameter': + {'fval': 1.4723, 'massd': -0.5, 'nmc': 0.0, 'ntt': 2.0}, + 'probability': 0.96}}], + 'modifications': [], + 'modified_peptide': 'SLNGEWR', + 'proteins': [{'num_tol_term': 2, + 'protein': 'sp|P00722|BGAL_ECOLI', + 'peptide_prev_aa': 'R', + 'protein_descr': 'BETA-GALACTOSIDASE (EC 3.2.1.23) ' + '(LACTASE) - Escherichia coli.', + 'peptide_next_aa': 'F'}], + 'calc_neutral_pep_mass': 860.892}]}, + {'precursor_neutral_mass': 677.392, + 'spectrum': 'pps_sl20060731_18mix_25ul_r1_1154456409.0040.0040.1', + 'start_scan': 40, + 'assumed_charge': 1, + 'index': 2, + 'end_scan': 40, + 'search_hit': [{'tot_num_ions': 10, + 'num_missed_cleavages': 1, + 'is_rejected': False, + 'hit_rank': 1, + 'num_matched_ions': 8, + 'search_score': { + 'sprank': 1.0, + 'deltacn': 0.165, + 'deltacnstar': 0.0, + 'spscore': 427.0, + 'xcorr': 1.644}, + 'num_tot_proteins': 1, + 'peptide': 'GKKFAK', + 'massdiff': -0.5, + 'analysis_result': [{'analysis': 'peptideprophet', + 'peptideprophet_result': { + 'all_ntt_prob': [0.0491, 0.548, 0.9656], + 'parameter': { + 'fval': 2.0779, 'massd': -0.5, 'nmc': 1.0, 'ntt': 1.0}, + 'probability': 0.548}}], + 'modifications': [], + 'modified_peptide': 'GKKFAK', + 'proteins': [{'num_tol_term': 1, + 'protein': 'gi|3212198|gb|AAC22319.1|', + 'peptide_prev_aa': 'N', + 'protein_descr': 'hemoglobin-binding protein ' + '[Haemophilus influenzae Rd]', + 'peptide_next_aa': 'I'}], + 'calc_neutral_pep_mass': 677.892}]}, + {'assumed_charge': 2, + 'end_scan': 1366, + 'index': 29, + 'precursor_neutral_mass': 718.4136, + 'retention_time_sec': 38.426123, + 'search_hit': [{'calc_neutral_pep_mass': 718.4126, + 'search_score': { + 'expect': 0.0, + 'homologyscore': 46.61, + 'identityscore': 25.38, + 'star': 0.0, + 'ionscore': 36.45}, + 'hit_rank': 1, + 'is_rejected': False, + 'massdiff': 0.0011, + 'modifications': [], + 'modified_peptide': 'VGQFIR', + 'num_matched_ions': 5, + 'num_missed_cleavages': 0, + 'num_tot_proteins': 1, + 'peptide': 'VGQFIR', + 'analysis_result': [{'analysis': 'peptideprophet', + 'peptideprophet_result': + {'all_ntt_prob': [0., 0.5741, 0.7264], + 'parameter': { + 'fval': 0.6052, 'massd': 0.001, 'nmc': 0.0, 'ntt': 2.0}, + 'probability': 0.7264}}], + 'proteins': [{'num_tol_term': 2, + 'peptide_next_aa': 'L', + 'peptide_prev_aa': 'K', + 'protein': 'IPI00200898', + 'protein_descr': None}], + 'tot_num_ions': 10}], + 'spectrum': 'MASCOT', + 'start_scan': 1366}, + {'assumed_charge': 2, + 'end_scan': 6862, + 'index': 49, + 'precursor_neutral_mass': 1404.7476, + 'search_hit': [{'search_score': { + 'bscore': 2.0, + 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description': '>IPI:IPI00554648.1|SWISS-PROT:P05787 Tax_Id=9606 Keratin, type II cytoskeletal 8', - 'releaseDate': '2006-02-22T09:30:47Z', - 'start': 23, - 'version': '3.15'}], - 'PeptideSequence': 'SYTSGPGSR', - 'ProteinScape:IntensityCoverage': 0.39717937427768873, - 'ProteinScape:SequestMetaScore': 4.159878401845841, - 'calculatedMassToCharge': 911.4144, - 'chargeState': 1, - 'experimentalMassToCharge': 911.415, - 'passThreshold': True, - 'rank': 1}, - {'Modification': [{'location': 10, "name": "Oxidation"}], - 'PeptideEvidenceRef': [{'DatabaseName': {'database IPI_human': ''}, - 'Modification': [{'location': 10, "name": "Oxidation"}], - 'PeptideSequence': 'YHTSQSGDEMTSLSEYVSR', - 'Seq': 'PEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASRMEEVD', - 'accession': 'IPI00414676.5', - 'decoy DB accession regexp': '^SHD', - 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', - 'end': 474, - 'isDecoy': False, - 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', - "decoy DB from IPI_human": '', "DB composition target+decoy": '', "decoy DB type shuffle": '', - 'numDatabaseSequences': 58099, - 'post': 'M', - 'pre': 'R', - 'protein description': '>IPI:IPI00414676.5|SWISS-PROT:P08238|TREMBL:Q5T9W7;Q6PK50;Q9H6X9|ENSEMBL:ENSP00000325875|REFSEQ:NP_031381|H-INV:HIT000008644;HIT000032091;HIT000034201;HIT000035963;HIT000036733;HIT000049765;HIT000057726|VEGA:OTTHUMP00000016517;OTTHUMP00000016518;OTTHUMP00000016519 Tax_Id=9606 Heat shock protein HSP 90-beta', - 'releaseDate': '2006-02-22T09:30:47Z', - 'start': 456, - 'version': '3.15'}], - 'PeptideSequence': 'YHTSQSGDEMTSLSEYVSR', - 'ProteinScape:IntensityCoverage': 0.136423966822031, - 'ProteinScape:SequestMetaScore': 5.725397508852668, - 'calculatedMassToCharge': 2192.932715, - 'chargeState': 1, - 'experimentalMassToCharge': 2192.9, - 'passThreshold': True, - 'rank': 2}], - 'location': 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'YQQKTRHDAFPRIQLALRAGAKSKEDLFSEPKLYEDKEQRISSELPEEALDDSSPSDTSLIAVEREISSNLRHSSTNYEEHLRKLKKDKYSEAVDPSGKPLGLLVILGNQYMREDEIATEERMPENKSTDISTYIKEFDGKEIAFPTENSYFPARGDKSKAVTAKWKRFTPFPLQTDDNSAAKLTEVFKIQLTTVGKLGKCSEGGENKEDKCTDNLCLNPPDELTEHREAPVTDTKPIMPEQIIITTKEISDSQLENRDETAPIALDLIALVSVNSLTGETNRKMEEYKSKKRRTTRLEETGFHILHNREVNMDNGECVFPIHYDAAQEMQPHTDSSKVMKASEFQKDIILMELIEKFDHNVKLLSKDCVEVQNSMANLELDKESEEQAVGDGSCLTRGTLVIKAQNGKNTGENDSTKETREYLRKKMDEAEDYGLVLKDDTYIEVWDVAVQITYLLKRSIEWPESECIDIEPFVHKAKSYINVEKETESHKLVQHKYKCRPLFRGENKDVTKRLLYGKILLEDKLSSASGLKSTELWDLDEDYEVTWRQEILLNKNKKVAPDEKETYIVLQNNLYPMQPVVMPSIPARMMSLENDILKMPIAAVRVKVVDITINKFLMGEINADDMEFPTSGFLEQHSDFGGLANGESQNDKPTEGQAREIEPIAKEEYVIDLEWGLRITQPTSEYGYDGELVVYVTKGMGKQTEPESLSYVCVVEGFAKAQLPERQITGKEDSGFIRRQQRLLEDDFSMKKKIFEGLDPILSEKKLDMQFRKFSMKWQYLKDILPADFDKEKEIFREFHKIEIKVSFGHKGMESKAALYIKFYETFERELKQFLSAEPRYRDDACEGLQLEV', - 'accession': 'SHD00382470.3', - 'decoy DB accession regexp': '^SHD', - 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', - 'end': 191, - 'isDecoy': True, - 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', - "decoy DB from IPI_human": '', "DB composition target+decoy": '', "decoy DB type shuffle": '', - 'numDatabaseSequences': 58099, - 'post': 'V', - 'pre': 'L', - 'protein description': '>SHD:SHD00382470.3|SWISS-PROT:P07900-2|TREMBL:Q86SX1|ENSEMBL:ENSP00000335153|REFSEQ:NP_001017963|VEGA:OTTHUMP00000041671 Tax_Id=9606 Gene_Symbol=HSP90AA1 heat shock protein 90kDa alpha (cytosolic), class A member 1 isoform 1', - 'releaseDate': '2006-02-22T09:30:47Z', - 'start': 183, - 'version': '3.15'}], - 'PeptideSequence': 'ENDILKMPIAAVR', - 'ProteinScape:IntensityCoverage': 0.2854129700126088, - 'ProteinScape:SequestMetaScore': 6.181682868401155, - 'calculatedMassToCharge': 1469.8071, - 'chargeState': 1, - 'experimentalMassToCharge': 1469.806, - 'passThreshold': True, - 'rank': 1}], - 'location': 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'end': 234, - 'isDecoy': True, - 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', - "decoy DB from IPI_human": '', "DB composition target+decoy": '', "decoy DB type shuffle": '', - 'numDatabaseSequences': 58099, - 'post': 'K', - 'pre': 'R', - 'protein description': '>SHD:SHD00382470.3|SWISS-PROT:P07900-2|TREMBL:Q86SX1|ENSEMBL:ENSP00000335153|REFSEQ:NP_001017963|VEGA:OTTHUMP00000041671 Tax_Id=9606 Gene_Symbol=HSP90AA1 heat shock protein 90kDa alpha (cytosolic), class A member 1 isoform 1', - 'releaseDate': '2006-02-22T09:30:47Z', - 'start': 223, - 'version': '3.15'}], - 'PeptideSequence': 'LLEDDFSMKK', - 'ProteinScape:IntensityCoverage': 0.29049959198538566, - 'ProteinScape:SequestMetaScore': 6.669916225794168, - 'calculatedMassToCharge': 1225.6059, - 'chargeState': 1, - 'experimentalMassToCharge': 1225.604, - 'passThreshold': True, - 'rank': 1}], - 'location': 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'databasekey=6'}, - {'FileFormat': 'Proteinscape spectra', - 'SpectrumIDFormat': 'spectrum from database nativeID format', - 'SpectrumIdentificationItem': [{'Modification': [{'location': 11, - "name": "Oxidation"}], - 'PeptideEvidenceRef': [{'DatabaseName': {'database IPI_human': ''}, - 'Modification': [{'location': 11, "name": "Oxidation"}], - 'PeptideSequence': 'TLTLVDTGIGMTK', - 'Seq': 'PEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASRMEEVD', - 'accession': 'IPI00414676.5', - 'decoy DB accession regexp': '^SHD', - 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', - 'end': 50, - 'isDecoy': False, - 'location': 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'proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X', - 'spectrumID': 'databasekey=11'}, - {'FileFormat': 'Proteinscape spectra', - 'SpectrumIDFormat': 'spectrum from database nativeID format', - 'SpectrumIdentificationItem': [{'PeptideEvidenceRef': [{'DatabaseName': {'database IPI_human': ''}, - 'PeptideSequence': 'HNDDEQYAWESSAGGSFTVR', - 'Seq': 'PEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASRMEEVD', - 'accession': 'IPI00414676.5', - 'decoy DB accession regexp': '^SHD', - 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', - 'end': 50, - 'isDecoy': False, - 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', - "decoy DB from IPI_human": '', "DB composition target+decoy": '', "decoy DB type shuffle": '', - 'numDatabaseSequences': 58099, - 'post': 'A', - 'pre': 'K', - 'protein description': '>IPI:IPI00414676.5|SWISS-PROT:P08238|TREMBL:Q5T9W7;Q6PK50;Q9H6X9|ENSEMBL:ENSP00000325875|REFSEQ:NP_031381|H-INV:HIT000008644;HIT000032091;HIT000034201;HIT000035963;HIT000036733;HIT000049765;HIT000057726|VEGA:OTTHUMP00000016517;OTTHUMP00000016518;OTTHUMP00000016519 Tax_Id=9606 Heat shock protein HSP 90-beta', - 'releaseDate': '2006-02-22T09:30:47Z', - 'start': 41, - 'version': '3.15'}], - 'PeptideSequence': 'HNDDEQYAWESSAGGSFTVR', - 'ProteinScape:IntensityCoverage': 0.0, - 'ProteinScape:MascotScore': 39.0, - 'calculatedMassToCharge': 2256.9515, - 'chargeState': 1, - 'experimentalMassToCharge': 2256.952, - 'passThreshold': True, - 'rank': 1}], - 'location': 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'isDecoy': False, - 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', - "decoy DB from IPI_human": '', "DB composition target+decoy": '', "decoy DB type shuffle": '', - 'numDatabaseSequences': 58099, - 'post': 'E', - 'pre': 'R', - 'protein description': '>IPI:IPI00554788.5|SWISS-PROT:P05783|ENSEMBL:ENSP00000373487;ENSP00000373489|REFSEQ:NP_000215;NP_954657|H-INV:HIT000280941|VEGA:OTTHUMP00000167632 Tax_Id=9606 Gene_Symbol=KRT18 Keratin, type I cytoskeletal 18', - 'releaseDate': '2006-02-22T09:30:47Z', - 'start': 55, - 'version': '3.15'}], - 'PeptideSequence': 'GGMGSGGLATGIAGGLAGMGGIQNEK', - 'calculatedMassToCharge': 2261.0939, - 'chargeState': 1, - 'experimentalMassToCharge': 2261.092, - 'passThreshold': True, - 'rank': 1}], - 'location': 'proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X', - 'spectrumID': 'databasekey=35'}, - {'FileFormat': 'Proteinscape spectra', - 'SpectrumIDFormat': 'spectrum from database nativeID format', - 'SpectrumIdentificationItem': [{'PeptideEvidenceRef': [{'DatabaseName': {'database IPI_human': ''}, - 'PeptideSequence': 'LRSEPVMGVK', - 'Seq': 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'end': 234, + 'isDecoy': True, + 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', + "decoy DB from IPI_human": '', + "DB composition target+decoy": '', + "decoy DB type shuffle": '', + 'numDatabaseSequences': 58099, + 'post': 'K', + 'pre': 'R', + 'protein description': '>SHD:SHD00382470.3|SWISS-PROT:P07900-2|TREMBL:Q86SX1|ENSEMBL:ENSP00000335153|REFSEQ:NP_001017963|VEGA:OTTHUMP00000041671 Tax_Id=9606 Gene_Symbol=HSP90AA1 heat shock protein 90kDa alpha (cytosolic), class A member 1 isoform 1', + 'releaseDate': '2006-02-22T09:30:47Z', + 'start': 223, + 'version': '3.15'}], + 'PeptideSequence': 'LLEDDFSMKK', + 'ProteinScape:IntensityCoverage': 0.29049959198538566, + 'ProteinScape:SequestMetaScore': 6.669916225794168, + 'calculatedMassToCharge': 1225.6059, + 'chargeState': 1, + 'experimentalMassToCharge': 1225.604, + 'passThreshold': True, + 'rank': 1}], + 'location': 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'MKIVPDERDRVQKKTFTKWVNKHLIKAQRHISDLYEDLRDGHNLISLLEVLSGDSLPREKGRMRFHKLQNVQIALDYLRHRQVKLVNIRNDDIADGNPKLTLGLIWTIILHFQISDIQVSGQSEDMTAKEKLLLWSQRMVEGYQGLRCDNFTSSWRDGRLFNAIIHRHKPLLIDMNKVYRQTNLENLDQAFSVAERDLGVTRLLDPEDVDVPQPDEKSIITYVSSLYDAMPRVPDVQDGVRANELQLRWQEYRELVLLLLQWMRHHTAAFEERRFPSSFEEIEILWSQFLKFKEMELPAKEADKNRSKGIYQSLEGAVQAGQLKVPPGYHPLDVEKEWGKLHVAILEREKQLRSEFERLECLQRIVTKLQMEAGLCEEQLNQADALLQSDVRLLAAGKVPQRAGEVERDLDKADSMIRLLFNDVQTLKDGRHPQGEQMYRRVYRLHERLVAIRTEYNLRLKAGVAAPATQVAQVTLQSVQRRPELEDSTLRYLQDLLAWVEENQHRVDGAEWGVDLPSVEAQLGSHRGLHQSIEEFRAKIERARSDEGQLSPATRGAYRDCLGRLDLQYAKLLNSSKARLRSLESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALMRELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHLKENAAYFQFFSDVREAEGQLQKLQEALRRKYSCDRSATVTRLEDLLQDAQDEKEQLNEYKGHLSGLAKRAKAVVQLKPRHPAHPMRGRLPLLAVCDYKQVEVTVHKGDECQLVGPAQPSHWKVLSSSGSEAAVPSVCFLVPPPNQEAQEAVTRLEAQHQALVTLWHQLHVDMKSLLAWQSLRRDVQLIRSWSLATFRTLKPEEQRQALHSLELHYQAFLRDSQDAGGFGPEDRLMAEREYGSCSHHYQQLLQSLEQGAQEESRCQRCISELKDIRLQLEACETRTVHRLRLPLDKEPARECAQRIAEQQKAQAEVEGLGKGVARLSAEAEKVLALPEPSPAAPTLRSELELTLGKLEQVRSLSAIYLEKLKTISLVIRGTQGAEEVLRAHEEQLKEAQAVPATLPELEATKASLKKLRAQAEAQQPTFDALRDELRGAQEVGERLQQRHGERDVEVERWRERVAQLLERWQAVLAQTDVRQRELEQLGRQLRYYRESADPLGAWLQDARRRQEQIQAMPLADSQAVREQLRQEQALLEEIERHGEKVEECQRFAKQYINAIKDYELQLVTYKAQLEPVASPAKKPKVQSGSESVIQEYVDLRTHYSELTTLTSQYIKFISETLRRMEEEERLAEQQRAEERERLAEVEAALEKQRQLAEAHAQAKAQAEREAKELQQRMQEEVVRREEAAVDAQQQKRSIQEELQQLRQSSEAEIQAKARQAEAAERSRLRIEEEIRVVRLQLEATERQRGGAEGELQALRARAEEAEAQKRQAQEEAERLRRQVQDESQRKRQAEVELASRVKAEAEAAREKQRALQALEELRLQAEEAERRLRQAEVERARQVQVALETAQRSAEAELQSKRASFAEKTAQLERSLQEEHVAVAQLREEAERRAQQQAEAERAREEAERELERWQLKANEALRLRLQAEEVAQQKSLAQAEAEKQKEEAEREARRRGKAEEQAVRQRELAEQELEKQRQLAEGTAQQRLAAEQELIRLRAETEQGEQQRQLLEEELARLQREAAAATQKRQELEAELAKVRAEMEVLLASKARAEEESRSTSEKSKQRLEAEAGRFRELAEEAARLRALAEEAKRQRQLAEEDAARQRAEAERVLAEKLAAIGEATRLKTEAEIALKEKEAENERLRRLAEDEAFQRRRLEEQAAQHKADIEERLAQLRKASDSELERQKGLVEDTLRQRRQVEEEILALKASFEKAAAGKAELELELGRIRSNAEDTLRSKEQAELEAARQRQLAAEEERRRREAEERVQKSLAAEEEAARQRKAALEEVERLKAKVEEARRLRERAEQESARQLQLAQEAAQKRLQAEEKAHAFAVQQKEQELQQTLQQEQSVLDQLRGEAEAARRAAEEAEEARVQAEREAAQSRRQVEEAERLKQSAEEQAQARAQAQAAAEKLRKEAEQEAARRAQAEQAALRQKQAADAEMEKHKKFAEQTLRQKAQVEQELTTLRLQLEETDHQKNLLDEELQRLKAEATEAARQRSQVEEELFSVRVQMEELSKLKARIEAENRALILRDKDNTQRFLQEEAEKMKQVAEEAARLSVAAQEAARLRQLAEEDLAQQRALAEKMLKEKMQAVQEATRLKAEAELLQQQKELAQEQARRLQEDKEQMAQQLAEETQGFQRTLEAERQRQLEMSAEAERLKLRVAEMSRAQARAEEDAQRFRKQAEEIGEKLHRTELATQEKVTLVQTLEIQRQQSDHDAERLREAIAELEREKEKLQQEAKLLQLKSEEMQTVQQEQLLQETQALQQSFLSEKDSLLQRERFIEQEKAKLEQLFQDEVAKAQQLREEQQRQQQQMEQERQRLVASMEEARRRQHEAEEGVRRKQEELQQLEQQRRQQEELLAEENQRLREQLQLLEEQHRAALAHSEEVTASQVAATKTLPNGRDALDGPAAEAEPEHSFDGLRRKVSAQRLQEAGILSAEELQRLAQGHTTVDELARREDVRHYLQGRSSIAGLLLKATNEKLSVYAALQRQLLSPGTALILLEAQAASGFLLDPVRNRRLTVNEAVKEGVVGPELHHKLLSAERAVTGYKDPYTGQQISLFQAMQKGLIVREHGIRLLEAQIATGGVIDPVHSHRVPVDVAYRRGYFDEEMNRVLADPSDDTKGFFDPNTHENLTYLQLLERCVEDPETGLCLLPLTDKAAKGGELVYTDSEARDVFEKATVSAPFGKFQGKTVTIWEIINSEYFTAEQRRDLLRQFRTGRITVEKIIKIIITVVEEQEQKGRLCFEGLRSLVPAAELLESRVIDRELYQQLQRGERSVRDVAEVDTVRRALRGANVIAGVWLEEAGQKLSIYNALKKDLLPSDMAVALLEAQAGTGHIIDPATSARLTVDEAVRAGLVGPEFHEKLLSAEKAVTGYRDPYTGQSVSLFQALKKGLIPREQGLRLLDAQLSTGGIVDPSKSHRVPLDVACARGCLDEETSRALSAPRADAKAYSDPSTGEPATYGELQQRCRPDQLTGLSLLPLSEKAARARQEELYSELQARETFEKTPVEVPVGGFKGRTVTVWELISSEYFTAEQRQELLRQFRTGKVTVEKVIKILITIVEEVETLRQERLSFSGLRAPVPASELLASGVLSRAQFEQLKDGKTTVKDLSELGSVRTLLQGSGCLAGIYLEDTKEKVSIYEAMRRGLLRATTAALLLEAQAATGFLVDPVRNQRLYVHEAVKAGVVGPELHEQLLSAEKAVTGYRDPYSGSTISLFQAMQKGLVLRQHGIRLLEAQIATGGIIDPVHSHRVPVDVAYQRGYFSEEMNRVLADPSDDTKGFFDPNTHENLTYRQLLERCVEDPETGLRLLPLKGAEKAEVVETTQVYTEEETRRAFEETQIDIPGGGSHGGSTMSLWEVMQSDLIPEEQRAQLMADFQAGRVTKERMIIIIIEIIEKTEIIRQQGLASYDYVRRRLTAEDLFEARIISLETYNLLREGTRSLREALEAESAWCYLYGTGSVAGVYLPGSRQTLSIYQALKKGLLSAEVARLLLEAQAATGFLLDPVKGERLTVDEAVRKGLVGPELHDRLLSAERAVTGYRDPYTEQTISLFQAMKKELIPTEEALRLLDAQLATGGIVDPRLGFHLPLEVAYQRGYLNKDTHDQLSEPSEVRSYVDPSTDERLSYTQLLRRCRRDDGTGQLLLPLSDARKLTFRGLRKQITMEELVRSQVMDEATALQLREGLTSIEEVTKNLQKFLEGTSCIAGVFVDATKERLSVYQAMKKGIIRPGTAFELLEAQAATGYVIDPIKGLKLTVEEAVRMGIVGPEFKDKLLSAERAVTGYKDPYSGKLISLFQAMKKGLILKDHGIRLLEAQIATGGIIDPEESHRLPVEVAYKRGLFDEEMNEILTDPSDDTKGFFDPNTEENLTYLQLMERCITDPQTGLCLLPLKEKKRERKTSSKSSVRKRRVVIVDPETGKEMSVYEAYRKGLIDHQTYLELSEQECEWEEITISSSDGVVKSMIIDRRSGRQYDIDDAIAKNLIDRSALDQYRAGTLSITEFADMLSGNAGGFRSRSSSVGSSSSYPISPAVSRTQLASWSDPTEETGPVAGILDTETLEKVSITEAMHRNLVDNITGQRLLEAQACTGGIIDPSTGERFPVTDAVNKGLVDKIMVDRINLAQKAFCGFEDPRTKTKMSAAQALKKGWLYYEAGQRFLEVQYLTGGLIEPDTPGRVPLDEALQRGTVDARTAQKLRDVGAYSKYLTCPKTKLKISYKDALDRSMVEEGTGLRLLEAAAQSTKGYYSPYSVSGSGSTAGSRTGSRTGSRAGSRRGSFDATGSGFSMTFSSSSYSSSGYGRRYASGSSASLGGPESAVA', + 'accession': 'IPI00398776.3', + 'decoy DB accession regexp': '^SHD', + 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', + 'end': 59, + 'isDecoy': False, + 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', + "decoy DB from IPI_human": '', + "DB composition target+decoy": '', + "decoy DB type shuffle": '', + 'numDatabaseSequences': 58099, + 'post': 'E', + 'pre': 'R', + 'protein description': '>IPI:IPI00398776.3|TREMBL:Q6S379;Q96IE3|REFSEQ:NP_958783 Tax_Id=9606 plectin 1 isoform 7', + 'releaseDate': '2006-02-22T09:30:47Z', + 'start': 40, + 'version': '3.15'}], + 'PeptideSequence': 'DGHNLISLLEVLSGDSLPR', + 'calculatedMassToCharge': 2035.0745, + 'chargeState': 1, + 'experimentalMassToCharge': 2035.075, + 'passThreshold': True, + 'rank': 1}], + 'location': 'proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X', + 'spectrumID': 'databasekey=2'}, + {'FileFormat': 'Proteinscape spectra', + 'SpectrumIDFormat': 'spectrum from database nativeID format', + 'SpectrumIdentificationItem': [ + {'PeptideEvidenceRef': [{'DatabaseName': {'database IPI_human': ''}, + 'PeptideSequence': 'QTNLENLDQAFSVAER', + 'Seq': 'MKIVPDERDRVQKKTFTKWVNKHLIKAQRHISDLYEDLRDGHNLISLLEVLSGDSLPREKGRMRFHKLQNVQIALDYLRHRQVKLVNIRNDDIADGNPKLTLGLIWTIILHFQISDIQVSGQSEDMTAKEKLLLWSQRMVEGYQGLRCDNFTSSWRDGRLFNAIIHRHKPLLIDMNKVYRQTNLENLDQAFSVAERDLGVTRLLDPEDVDVPQPDEKSIITYVSSLYDAMPRVPDVQDGVRANELQLRWQEYRELVLLLLQWMRHHTAAFEERRFPSSFEEIEILWSQFLKFKEMELPAKEADKNRSKGIYQSLEGAVQAGQLKVPPGYHPLDVEKEWGKLHVAILEREKQLRSEFERLECLQRIVTKLQMEAGLCEEQLNQADALLQSDVRLLAAGKVPQRAGEVERDLDKADSMIRLLFNDVQTLKDGRHPQGEQMYRRVYRLHERLVAIRTEYNLRLKAGVAAPATQVAQVTLQSVQRRPELEDSTLRYLQDLLAWVEENQHRVDGAEWGVDLPSVEAQLGSHRGLHQSIEEFRAKIERARSDEGQLSPATRGAYRDCLGRLDLQYAKLLNSSKARLRSLESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALMRELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHLKENAAYFQFFSDVREAEGQLQKLQEALRRKYSCDRSATVTRLEDLLQDAQDEKEQLNEYKGHLSGLAKRAKAVVQLKPRHPAHPMRGRLPLLAVCDYKQVEVTVHKGDECQLVGPAQPSHWKVLSSSGSEAAVPSVCFLVPPPNQEAQEAVTRLEAQHQALVTLWHQLHVDMKSLLAWQSLRRDVQLIRSWSLATFRTLKPEEQRQALHSLELHYQAFLRDSQDAGGFGPEDRLMAEREYGSCSHHYQQLLQSLEQGAQEESRCQRCISELKDIRLQLEACETRTVHRLRLPLDKEPARECAQRIAEQQKAQAEVEGLGKGVARLSAEAEKVLALPEPSPAAPTLRSELELTLGKLEQVRSLSAIYLEKLKTISLVIRGTQGAEEVLRAHEEQLKEAQAVPATLPELEATKASLKKLRAQAEAQQPTFDALRDELRGAQEVGERLQQRHGERDVEVERWRERVAQLLERWQAVLAQTDVRQRELEQLGRQLRYYRESADPLGAWLQDARRRQEQIQAMPLADSQAVREQLRQEQALLEEIERHGEKVEECQRFAKQYINAIKDYELQLVTYKAQLEPVASPAKKPKVQSGSESVIQEYVDLRTHYSELTTLTSQYIKFISETLRRMEEEERLAEQQRAEERERLAEVEAALEKQRQLAEAHAQAKAQAEREAKELQQRMQEEVVRREEAAVDAQQQKRSIQEELQQLRQSSEAEIQAKARQAEAAERSRLRIEEEIRVVRLQLEATERQRGGAEGELQALRARAEEAEAQKRQAQEEAERLRRQVQDESQRKRQAEVELASRVKAEAEAAREKQRALQALEELRLQAEEAERRLRQAEVERARQVQVALETAQRSAEAELQSKRASFAEKTAQLERSLQEEHVAVAQLREEAERRAQQQAEAERAREEAERELERWQLKANEALRLRLQAEEVAQQKSLAQAEAEKQKEEAEREARRRGKAEEQAVRQRELAEQELEKQRQLAEGTAQQRLAAEQELIRLRAETEQGEQQRQLLEEELARLQREAAAATQKRQELEAELAKVRAEMEVLLASKARAEEESRSTSEKSKQRLEAEAGRFRELAEEAARLRALAEEAKRQRQLAEEDAARQRAEAERVLAEKLAAIGEATRLKTEAEIALKEKEAENERLRRLAEDEAFQRRRLEEQAAQHKADIEERLAQLRKASDSELERQKGLVEDTLRQRRQVEEEILALKASFEKAAAGKAELELELGRIRSNAEDTLRSKEQAELEAARQRQLAAEEERRRREAEERVQKSLAAEEEAARQRKAALEEVERLKAKVEEARRLRERAEQESARQLQLAQEAAQKRLQAEEKAHAFAVQQKEQELQQTLQQEQSVLDQLRGEAEAARRAAEEAEEARVQAEREAAQSRRQVEEAERLKQSAEEQAQARAQAQAAAEKLRKEAEQEAARRAQAEQAALRQKQAADAEMEKHKKFAEQTLRQKAQVEQELTTLRLQLEETDHQKNLLDEELQRLKAEATEAARQRSQVEEELFSVRVQMEELSKLKARIEAENRALILRDKDNTQRFLQEEAEKMKQVAEEAARLSVAAQEAARLRQLAEEDLAQQRALAEKMLKEKMQAVQEATRLKAEAELLQQQKELAQEQARRLQEDKEQMAQQLAEETQGFQRTLEAERQRQLEMSAEAERLKLRVAEMSRAQARAEEDAQRFRKQAEEIGEKLHRTELATQEKVTLVQTLEIQRQQSDHDAERLREAIAELEREKEKLQQEAKLLQLKSEEMQTVQQEQLLQETQALQQSFLSEKDSLLQRERFIEQEKAKLEQLFQDEVAKAQQLREEQQRQQQQMEQERQRLVASMEEARRRQHEAEEGVRRKQEELQQLEQQRRQQEELLAEENQRLREQLQLLEEQHRAALAHSEEVTASQVAATKTLPNGRDALDGPAAEAEPEHSFDGLRRKVSAQRLQEAGILSAEELQRLAQGHTTVDELARREDVRHYLQGRSSIAGLLLKATNEKLSVYAALQRQLLSPGTALILLEAQAASGFLLDPVRNRRLTVNEAVKEGVVGPELHHKLLSAERAVTGYKDPYTGQQISLFQAMQKGLIVREHGIRLLEAQIATGGVIDPVHSHRVPVDVAYRRGYFDEEMNRVLADPSDDTKGFFDPNTHENLTYLQLLERCVEDPETGLCLLPLTDKAAKGGELVYTDSEARDVFEKATVSAPFGKFQGKTVTIWEIINSEYFTAEQRRDLLRQFRTGRITVEKIIKIIITVVEEQEQKGRLCFEGLRSLVPAAELLESRVIDRELYQQLQRGERSVRDVAEVDTVRRALRGANVIAGVWLEEAGQKLSIYNALKKDLLPSDMAVALLEAQAGTGHIIDPATSARLTVDEAVRAGLVGPEFHEKLLSAEKAVTGYRDPYTGQSVSLFQALKKGLIPREQGLRLLDAQLSTGGIVDPSKSHRVPLDVACARGCLDEETSRALSAPRADAKAYSDPSTGEPATYGELQQRCRPDQLTGLSLLPLSEKAARARQEELYSELQARETFEKTPVEVPVGGFKGRTVTVWELISSEYFTAEQRQELLRQFRTGKVTVEKVIKILITIVEEVETLRQERLSFSGLRAPVPASELLASGVLSRAQFEQLKDGKTTVKDLSELGSVRTLLQGSGCLAGIYLEDTKEKVSIYEAMRRGLLRATTAALLLEAQAATGFLVDPVRNQRLYVHEAVKAGVVGPELHEQLLSAEKAVTGYRDPYSGSTISLFQAMQKGLVLRQHGIRLLEAQIATGGIIDPVHSHRVPVDVAYQRGYFSEEMNRVLADPSDDTKGFFDPNTHENLTYRQLLERCVEDPETGLRLLPLKGAEKAEVVETTQVYTEEETRRAFEETQIDIPGGGSHGGSTMSLWEVMQSDLIPEEQRAQLMADFQAGRVTKERMIIIIIEIIEKTEIIRQQGLASYDYVRRRLTAEDLFEARIISLETYNLLREGTRSLREALEAESAWCYLYGTGSVAGVYLPGSRQTLSIYQALKKGLLSAEVARLLLEAQAATGFLLDPVKGERLTVDEAVRKGLVGPELHDRLLSAERAVTGYRDPYTEQTISLFQAMKKELIPTEEALRLLDAQLATGGIVDPRLGFHLPLEVAYQRGYLNKDTHDQLSEPSEVRSYVDPSTDERLSYTQLLRRCRRDDGTGQLLLPLSDARKLTFRGLRKQITMEELVRSQVMDEATALQLREGLTSIEEVTKNLQKFLEGTSCIAGVFVDATKERLSVYQAMKKGIIRPGTAFELLEAQAATGYVIDPIKGLKLTVEEAVRMGIVGPEFKDKLLSAERAVTGYKDPYSGKLISLFQAMKKGLILKDHGIRLLEAQIATGGIIDPEESHRLPVEVAYKRGLFDEEMNEILTDPSDDTKGFFDPNTEENLTYLQLMERCITDPQTGLCLLPLKEKKRERKTSSKSSVRKRRVVIVDPETGKEMSVYEAYRKGLIDHQTYLELSEQECEWEEITISSSDGVVKSMIIDRRSGRQYDIDDAIAKNLIDRSALDQYRAGTLSITEFADMLSGNAGGFRSRSSSVGSSSSYPISPAVSRTQLASWSDPTEETGPVAGILDTETLEKVSITEAMHRNLVDNITGQRLLEAQACTGGIIDPSTGERFPVTDAVNKGLVDKIMVDRINLAQKAFCGFEDPRTKTKMSAAQALKKGWLYYEAGQRFLEVQYLTGGLIEPDTPGRVPLDEALQRGTVDARTAQKLRDVGAYSKYLTCPKTKLKISYKDALDRSMVEEGTGLRLLEAAAQSTKGYYSPYSVSGSGSTAGSRTGSRTGSRAGSRRGSFDATGSGFSMTFSSSSYSSSGYGRRYASGSSASLGGPESAVA', + 'accession': 'IPI00398776.3', + 'decoy DB accession regexp': '^SHD', + 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', + 'end': 197, + 'isDecoy': False, + 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', + "decoy DB from IPI_human": '', + "DB composition target+decoy": '', + "decoy DB type shuffle": '', + 'numDatabaseSequences': 58099, + 'post': 'D', + 'pre': 'R', + 'protein description': '>IPI:IPI00398776.3|TREMBL:Q6S379;Q96IE3|REFSEQ:NP_958783 Tax_Id=9606 plectin 1 isoform 7', + 'releaseDate': '2006-02-22T09:30:47Z', + 'start': 181, + 'version': '3.15'}], + 'PeptideSequence': 'QTNLENLDQAFSVAER', + 'calculatedMassToCharge': 1834.8856, + 'chargeState': 1, + 'experimentalMassToCharge': 1834.884, + 'passThreshold': True, + 'rank': 1}], + 'location': 'proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X', + 'spectrumID': 'databasekey=3'}, + {'FileFormat': 'Proteinscape spectra', + 'SpectrumIDFormat': 'spectrum from database nativeID format', + 'SpectrumIdentificationItem': [ + {'PeptideEvidenceRef': [{'DatabaseName': {'database IPI_human': ''}, + 'PeptideSequence': 'HHTAAFEER', + 'Seq': 'MKIVPDERDRVQKKTFTKWVNKHLIKAQRHISDLYEDLRDGHNLISLLEVLSGDSLPREKGRMRFHKLQNVQIALDYLRHRQVKLVNIRNDDIADGNPKLTLGLIWTIILHFQISDIQVSGQSEDMTAKEKLLLWSQRMVEGYQGLRCDNFTSSWRDGRLFNAIIHRHKPLLIDMNKVYRQTNLENLDQAFSVAERDLGVTRLLDPEDVDVPQPDEKSIITYVSSLYDAMPRVPDVQDGVRANELQLRWQEYRELVLLLLQWMRHHTAAFEERRFPSSFEEIEILWSQFLKFKEMELPAKEADKNRSKGIYQSLEGAVQAGQLKVPPGYHPLDVEKEWGKLHVAILEREKQLRSEFERLECLQRIVTKLQMEAGLCEEQLNQADALLQSDVRLLAAGKVPQRAGEVERDLDKADSMIRLLFNDVQTLKDGRHPQGEQMYRRVYRLHERLVAIRTEYNLRLKAGVAAPATQVAQVTLQSVQRRPELEDSTLRYLQDLLAWVEENQHRVDGAEWGVDLPSVEAQLGSHRGLHQSIEEFRAKIERARSDEGQLSPATRGAYRDCLGRLDLQYAKLLNSSKARLRSLESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALMRELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHLKENAAYFQFFSDVREAEGQLQKLQEALRRKYSCDRSATVTRLEDLLQDAQDEKEQLNEYKGHLSGLAKRAKAVVQLKPRHPAHPMRGRLPLLAVCDYKQVEVTVHKGDECQLVGPAQPSHWKVLSSSGSEAAVPSVCFLVPPPNQEAQEAVTRLEAQHQALVTLWHQLHVDMKSLLAWQSLRRDVQLIRSWSLATFRTLKPEEQRQALHSLELHYQAFLRDSQDAGGFGPEDRLMAEREYGSCSHHYQQLLQSLEQGAQEESRCQRCISELKDIRLQLEACETRTVHRLRLPLDKEPARECAQRIAEQQKAQAEVEGLGKGVARLSAEAEKVLALPEPSPAAPTLRSELELTLGKLEQVRSLSAIYLEKLKTISLVIRGTQGAEEVLRAHEEQLKEAQAVPATLPELEATKASLKKLRAQAEAQQPTFDALRDELRGAQEVGERLQQRHGERDVEVERWRERVAQLLERWQAVLAQTDVRQRELEQLGRQLRYYRESADPLGAWLQDARRRQEQIQAMPLADSQAVREQLRQEQALLEEIERHGEKVEECQRFAKQYINAIKDYELQLVTYKAQLEPVASPAKKPKVQSGSESVIQEYVDLRTHYSELTTLTSQYIKFISETLRRMEEEERLAEQQRAEERERLAEVEAALEKQRQLAEAHAQAKAQAEREAKELQQRMQEEVVRREEAAVDAQQQKRSIQEELQQLRQSSEAEIQAKARQAEAAERSRLRIEEEIRVVRLQLEATERQRGGAEGELQALRARAEEAEAQKRQAQEEAERLRRQVQDESQRKRQAEVELASRVKAEAEAAREKQRALQALEELRLQAEEAERRLRQAEVERARQVQVALETAQRSAEAELQSKRASFAEKTAQLERSLQEEHVAVAQLREEAERRAQQQAEAERAREEAERELERWQLKANEALRLRLQAEEVAQQKSLAQAEAEKQKEEAEREARRRGKAEEQAVRQRELAEQELEKQRQLAEGTAQQRLAAEQELIRLRAETEQGEQQRQLLEEELARLQREAAAATQKRQELEAELAKVRAEMEVLLASKARAEEESRSTSEKSKQRLEAEAGRFRELAEEAARLRALAEEAKRQRQLAEEDAARQRAEAERVLAEKLAAIGEATRLKTEAEIALKEKEAENERLRRLAEDEAFQRRRLEEQAAQHKADIEERLAQLRKASDSELERQKGLVEDTLRQRRQVEEEILALKASFEKAAAGKAELELELGRIRSNAEDTLRSKEQAELEAARQRQLAAEEERRRREAEERVQKSLAAEEEAARQRKAALEEVERLKAKVEEARRLRERAEQESARQLQLAQEAAQKRLQAEEKAHAFAVQQKEQELQQTLQQEQSVLDQLRGEAEAARRAAEEAEEARVQAEREAAQSRRQVEEAERLKQSAEEQAQARAQAQAAAEKLRKEAEQEAARRAQAEQAALRQKQAADAEMEKHKKFAEQTLRQKAQVEQELTTLRLQLEETDHQKNLLDEELQRLKAEATEAARQRSQVEEELFSVRVQMEELSKLKARIEAENRALILRDKDNTQRFLQEEAEKMKQVAEEAARLSVAAQEAARLRQLAEEDLAQQRALAEKMLKEKMQAVQEATRLKAEAELLQQQKELAQEQARRLQEDKEQMAQQLAEETQGFQRTLEAERQRQLEMSAEAERLKLRVAEMSRAQARAEEDAQRFRKQAEEIGEKLHRTELATQEKVTLVQTLEIQRQQSDHDAERLREAIAELEREKEKLQQEAKLLQLKSEEMQTVQQEQLLQETQALQQSFLSEKDSLLQRERFIEQEKAKLEQLFQDEVAKAQQLREEQQRQQQQMEQERQRLVASMEEARRRQHEAEEGVRRKQEELQQLEQQRRQQEELLAEENQRLREQLQLLEEQHRAALAHSEEVTASQVAATKTLPNGRDALDGPAAEAEPEHSFDGLRRKVSAQRLQEAGILSAEELQRLAQGHTTVDELARREDVRHYLQGRSSIAGLLLKATNEKLSVYAALQRQLLSPGTALILLEAQAASGFLLDPVRNRRLTVNEAVKEGVVGPELHHKLLSAERAVTGYKDPYTGQQISLFQAMQKGLIVREHGIRLLEAQIATGGVIDPVHSHRVPVDVAYRRGYFDEEMNRVLADPSDDTKGFFDPNTHENLTYLQLLERCVEDPETGLCLLPLTDKAAKGGELVYTDSEARDVFEKATVSAPFGKFQGKTVTIWEIINSEYFTAEQRRDLLRQFRTGRITVEKIIKIIITVVEEQEQKGRLCFEGLRSLVPAAELLESRVIDRELYQQLQRGERSVRDVAEVDTVRRALRGANVIAGVWLEEAGQKLSIYNALKKDLLPSDMAVALLEAQAGTGHIIDPATSARLTVDEAVRAGLVGPEFHEKLLSAEKAVTGYRDPYTGQSVSLFQALKKGLIPREQGLRLLDAQLSTGGIVDPSKSHRVPLDVACARGCLDEETSRALSAPRADAKAYSDPSTGEPATYGELQQRCRPDQLTGLSLLPLSEKAARARQEELYSELQARETFEKTPVEVPVGGFKGRTVTVWELISSEYFTAEQRQELLRQFRTGKVTVEKVIKILITIVEEVETLRQERLSFSGLRAPVPASELLASGVLSRAQFEQLKDGKTTVKDLSELGSVRTLLQGSGCLAGIYLEDTKEKVSIYEAMRRGLLRATTAALLLEAQAATGFLVDPVRNQRLYVHEAVKAGVVGPELHEQLLSAEKAVTGYRDPYSGSTISLFQAMQKGLVLRQHGIRLLEAQIATGGIIDPVHSHRVPVDVAYQRGYFSEEMNRVLADPSDDTKGFFDPNTHENLTYRQLLERCVEDPETGLRLLPLKGAEKAEVVETTQVYTEEETRRAFEETQIDIPGGGSHGGSTMSLWEVMQSDLIPEEQRAQLMADFQAGRVTKERMIIIIIEIIEKTEIIRQQGLASYDYVRRRLTAEDLFEARIISLETYNLLREGTRSLREALEAESAWCYLYGTGSVAGVYLPGSRQTLSIYQALKKGLLSAEVARLLLEAQAATGFLLDPVKGERLTVDEAVRKGLVGPELHDRLLSAERAVTGYRDPYTEQTISLFQAMKKELIPTEEALRLLDAQLATGGIVDPRLGFHLPLEVAYQRGYLNKDTHDQLSEPSEVRSYVDPSTDERLSYTQLLRRCRRDDGTGQLLLPLSDARKLTFRGLRKQITMEELVRSQVMDEATALQLREGLTSIEEVTKNLQKFLEGTSCIAGVFVDATKERLSVYQAMKKGIIRPGTAFELLEAQAATGYVIDPIKGLKLTVEEAVRMGIVGPEFKDKLLSAERAVTGYKDPYSGKLISLFQAMKKGLILKDHGIRLLEAQIATGGIIDPEESHRLPVEVAYKRGLFDEEMNEILTDPSDDTKGFFDPNTEENLTYLQLMERCITDPQTGLCLLPLKEKKRERKTSSKSSVRKRRVVIVDPETGKEMSVYEAYRKGLIDHQTYLELSEQECEWEEITISSSDGVVKSMIIDRRSGRQYDIDDAIAKNLIDRSALDQYRAGTLSITEFADMLSGNAGGFRSRSSSVGSSSSYPISPAVSRTQLASWSDPTEETGPVAGILDTETLEKVSITEAMHRNLVDNITGQRLLEAQACTGGIIDPSTGERFPVTDAVNKGLVDKIMVDRINLAQKAFCGFEDPRTKTKMSAAQALKKGWLYYEAGQRFLEVQYLTGGLIEPDTPGRVPLDEALQRGTVDARTAQKLRDVGAYSKYLTCPKTKLKISYKDALDRSMVEEGTGLRLLEAAAQSTKGYYSPYSVSGSGSTAGSRTGSRTGSRAGSRRGSFDATGSGFSMTFSSSSYSSSGYGRRYASGSSASLGGPESAVA', + 'accession': 'IPI00398776.3', + 'decoy DB accession regexp': '^SHD', + 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', + 'end': 274, + 'isDecoy': False, + 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', + "decoy DB from IPI_human": '', + "DB composition target+decoy": '', + "decoy DB type shuffle": '', + 'numDatabaseSequences': 58099, + 'post': 'R', + 'pre': 'R', + 'protein description': '>IPI:IPI00398776.3|TREMBL:Q6S379;Q96IE3|REFSEQ:NP_958783 Tax_Id=9606 plectin 1 isoform 7', + 'releaseDate': '2006-02-22T09:30:47Z', + 'start': 265, + 'version': '3.15'}], + 'PeptideSequence': 'HHTAAFEER', + 'calculatedMassToCharge': 1097.5049, + 'chargeState': 1, + 'experimentalMassToCharge': 1097.503, + 'passThreshold': True, + 'rank': 1}], + 'location': 'proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X', + 'spectrumID': 'databasekey=4'}, + {'FileFormat': 'Proteinscape spectra', + 'SpectrumIDFormat': 'spectrum from database nativeID format', + 'SpectrumIdentificationItem': [ + {'PeptideEvidenceRef': [{'DatabaseName': {'database IPI_human': ''}, + 'PeptideSequence': 'STFSTNYR', + 'Seq': 'MSFTTRSTFSTNYRSLGSVQAPSYGARPVSSAASVYAGAGGSGSRISVSRSTSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDRLASYLDRVRSLETENRRLESKIREHLEKKGPQVRDWSHYFKIIEDLRAQIFANTVDNARIVLQIDNARLAADDFRVKYETELAMRQSVENDIHGLRKVIDDTNITRLQLETEIEALKEELLFMKKNHEEEVKGLQAQIASSGLTVEVDAPKSQDLAKIMADIRAQYDELARKNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRRTVQSLEIDLDSMRNLKASLENSLREVEARYALQMEQLNGILLHLESELAQTRAEGQRQAQEYEALLNIKVKLEAEIATYRRLLEDGEDFNLGDALDSSNSMQTIQKTTTRRIVDGKVVSETNDTKVLRH', + 'accession': 'IPI00554788.5', + 'decoy DB accession regexp': '^SHD', + 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', + 'end': 15, + 'isDecoy': False, + 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', + "decoy DB from IPI_human": '', + "DB composition target+decoy": '', + "decoy DB type shuffle": '', + 'numDatabaseSequences': 58099, + 'post': 'S', + 'pre': 'R', + 'protein description': '>IPI:IPI00554788.5|SWISS-PROT:P05783|ENSEMBL:ENSP00000373487;ENSP00000373489|REFSEQ:NP_000215;NP_954657|H-INV:HIT000280941|VEGA:OTTHUMP00000167632 Tax_Id=9606 Gene_Symbol=KRT18 Keratin, type I cytoskeletal 18', + 'releaseDate': '2006-02-22T09:30:47Z', + 'start': 7, + 'version': '3.15'}], + 'PeptideSequence': 'STFSTNYR', + 'calculatedMassToCharge': 975.4457, + 'chargeState': 1, + 'experimentalMassToCharge': 975.446, + 'passThreshold': True, + 'rank': 1}, + {'PeptideEvidenceRef': [{'DatabaseName': {'database IPI_human': ''}, + 'PeptideSequence': 'MYGPMGTR', + 'Seq': 'PSKYTHAFFHGGTVLFTYVDGLIAESLQLVTQSPPAAGVAGMYDGTSPTTTDIADFEGGPVKEDDEQKLLSSCPRVKGSEPKSPDHGACPSKGLNCKEAHAACCAVFYDYGVEVELVSALSATGAVVHKTASCTLDVTYPEDTIDGDPTAGRKTKKCKGSKATPPDYVRGEKVEIAARGPNDKLYYFEVVSREKPLGAFKCGNQKVNIVYEGVVVVGELEAKILDEVQGTTDGVVGSKDTTQINVIVFNLPCKTGSFVCNRAYKCDKPMDAEGPVVAKLNPGRAALVLHHPEQDKGLNLTGGVHNDTPDGVQKGLDITPTSVAPPMKQQVHNVVMRKKDTLDSKAQIATPETAFVNADAEPVSPWSELIVSEKLGENALGTLQPFHQAVDTTVAKPYRAPLAPWGAVVVNEQFVPAVSVNIGAERESEYILQTAGKCIADDLEGITETNKAVTTREDGPSISYIPSGGDAVSYDTQNRVGTTSLSPWKVDRGVSLSVGALKLLRIVWNDFCADTPVCVAGEVSYSTVGRGVSAGVAAPNPPVKAMVSRPIGTVSRIGGSDTRAGMKFSMHTGGIHTTKSKDDGESGSSYGGDTTVIEYGVEGGSTTVQELAIAPVGAYNLSAQPFGVKGRNEETKKTYSFQVAFVFGVLIFPESPRSREIQNPPAPIVYFVKSGDAQDKGGKEKAGTALIPFMVDPASGLKMYGPMGTRNQNDLGQESQGGTPSKTSEDDVSYNETKQLRATGGAGEETSDADSPKRLSEHGASASPMVQMGIGVINLEYGAPSVTPTVEPCRVTEYVSSSDSEGYAGTRVSAGVDQIDVKPLITLQIYPRSLYQVQENKCLATQAAIVYSSADVVPVVVLNKSGHGKFKVDRTDRKQHEVHYGNKCDDTNGDKNIGGNPSTVLESKDCCGISCVPLKVKTGKGVGPVTMSPPMGPAVHGGDIVHSLREVVVVSAVGKSDVVRGAGVAESKVISKRVAVTMADFSYVEKGIGRKGFSETDFGHKGPGDGRVVGSSRKVSSFFVIFQPAGGWKVIEVILHDAIIGGDGQIGGTANPFVGYTLKEASGVDYADVPVIGVLAYYVAELYRDQHGTDQGPGPEGNEITADPGVGTGAEDGRASGYGAGIVTTKTTDSTGCPHRPVQAERLGRKLRSEPVMGVKPGVGGTHCNEDINEKTGIALDVVRAPPAFQPSISGVHTKSSATDVGPDVFDTGGVALVCQPVVGSVVSPYYCPPFGAGVIECYPMSTDPADSSRRNFKPPQRVVTTTEAGDDSGAYVYRYFGPGADMKLPKDSSDVVGNGDCESDPPKLSGNVPQHPEQYSTPAESMRGDPAVSDSLVMANVEFPKCEPDQNYGGHDGKVAPFFDRENEQVDVGLPNDSKGPCVRGVFPLFHYIGSVAPRAVIKCPTTLGPIGQTGGFPGFKSIAYLLIGTGCFQKLLKYVITELVDNCDGCRAKYGSDSTGSFVMEAKGLPIQGFKGKSGTDKCNHEKVDIELTTSGKRPRPPANQAKIEDVLPNAVTDVKECTAVYVDREIELDEIDPHTAQGHRYKRGPKEPIAWSIELSPSGRYMVELLVEISVAFVPPIPIFGTEVAPVGAPAISTSGSPGPAIGRVTLGQKAALPTEPEPSNSYARVDRQEEKRTPEGCGEAAKAHHPPFGINPLAQVIEDQDAYHFDHVGARIGLERGTSCDGESEAIEGPVLYAAPAKAAPSGEVHIARQDVKDPLAGGELHTVLDRCDAVSYESSKSQPLHTITFSKPEPGKSDAMITPPVIEPIVFIWIQRAHFPNGETSLGSSRAFAGKRVSKTYGGSDLRECWIGGGPKKNLKPCQPGEGTGKPITGEPLGMVIVRTLPRWELVKHFLVAPGTVIGTTGHADHVSRPGKPVLIPTERANWPVPRHYTELHDGREVKCTREGVKFHRLDTVNAAVHKNYRHPSSKSSCLWHGVVTKEQAGQISIREFVEDVSPGSIIVDIVNLVAVQGPSSTGSGLGVVHAYPLTYYTVKDIVVALKLSSASFIMVNKKAVVTVCFSDVQSGFKKNVASPPGVLSVSIGLDTYEGDPGIATNWWPSTDEKPCGNVLEDSGPDENHSNPNTAWEFTGLGDTKEGRPNTAFVESEMVLLPVAYVLEQKHPGQGQVGNTMLKDGICEGSTSHVGAVDPSEVQPLGFPGRLITKKFLETFIFCYPSEPIGKGKKVDGKLTSSYSSELAERELVLALAVGIGDAVYYYAFGAGPKIHVFTGDGGGVKNGILVLEGPFHGDEPDLGPFNPGPTQGVERGYSGGEKLATPTVTTYVPELVGLVVVGGTDGIGVHAAVVERWGTYDGKVSPQSVYTTKPGPLSGSDDIHLNVKTVKYLHDEGYTFTIPPHGEKVVEVVEAEQVGRQSDGTTYVTQNNAQAIPVKLRRTAPYGELGHVKLDQVGEEYFGIKFHVNGCDGPGTGPENATYVEQTSGVPPRTPVFGFSVEGTLIQSPQIALNKGRHAVTTIIKQARPFLGGVKGTTDQTPDAFVPHKQTEPLVAACKYVGGWYNHVVPKGKAGEGQGQHRPAVKRANPSDEQAMQSMKKPSPPTPQGEEVSTSVKDLEPESYFQQNVYVNVPAHIGKKLPGIECNQND', + 'accession': 'SHD00644576.1', + 'decoy DB accession regexp': '^SHD', + 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', + 'end': 710, + 'isDecoy': True, + 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', + "decoy DB from IPI_human": '', + "DB composition target+decoy": '', + "decoy DB type shuffle": '', + 'numDatabaseSequences': 58099, + 'post': 'N', + 'pre': 'K', + 'protein description': '>SHD:SHD00644576.1|TREMBL:Q5HY54;Q86TQ3;Q96C61|ENSEMBL:ENSP00000358863|VEGA:OTTHUMP00000064890 Tax_Id=9606 Gene_Symbol=FLNA Filamin A, alpha', + 'releaseDate': '2006-02-22T09:30:47Z', + 'start': 702, + 'version': '3.15'}], + 'PeptideSequence': 'MYGPMGTR', + 'calculatedMassToCharge': 912.3993, + 'chargeState': 1, + 'experimentalMassToCharge': 912.29, + 'passThreshold': True, + 'rank': 1}], + 'location': 'proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X', + 'spectrumID': 'databasekey=6'}, + {'FileFormat': 'Proteinscape spectra', + 'SpectrumIDFormat': 'spectrum from database nativeID format', + 'SpectrumIdentificationItem': [{'Modification': [{'location': 11, + "name": "Oxidation"}], + 'PeptideEvidenceRef': [ + {'DatabaseName': {'database IPI_human': ''}, + 'Modification': [ + {'location': 11, "name": "Oxidation"}], + 'PeptideSequence': 'TLTLVDTGIGMTK', + 'Seq': 'PEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASRMEEVD', + 'accession': 'IPI00414676.5', + 'decoy DB accession regexp': '^SHD', + 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', + 'end': 50, + 'isDecoy': False, + 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', + "decoy DB from IPI_human": '', + "DB composition target+decoy": '', + "decoy DB type shuffle": '', + 'numDatabaseSequences': 58099, + 'post': 'A', + 'pre': 'R', + 'protein description': '>IPI:IPI00414676.5|SWISS-PROT:P08238|TREMBL:Q5T9W7;Q6PK50;Q9H6X9|ENSEMBL:ENSP00000325875|REFSEQ:NP_031381|H-INV:HIT000008644;HIT000032091;HIT000034201;HIT000035963;HIT000036733;HIT000049765;HIT000057726|VEGA:OTTHUMP00000016517;OTTHUMP00000016518;OTTHUMP00000016519 Tax_Id=9606 Heat shock protein HSP 90-beta', + 'releaseDate': '2006-02-22T09:30:47Z', + 'start': 41, + 'version': '3.15'}], + 'PeptideSequence': 'TLTLVDTGIGMTK', + 'ProteinScape:IntensityCoverage': 0.0, + 'ProteinScape:MascotScore': 33.82, + 'calculatedMassToCharge': 1365.722015, + 'chargeState': 1, + 'experimentalMassToCharge': 1365.721, + 'passThreshold': True, + 'rank': 1}], + 'location': 'proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X', + 'spectrumID': 'databasekey=11'}, + {'FileFormat': 'Proteinscape spectra', + 'SpectrumIDFormat': 'spectrum from database nativeID format', + 'SpectrumIdentificationItem': [ + {'PeptideEvidenceRef': [{'DatabaseName': {'database IPI_human': ''}, + 'PeptideSequence': 'HNDDEQYAWESSAGGSFTVR', + 'Seq': 'PEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASRMEEVD', + 'accession': 'IPI00414676.5', + 'decoy DB accession regexp': '^SHD', + 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', + 'end': 50, + 'isDecoy': False, + 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', + "decoy DB from IPI_human": '', + "DB composition target+decoy": '', + "decoy DB type shuffle": '', + 'numDatabaseSequences': 58099, + 'post': 'A', + 'pre': 'K', + 'protein description': '>IPI:IPI00414676.5|SWISS-PROT:P08238|TREMBL:Q5T9W7;Q6PK50;Q9H6X9|ENSEMBL:ENSP00000325875|REFSEQ:NP_031381|H-INV:HIT000008644;HIT000032091;HIT000034201;HIT000035963;HIT000036733;HIT000049765;HIT000057726|VEGA:OTTHUMP00000016517;OTTHUMP00000016518;OTTHUMP00000016519 Tax_Id=9606 Heat shock protein HSP 90-beta', + 'releaseDate': '2006-02-22T09:30:47Z', + 'start': 41, + 'version': '3.15'}], + 'PeptideSequence': 'HNDDEQYAWESSAGGSFTVR', + 'ProteinScape:IntensityCoverage': 0.0, + 'ProteinScape:MascotScore': 39.0, + 'calculatedMassToCharge': 2256.9515, + 'chargeState': 1, + 'experimentalMassToCharge': 2256.952, + 'passThreshold': True, + 'rank': 1}], + 'location': 'proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X', + 'spectrumID': 'databasekey=12'}, + {'FileFormat': 'Proteinscape spectra', + 'SpectrumIDFormat': 'spectrum from database nativeID format', + 'SpectrumIdentificationItem': [ + {'PeptideEvidenceRef': [{'DatabaseName': {'database IPI_human': ''}, + 'PeptideSequence': 'GGMGSGGLATGIAGGLAGMGGIQNEK', + 'Seq': 'MSFTTRSTFSTNYRSLGSVQAPSYGARPVSSAASVYAGAGGSGSRISVSRSTSFRGGMGSGGLATGIAGGLAGMGGIQNEKETMQSLNDRLASYLDRVRSLETENRRLESKIREHLEKKGPQVRDWSHYFKIIEDLRAQIFANTVDNARIVLQIDNARLAADDFRVKYETELAMRQSVENDIHGLRKVIDDTNITRLQLETEIEALKEELLFMKKNHEEEVKGLQAQIASSGLTVEVDAPKSQDLAKIMADIRAQYDELARKNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRRTVQSLEIDLDSMRNLKASLENSLREVEARYALQMEQLNGILLHLESELAQTRAEGQRQAQEYEALLNIKVKLEAEIATYRRLLEDGEDFNLGDALDSSNSMQTIQKTTTRRIVDGKVVSETNDTKVLRH', + 'accession': 'IPI00554788.5', + 'decoy DB accession regexp': '^SHD', + 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', + 'end': 81, + 'isDecoy': False, + 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', + "decoy DB from IPI_human": '', + "DB composition target+decoy": '', + "decoy DB type shuffle": '', + 'numDatabaseSequences': 58099, + 'post': 'E', + 'pre': 'R', + 'protein description': '>IPI:IPI00554788.5|SWISS-PROT:P05783|ENSEMBL:ENSP00000373487;ENSP00000373489|REFSEQ:NP_000215;NP_954657|H-INV:HIT000280941|VEGA:OTTHUMP00000167632 Tax_Id=9606 Gene_Symbol=KRT18 Keratin, type I cytoskeletal 18', + 'releaseDate': '2006-02-22T09:30:47Z', + 'start': 55, + 'version': '3.15'}], + 'PeptideSequence': 'GGMGSGGLATGIAGGLAGMGGIQNEK', + 'calculatedMassToCharge': 2261.0939, + 'chargeState': 1, + 'experimentalMassToCharge': 2261.092, + 'passThreshold': True, + 'rank': 1}], + 'location': 'proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X', + 'spectrumID': 'databasekey=35'}, + {'FileFormat': 'Proteinscape spectra', + 'SpectrumIDFormat': 'spectrum from database nativeID format', + 'SpectrumIdentificationItem': [ + {'PeptideEvidenceRef': [{'DatabaseName': {'database IPI_human': ''}, + 'PeptideSequence': 'LRSEPVMGVK', + 'Seq': 'PSKYTHAFFHGGTVLFTYVDGLIAESLQLVTQSPPAAGVAGMYDGTSPTTTDIADFEGGPVKEDDEQKLLSSCPRVKGSEPKSPDHGACPSKGLNCKEAHAACCAVFYDYGVEVELVSALSATGAVVHKTASCTLDVTYPEDTIDGDPTAGRKTKKCKGSKATPPDYVRGEKVEIAARGPNDKLYYFEVVSREKPLGAFKCGNQKVNIVYEGVVVVGELEAKILDEVQGTTDGVVGSKDTTQINVIVFNLPCKTGSFVCNRAYKCDKPMDAEGPVVAKLNPGRAALVLHHPEQDKGLNLTGGVHNDTPDGVQKGLDITPTSVAPPMKQQVHNVVMRKKDTLDSKAQIATPETAFVNADAEPVSPWSELIVSEKLGENALGTLQPFHQAVDTTVAKPYRAPLAPWGAVVVNEQFVPAVSVNIGAERESEYILQTAGKCIADDLEGITETNKAVTTREDGPSISYIPSGGDAVSYDTQNRVGTTSLSPWKVDRGVSLSVGALKLLRIVWNDFCADTPVCVAGEVSYSTVGRGVSAGVAAPNPPVKAMVSRPIGTVSRIGGSDTRAGMKFSMHTGGIHTTKSKDDGESGSSYGGDTTVIEYGVEGGSTTVQELAIAPVGAYNLSAQPFGVKGRNEETKKTYSFQVAFVFGVLIFPESPRSREIQNPPAPIVYFVKSGDAQDKGGKEKAGTALIPFMVDPASGLKMYGPMGTRNQNDLGQESQGGTPSKTSEDDVSYNETKQLRATGGAGEETSDADSPKRLSEHGASASPMVQMGIGVINLEYGAPSVTPTVEPCRVTEYVSSSDSEGYAGTRVSAGVDQIDVKPLITLQIYPRSLYQVQENKCLATQAAIVYSSADVVPVVVLNKSGHGKFKVDRTDRKQHEVHYGNKCDDTNGDKNIGGNPSTVLESKDCCGISCVPLKVKTGKGVGPVTMSPPMGPAVHGGDIVHSLREVVVVSAVGKSDVVRGAGVAESKVISKRVAVTMADFSYVEKGIGRKGFSETDFGHKGPGDGRVVGSSRKVSSFFVIFQPAGGWKVIEVILHDAIIGGDGQIGGTANPFVGYTLKEASGVDYADVPVIGVLAYYVAELYRDQHGTDQGPGPEGNEITADPGVGTGAEDGRASGYGAGIVTTKTTDSTGCPHRPVQAERLGRKLRSEPVMGVKPGVGGTHCNEDINEKTGIALDVVRAPPAFQPSISGVHTKSSATDVGPDVFDTGGVALVCQPVVGSVVSPYYCPPFGAGVIECYPMSTDPADSSRRNFKPPQRVVTTTEAGDDSGAYVYRYFGPGADMKLPKDSSDVVGNGDCESDPPKLSGNVPQHPEQYSTPAESMRGDPAVSDSLVMANVEFPKCEPDQNYGGHDGKVAPFFDRENEQVDVGLPNDSKGPCVRGVFPLFHYIGSVAPRAVIKCPTTLGPIGQTGGFPGFKSIAYLLIGTGCFQKLLKYVITELVDNCDGCRAKYGSDSTGSFVMEAKGLPIQGFKGKSGTDKCNHEKVDIELTTSGKRPRPPANQAKIEDVLPNAVTDVKECTAVYVDREIELDEIDPHTAQGHRYKRGPKEPIAWSIELSPSGRYMVELLVEISVAFVPPIPIFGTEVAPVGAPAISTSGSPGPAIGRVTLGQKAALPTEPEPSNSYARVDRQEEKRTPEGCGEAAKAHHPPFGINPLAQVIEDQDAYHFDHVGARIGLERGTSCDGESEAIEGPVLYAAPAKAAPSGEVHIARQDVKDPLAGGELHTVLDRCDAVSYESSKSQPLHTITFSKPEPGKSDAMITPPVIEPIVFIWIQRAHFPNGETSLGSSRAFAGKRVSKTYGGSDLRECWIGGGPKKNLKPCQPGEGTGKPITGEPLGMVIVRTLPRWELVKHFLVAPGTVIGTTGHADHVSRPGKPVLIPTERANWPVPRHYTELHDGREVKCTREGVKFHRLDTVNAAVHKNYRHPSSKSSCLWHGVVTKEQAGQISIREFVEDVSPGSIIVDIVNLVAVQGPSSTGSGLGVVHAYPLTYYTVKDIVVALKLSSASFIMVNKKAVVTVCFSDVQSGFKKNVASPPGVLSVSIGLDTYEGDPGIATNWWPSTDEKPCGNVLEDSGPDENHSNPNTAWEFTGLGDTKEGRPNTAFVESEMVLLPVAYVLEQKHPGQGQVGNTMLKDGICEGSTSHVGAVDPSEVQPLGFPGRLITKKFLETFIFCYPSEPIGKGKKVDGKLTSSYSSELAERELVLALAVGIGDAVYYYAFGAGPKIHVFTGDGGGVKNGILVLEGPFHGDEPDLGPFNPGPTQGVERGYSGGEKLATPTVTTYVPELVGLVVVGGTDGIGVHAAVVERWGTYDGKVSPQSVYTTKPGPLSGSDDIHLNVKTVKYLHDEGYTFTIPPHGEKVVEVVEAEQVGRQSDGTTYVTQNNAQAIPVKLRRTAPYGELGHVKLDQVGEEYFGIKFHVNGCDGPGTGPENATYVEQTSGVPPRTPVFGFSVEGTLIQSPQIALNKGRHAVTTIIKQARPFLGGVKGTTDQTPDAFVPHKQTEPLVAACKYVGGWYNHVVPKGKAGEGQGQHRPAVKRANPSDEQAMQSMKKPSPPTPQGEEVSTSVKDLEPESYFQQNVYVNVPAHIGKKLPGIECNQND', + 'accession': 'SHD00644576.1', + 'decoy DB accession regexp': '^SHD', + 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', + 'end': 1159, + 'isDecoy': True, + 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', + "decoy DB from IPI_human": '', + "DB composition target+decoy": '', + "decoy DB type shuffle": '', + 'numDatabaseSequences': 58099, + 'post': 'P', + 'pre': 'K', + 'protein description': '>SHD:SHD00644576.1|TREMBL:Q5HY54;Q86TQ3;Q96C61|ENSEMBL:ENSP00000358863|VEGA:OTTHUMP00000064890 Tax_Id=9606 Gene_Symbol=FLNA Filamin A, alpha', + 'releaseDate': '2006-02-22T09:30:47Z', + 'start': 1150, + 'version': '3.15'}], + 'PeptideSequence': 'LRSEPVMGVK', + 'calculatedMassToCharge': 1115.6168, + 'chargeState': 1, + 'experimentalMassToCharge': 1115.617, + 'passThreshold': True, + 'rank': 1}], + 'location': 'proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X', + 'spectrumID': 'databasekey=36'}, + {'FileFormat': 'Proteinscape spectra', + 'SpectrumIDFormat': 'spectrum from database nativeID format', + 'SpectrumIdentificationItem': [ + {'PeptideEvidenceRef': [{'DatabaseName': {'database IPI_human': ''}, + 'PeptideSequence': 'QSDGTTYVTQNNAQAIPVK', + 'Seq': 'PSKYTHAFFHGGTVLFTYVDGLIAESLQLVTQSPPAAGVAGMYDGTSPTTTDIADFEGGPVKEDDEQKLLSSCPRVKGSEPKSPDHGACPSKGLNCKEAHAACCAVFYDYGVEVELVSALSATGAVVHKTASCTLDVTYPEDTIDGDPTAGRKTKKCKGSKATPPDYVRGEKVEIAARGPNDKLYYFEVVSREKPLGAFKCGNQKVNIVYEGVVVVGELEAKILDEVQGTTDGVVGSKDTTQINVIVFNLPCKTGSFVCNRAYKCDKPMDAEGPVVAKLNPGRAALVLHHPEQDKGLNLTGGVHNDTPDGVQKGLDITPTSVAPPMKQQVHNVVMRKKDTLDSKAQIATPETAFVNADAEPVSPWSELIVSEKLGENALGTLQPFHQAVDTTVAKPYRAPLAPWGAVVVNEQFVPAVSVNIGAERESEYILQTAGKCIADDLEGITETNKAVTTREDGPSISYIPSGGDAVSYDTQNRVGTTSLSPWKVDRGVSLSVGALKLLRIVWNDFCADTPVCVAGEVSYSTVGRGVSAGVAAPNPPVKAMVSRPIGTVSRIGGSDTRAGMKFSMHTGGIHTTKSKDDGESGSSYGGDTTVIEYGVEGGSTTVQELAIAPVGAYNLSAQPFGVKGRNEETKKTYSFQVAFVFGVLIFPESPRSREIQNPPAPIVYFVKSGDAQDKGGKEKAGTALIPFMVDPASGLKMYGPMGTRNQNDLGQESQGGTPSKTSEDDVSYNETKQLRATGGAGEETSDADSPKRLSEHGASASPMVQMGIGVINLEYGAPSVTPTVEPCRVTEYVSSSDSEGYAGTRVSAGVDQIDVKPLITLQIYPRSLYQVQENKCLATQAAIVYSSADVVPVVVLNKSGHGKFKVDRTDRKQHEVHYGNKCDDTNGDKNIGGNPSTVLESKDCCGISCVPLKVKTGKGVGPVTMSPPMGPAVHGGDIVHSLREVVVVSAVGKSDVVRGAGVAESKVISKRVAVTMADFSYVEKGIGRKGFSETDFGHKGPGDGRVVGSSRKVSSFFVIFQPAGGWKVIEVILHDAIIGGDGQIGGTANPFVGYTLKEASGVDYADVPVIGVLAYYVAELYRDQHGTDQGPGPEGNEITADPGVGTGAEDGRASGYGAGIVTTKTTDSTGCPHRPVQAERLGRKLRSEPVMGVKPGVGGTHCNEDINEKTGIALDVVRAPPAFQPSISGVHTKSSATDVGPDVFDTGGVALVCQPVVGSVVSPYYCPPFGAGVIECYPMSTDPADSSRRNFKPPQRVVTTTEAGDDSGAYVYRYFGPGADMKLPKDSSDVVGNGDCESDPPKLSGNVPQHPEQYSTPAESMRGDPAVSDSLVMANVEFPKCEPDQNYGGHDGKVAPFFDRENEQVDVGLPNDSKGPCVRGVFPLFHYIGSVAPRAVIKCPTTLGPIGQTGGFPGFKSIAYLLIGTGCFQKLLKYVITELVDNCDGCRAKYGSDSTGSFVMEAKGLPIQGFKGKSGTDKCNHEKVDIELTTSGKRPRPPANQAKIEDVLPNAVTDVKECTAVYVDREIELDEIDPHTAQGHRYKRGPKEPIAWSIELSPSGRYMVELLVEISVAFVPPIPIFGTEVAPVGAPAISTSGSPGPAIGRVTLGQKAALPTEPEPSNSYARVDRQEEKRTPEGCGEAAKAHHPPFGINPLAQVIEDQDAYHFDHVGARIGLERGTSCDGESEAIEGPVLYAAPAKAAPSGEVHIARQDVKDPLAGGELHTVLDRCDAVSYESSKSQPLHTITFSKPEPGKSDAMITPPVIEPIVFIWIQRAHFPNGETSLGSSRAFAGKRVSKTYGGSDLRECWIGGGPKKNLKPCQPGEGTGKPITGEPLGMVIVRTLPRWELVKHFLVAPGTVIGTTGHADHVSRPGKPVLIPTERANWPVPRHYTELHDGREVKCTREGVKFHRLDTVNAAVHKNYRHPSSKSSCLWHGVVTKEQAGQISIREFVEDVSPGSIIVDIVNLVAVQGPSSTGSGLGVVHAYPLTYYTVKDIVVALKLSSASFIMVNKKAVVTVCFSDVQSGFKKNVASPPGVLSVSIGLDTYEGDPGIATNWWPSTDEKPCGNVLEDSGPDENHSNPNTAWEFTGLGDTKEGRPNTAFVESEMVLLPVAYVLEQKHPGQGQVGNTMLKDGICEGSTSHVGAVDPSEVQPLGFPGRLITKKFLETFIFCYPSEPIGKGKKVDGKLTSSYSSELAERELVLALAVGIGDAVYYYAFGAGPKIHVFTGDGGGVKNGILVLEGPFHGDEPDLGPFNPGPTQGVERGYSGGEKLATPTVTTYVPELVGLVVVGGTDGIGVHAAVVERWGTYDGKVSPQSVYTTKPGPLSGSDDIHLNVKTVKYLHDEGYTFTIPPHGEKVVEVVEAEQVGRQSDGTTYVTQNNAQAIPVKLRRTAPYGELGHVKLDQVGEEYFGIKFHVNGCDGPGTGPENATYVEQTSGVPPRTPVFGFSVEGTLIQSPQIALNKGRHAVTTIIKQARPFLGGVKGTTDQTPDAFVPHKQTEPLVAACKYVGGWYNHVVPKGKAGEGQGQHRPAVKRANPSDEQAMQSMKKPSPPTPQGEEVSTSVKDLEPESYFQQNVYVNVPAHIGKKLPGIECNQND', + 'accession': 'SHD00644576.1', + 'decoy DB accession regexp': '^SHD', + 'decoy DB generation algorithm': 'PeakQuant.DecoyDatabaseBuilder', + 'end': 2397, + 'isDecoy': True, + 'location': 'file://www.medizinisches-proteom-center.de/DBServer/ipi.HUMAN/3.15/ipi.HUMAN_decoy.fasta', + "decoy DB from IPI_human": '', + "DB composition target+decoy": '', + "decoy DB type shuffle": '', + 'numDatabaseSequences': 58099, + 'post': 'L', + 'pre': 'R', + 'protein description': '>SHD:SHD00644576.1|TREMBL:Q5HY54;Q86TQ3;Q96C61|ENSEMBL:ENSP00000358863|VEGA:OTTHUMP00000064890 Tax_Id=9606 Gene_Symbol=FLNA Filamin A, alpha', + 'releaseDate': '2006-02-22T09:30:47Z', + 'start': 2378, + 'version': '3.15'}], + 'PeptideSequence': 'QSDGTTYVTQNNAQAIPVK', + 'calculatedMassToCharge': 2035.0017, + 'chargeState': 1, + 'experimentalMassToCharge': 2035.002, + 'passThreshold': True, + 'rank': 1}], + 'location': 'proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X', + 'spectrumID': 'databasekey=40'}]} mzml_mz_array = np.load('test_mzml_mz.npy') mzml_int_array = np.load('test_mzml_intensity.npy') mzml_spectra = [{'MSn spectrum': '', - 'base peak intensity': 1471973.875, - 'base peak m/z': 810.415283203125, - 'count': 2, - 'defaultArrayLength': 19914, - 'highest observed m/z': 2000.0099466203771, - 'id': 'controllerType=0 controllerNumber=1 scan=1', - 'index': 0, - 'intensity array': makeCA(mzml_int_array), - 'lowest observed m/z': 200.00018816645022, - 'm/z array': makeCA(mzml_mz_array), - 'ms level': 1, - 'positive scan': '', - 'profile spectrum': '', - 'scanList': {'count': 1, - 'no combination': '', - 'scan': [{'[Thermo Trailer Extra]Monoisotopic M/Z:': 810.4152221679688, - 'filter string': 'FTMS + p ESI Full ms [200.00-2000.00]', - 'instrumentConfigurationRef': 'IC1', - 'preset scan configuration': 1.0, - 'scan start time': 0.004935, - 'scanWindowList': {'count': 1, - 'scanWindow': [{'scan window lower limit': 200.0, - 'scan window upper limit': 2000.0}]}}]}, - 'total ion current': 15245068.0}, - {'MSn spectrum': '', - 'base peak intensity': 1471973.875, - 'base peak m/z': 810.415283203125, - 'count': 2, - 'defaultArrayLength': 19914, - 'highest observed m/z': 2000.0099466203771, - 'id': 'controllerType=0 controllerNumber=1 scan=2', - 'index': 1, - 'intensity array': makeCA(mzml_int_array), - 'lowest observed m/z': 200.00018816645022, - 'm/z array': makeCA(mzml_mz_array), - 'ms level': 1, - 'positive scan': '', - 'profile spectrum': '', - 'scanList': {'count': 1, - 'no combination': '', - 'scan': [{'[Thermo Trailer Extra]Monoisotopic M/Z:': 810.4152221679688, - 'filter string': 'FTMS + p ESI Full ms [200.00-2000.00]', - 'instrumentConfigurationRef': 'IC1', - 'preset scan configuration': 1.0, - 'scan start time': 0.005935, - 'scanWindowList': {'count': 1, - 'scanWindow': [{'scan window lower limit': 200.0, - 'scan window upper limit': 2000.0}]}}]}, - 'total ion current': 15245068.0}] + 'base peak intensity': 1471973.875, + 'base peak m/z': 810.415283203125, + 'count': 2, + 'defaultArrayLength': 19914, + 'highest observed m/z': 2000.0099466203771, + 'id': 'controllerType=0 controllerNumber=1 scan=1', + 'index': 0, + 'intensity array': makeCA(mzml_int_array), + 'lowest observed m/z': 200.00018816645022, + 'm/z array': makeCA(mzml_mz_array), + 'ms level': 1, + 'positive scan': '', + 'profile spectrum': '', + 'scanList': {'count': 1, + 'no combination': '', + 'scan': [{'[Thermo Trailer Extra]Monoisotopic M/Z:': 810.4152221679688, + 'filter string': 'FTMS + p ESI Full ms [200.00-2000.00]', + 'instrumentConfigurationRef': 'IC1', + 'preset scan configuration': 1.0, + 'scan start time': 0.004935, + 'scanWindowList': {'count': 1, + 'scanWindow': [{'scan window lower limit': 200.0, + 'scan window upper limit': 2000.0}]}}]}, + 'total ion current': 15245068.0}, + {'MSn spectrum': '', + 'base peak intensity': 1471973.875, + 'base peak m/z': 810.415283203125, + 'count': 2, + 'defaultArrayLength': 19914, + 'highest observed m/z': 2000.0099466203771, + 'id': 'controllerType=0 controllerNumber=1 scan=2', + 'index': 1, + 'intensity array': makeCA(mzml_int_array), + 'lowest observed m/z': 200.00018816645022, + 'm/z array': makeCA(mzml_mz_array), + 'ms level': 1, + 'positive scan': '', + 'profile spectrum': '', + 'scanList': {'count': 1, + 'no combination': '', + 'scan': [{'[Thermo Trailer Extra]Monoisotopic M/Z:': 810.4152221679688, + 'filter string': 'FTMS + p ESI Full ms [200.00-2000.00]', + 'instrumentConfigurationRef': 'IC1', + 'preset scan configuration': 1.0, + 'scan start time': 0.005935, + 'scanWindowList': {'count': 1, + 'scanWindow': [{'scan window lower limit': 200.0, + 'scan window upper limit': 2000.0}]}}]}, + 'total ion current': 15245068.0}] - -mgf_int = [np.array([ 73., 44., 67., 291., 54., 49.]), - np.array([ 237., 128., 108., 1007., 974., 79.])] -mgf_mz = [np.array([ 846.6, 846.8, 847.6, 1640.1, 1640.6, 1895.5]), - np.array([ 345.1, 370.2, 460.2, 1673.3, 1674. , 1675.3])] -mgf_ch = [np.ma.masked_equal([0]*6, 0), - np.array([ 3., 2., 1., 1., 1., 1.])] +mgf_int = [np.array([73., 44., 67., 291., 54., 49.]), + np.array([237., 128., 108., 1007., 974., 79.])] +mgf_mz = [np.array([846.6, 846.8, 847.6, 1640.1, 1640.6, 1895.5]), + np.array([345.1, 370.2, 460.2, 1673.3, 1674., 1675.3])] +mgf_ch = [np.ma.masked_equal([0] * 6, 0), + np.array([3., 2., 1., 1., 1., 1.])] mgf_spectra_long = [{'intensity array': makeCA(mgf_int[0]), - 'm/z array': makeCA(mgf_mz[0]), - 'charge array': makeCA(mgf_ch[0]), - 'params': {'charge': [2], - 'com': 'Based on http://www.matrixscience.com/help/data_file_help.html', - 'it_mods': 'Oxidation (M)', - 'itol': '1', - 'itolu': 'Da', - 'mass': 'Monoisotopic', - 'mods': 'Carbamidomethyl (C)', - 'pepmass': (983.6, None), - 'title': 'Spectrum 1', - 'useremail': 'leu@altered-state.edu', - 'username': 'Lou Scene'}}, - {'intensity array': makeCA(mgf_int[1]), - 'm/z array': makeCA(mgf_mz[1]), - 'charge array': makeCA(mgf_ch[1]), - 'params': {'charge': [2, 3], - 'com': 'Based on http://www.matrixscience.com/help/data_file_help.html', - 'it_mods': 'Oxidation (M)', - 'itol': '1', - 'itolu': 'Da', - 'mass': 'Monoisotopic', - 'mods': 'Carbamidomethyl (C)', - 'pepmass': (1084.9, 1234.0), - 'rtinseconds': 25.0, - 'scans': '3', - 'title': 'Spectrum 2', - 'useremail': 'leu@altered-state.edu', - 'username': 'Lou Scene'}}] + 'm/z array': makeCA(mgf_mz[0]), + 'charge array': makeCA(mgf_ch[0]), + 'params': {'charge': [2], + 'com': 'Based on http://www.matrixscience.com/help/data_file_help.html', + 'it_mods': 'Oxidation (M)', + 'itol': '1', + 'itolu': 'Da', + 'mass': 'Monoisotopic', + 'mods': 'Carbamidomethyl (C)', + 'pepmass': (983.6, None), + 'title': 'Spectrum 1', + 'useremail': 'leu@altered-state.edu', + 'username': 'Lou Scene'}}, + {'intensity array': makeCA(mgf_int[1]), + 'm/z array': makeCA(mgf_mz[1]), + 'charge array': makeCA(mgf_ch[1]), + 'params': {'charge': [2, 3], + 'com': 'Based on http://www.matrixscience.com/help/data_file_help.html', + 'it_mods': 'Oxidation (M)', + 'itol': '1', + 'itolu': 'Da', + 'mass': 'Monoisotopic', + 'mods': 'Carbamidomethyl (C)', + 'pepmass': (1084.9, 1234.0), + 'rtinseconds': 25.0, + 'scans': '3', + 'title': 'Spectrum 2', + 'useremail': 'leu@altered-state.edu', + 'username': 'Lou Scene'}}] mgf_spectra_short = [{'intensity array': makeCA(mgf_int[0]), - 'charge array': makeCA(mgf_ch[0]), - 'm/z array': makeCA(mgf_mz[0]), - 'params': {'pepmass': (983.6, None), 'title': 'Spectrum 1', - 'charge': [2]}}, - {'intensity array': makeCA(mgf_int[1]), - 'm/z array': makeCA(mgf_mz[1]), - 'charge array': makeCA(mgf_ch[1]), - 'params': {'pepmass': (1084.9, 1234.0), - 'rtinseconds': 25.0, - 'scans': '3', - 'title': 'Spectrum 2'}}] + 'charge array': makeCA(mgf_ch[0]), + 'm/z array': makeCA(mgf_mz[0]), + 'params': {'pepmass': (983.6, None), 'title': 'Spectrum 1', + 'charge': [2]}}, + {'intensity array': makeCA(mgf_int[1]), + 'm/z array': makeCA(mgf_mz[1]), + 'charge array': makeCA(mgf_ch[1]), + 'params': {'pepmass': (1084.9, 1234.0), + 'rtinseconds': 25.0, + 'scans': '3', + 'title': 'Spectrum 2'}}] mgf_spectra_short_no_charges = deepcopy(mgf_spectra_short) for s in mgf_spectra_short_no_charges: @@ -1337,6 +1420,32 @@ def makeCA(arr): for key in ['m/z array', 'intensity array', 'charge array']: s[key] = list(s[key]) +mgf_annotated_int = [np.array([0.013, 0.049, 0.059, 0.012, 0.454, 0.002, 0.956, 0.098]), + np.array([0.597, 0.091, 0.063, 0.177, 0.165, 0.038, 0.043, 0.026, 0.213, 0.288, 0.177])] +mgf_annotated_mz = [np.array([138.0, 153.5, 375.1, 484.2, 662.8, 698.3, 1130.2, 1395.4]), + np.array([156.0, 157.1, 162.5, 211.1, 227.1, 228.1, 418.1, 698.3, 835.3, 949.4, 1112.7])] +mgf_annotated_ions = [np.array(["b1+1", "b3+2", "y3+1", "y7+2", "y10+2", "y11+2", "y8+1", "y11+1"]), + np.array(["y1+1", "b1+1", "y3+2", "y4+2", "y2+1", "b2+1", "b6+2", "y6+1", "b6+1", "b7+1", + "b8+1"])] + +mgf_spectra_annotated_long = [{'intensity array': makeCA(mgf_annotated_int[0]), + 'm/z array': makeCA(mgf_annotated_mz[0]), + 'ion array': mgf_annotated_ions[0], + 'params': {'charge': [2], + 'pepmass': (766.84948, None), + 'min_mz': '69.5367320', + 'max_mz': '1395.63277', + 'title': 'HAPPYNEWYEAR||2'}}, + {'intensity array': makeCA(mgf_annotated_int[1]), + 'm/z array': makeCA(mgf_annotated_mz[1]), + 'ion array': mgf_annotated_ions[1], + 'params': {'charge': [3], + 'pepmass': (511.56875, None), + 'title': 'RAEYWENYPPAH||3', + 'min_mz': '69.5367320', + 'max_mz': '1395.63277', + }}] + def decode_dict(d, encoding='utf-8'): """Recursively decode all strings in a dict""" @@ -1357,1139 +1466,1536 @@ def decode_dict(d, encoding='utf-8'): out[newk] = v return out + mgf_spectra_long_decoded = [decode_dict(s) for s in mgf_spectra_long - ] if sys.version_info.major == 2 else mgf_spectra_long + ] if sys.version_info.major == 2 else mgf_spectra_long mgf_spectra_short_decoded = [decode_dict(s) for s in mgf_spectra_short - ] if sys.version_info.major == 2 else mgf_spectra_short + ] if sys.version_info.major == 2 else mgf_spectra_short tandem_spectra = [{'act': '0', - 'expect': 1.5e-07, - 'fI': 48232.2, - 'id': '11745', - 'maxI': 4823220.0, - 'mh': 800.418907, - 'protein': [{'expect': -989.8, - 'file': {'URL': '/home/lab006/fasta/uniprot_sprot.fasta', - 'type': 'peptide'}, - 'id': '11745.1', - 'label': 'sp|P35579|MYH9_HUMAN Myosin-9 OS=Homo sapiens GN=MYH9 PE=1 SV=4', - 'note': 'sp|P35579|MYH9_HUMAN Myosin-9 OS=Homo sapiens GN=MYH9 PE=1 SV=4', - 'peptide': {'b_ions': 2, - 'b_score': 8.2, - 'delta': 0.0, - 'end': 14, - 'expect': 1.5e-07, - 'hyperscore': 16.4, - 'id': '11745.1.1', - 'mh': 800.4189, - 'missed_cleavages': 0, - 'nextscore': 16.4, - 'post': 'NFIN', - 'pre': 'AADK', - 'seq': 'YLYVDK', - 'start': 9, - 'y_ions': 3, - 'y_score': 11.8}, - 'sumI': 8.29, - 'uid': '249282'}, - {'expect': -784.7, - 'file': {'URL': '/home/lab006/fasta/uniprot_sprot.fasta', - 'type': 'peptide'}, - 'id': '11745.2', - 'label': 'sp|Q258K2|MYH9_CANFA Myosin-9 OS=Canis familiaris GN=MYH9 PE=2 SV=1', - 'note': 'sp|Q258K2|MYH9_CANFA Myosin-9 OS=Canis familiaris GN=MYH9 PE=2 SV=1', - 'peptide': {'b_ions': 2, - 'b_score': 8.2, - 'delta': 0.0, - 'end': 14, - 'expect': 1.5e-07, - 'hyperscore': 16.4, - 'id': '11745.2.1', - 'mh': 800.4189, - 'missed_cleavages': 0, - 'nextscore': 16.4, - 'post': 'NFIN', - 'pre': 'AADK', - 'seq': 'YLYVDK', - 'start': 9, - 'y_ions': 3, - 'y_score': 11.8}, - 'sumI': 8.24, - 'uid': '249280'}, - {'expect': -660.7, - 'file': {'URL': '/home/lab006/fasta/uniprot_sprot.fasta', - 'type': 'peptide'}, - 'id': '11745.3', - 'label': 'sp|Q8VDD5|MYH9_MOUSE Myosin-9 OS=Mus musculus GN=Myh9 PE=1 SV=4', - 'note': 'sp|Q8VDD5|MYH9_MOUSE Myosin-9 OS=Mus musculus GN=Myh9 PE=1 SV=4', - 'peptide': {'b_ions': 2, - 'b_score': 8.2, - 'delta': 0.0, - 'end': 14, - 'expect': 1.5e-07, - 'hyperscore': 16.4, - 'id': '11745.3.1', - 'mh': 800.4189, - 'missed_cleavages': 0, - 'nextscore': 16.4, - 'post': 'NFIN', - 'pre': 'AADK', - 'seq': 'YLYVDK', - 'start': 9, - 'y_ions': 3, - 'y_score': 11.8}, - 'sumI': 8.19, - 'uid': '249283'}, - {'expect': -654.3, - 'file': {'URL': '/home/lab006/fasta/uniprot_sprot.fasta', - 'type': 'peptide'}, - 'id': '11745.4', - 'label': 'sp|Q62812|MYH9_RAT Myosin-9 OS=Rattus norvegicus GN=Myh9 PE=1 SV=3', - 'note': 'sp|Q62812|MYH9_RAT Myosin-9 OS=Rattus norvegicus GN=Myh9 PE=1 SV=3', - 'peptide': {'b_ions': 2, - 'b_score': 8.2, - 'delta': 0.0, - 'end': 14, - 'expect': 1.5e-07, - 'hyperscore': 16.4, - 'id': '11745.4.1', - 'mh': 800.4189, - 'missed_cleavages': 0, - 'nextscore': 16.4, - 'post': 'NFIN', - 'pre': 'AADK', - 'seq': 'YLYVDK', - 'start': 9, - 'y_ions': 3, - 'y_score': 11.8}, - 'sumI': 8.15, - 'uid': '249284'}, - {'expect': -463.3, - 'file': {'URL': '/home/lab006/fasta/uniprot_sprot.fasta', - 'type': 'peptide'}, - 'id': '11745.5', - 'label': 'sp|P14105|MYH9_CHICK Myosin-9 OS=Gallus gallus GN=MYH9 PE=2 SV=1', - 'note': 'sp|P14105|MYH9_CHICK Myosin-9 OS=Gallus gallus GN=MYH9 PE=2 SV=1', - 'peptide': {'b_ions': 2, - 'b_score': 8.2, - 'delta': 0.0, - 'end': 14, - 'expect': 1.5e-07, - 'hyperscore': 16.4, - 'id': '11745.5.1', - 'mh': 800.4189, - 'missed_cleavages': 0, - 'nextscore': 16.4, - 'post': 'NIIN', - 'pre': 'DADK', - 'seq': 'YLYVDK', - 'start': 9, - 'y_ions': 3, - 'y_score': 11.8}, - 'sumI': 8.05, - 'uid': '249281'}], - 'rt': 42.0, - 'sumI': 6.93, - 'support': {'fragment ion mass spectrum': {'M+H': 800.419, - 'Xdata': {'units': 'MASSTOCHARGERATIO', - 'values': makeCA(np.array([ 174.759, 249.16 , 262.135, 277.155, 361.208, 378.203, - 401.716, 440.218, 472.624, 495.27 , 504.276, 524.271, - 526.277, 637.355]))}, - 'Ydata': {'units': 'UNKNOWN', - 'values': makeCA(np.array([ 2., 22., 3., 13., 4., 1., 5., 2., 2., - 2., 10., 100., 4., 6.]))}, - 'charge': 2, - 'id': '11745', - 'label': '11745.spectrum', - 'note': 'YLYVDK'}, - 'supporting data': {'b ion histogram': {'Xdata': {'units': 'number of ions', - 'values': makeCA(np.array([0, 1, 2, 3]))}, - 'Ydata': {'units': 'counts', 'values': makeCA(np.array([346, 64, 21, 0]))}, - 'label': '11745.b'}, - 'convolution survival function': {'Xdata': {'units': 'score', - 'values': makeCA(np.array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13]))}, - 'Ydata': {'units': 'counts', - 'values': makeCA(np.array([351, 351, 351, 309, 99, 20, 1, 0, 0, 0, 80, 0, 43, 0]))}, - 'label': '11745.convolute'}, - 'hyperscore expectation function': {'Xdata': {'units': 'score', - 'values': makeCA(np.array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, - 17]))}, - 'Ydata': {'units': 'counts', - 'values': makeCA(np.array([350, 350, 350, 308, 98, 19, 0, 81, 0, 0, 80, 3, 0, - 47, 4, 0, 10, 0]))}, - 'a0': 4.84111, - 'a1': -0.712472, - 'label': '11745.hyper'}, - 'y ion histogram': {'Xdata': {'units': 'number of ions', - 'values': makeCA(np.array([0, 1, 2, 3, 4]))}, - 'Ydata': {'units': 'counts', 'values': makeCA(np.array([ 2, 381, 38, 10, 0]))}, - 'label': '11745.y'}}}, - 'z': 2}] + 'expect': 1.5e-07, + 'fI': 48232.2, + 'id': '11745', + 'maxI': 4823220.0, + 'mh': 800.418907, + 'protein': [{'expect': -989.8, + 'file': {'URL': '/home/lab006/fasta/uniprot_sprot.fasta', + 'type': 'peptide'}, + 'id': '11745.1', + 'label': 'sp|P35579|MYH9_HUMAN Myosin-9 OS=Homo sapiens GN=MYH9 PE=1 SV=4', + 'note': 'sp|P35579|MYH9_HUMAN Myosin-9 OS=Homo sapiens GN=MYH9 PE=1 SV=4', + 'peptide': {'b_ions': 2, + 'b_score': 8.2, + 'delta': 0.0, + 'end': 14, + 'expect': 1.5e-07, + 'hyperscore': 16.4, + 'id': '11745.1.1', + 'mh': 800.4189, + 'missed_cleavages': 0, + 'nextscore': 16.4, + 'post': 'NFIN', + 'pre': 'AADK', + 'seq': 'YLYVDK', + 'start': 9, + 'y_ions': 3, + 'y_score': 11.8}, + 'sumI': 8.29, + 'uid': '249282'}, + {'expect': -784.7, + 'file': {'URL': '/home/lab006/fasta/uniprot_sprot.fasta', + 'type': 'peptide'}, + 'id': '11745.2', + 'label': 'sp|Q258K2|MYH9_CANFA Myosin-9 OS=Canis familiaris GN=MYH9 PE=2 SV=1', + 'note': 'sp|Q258K2|MYH9_CANFA Myosin-9 OS=Canis familiaris GN=MYH9 PE=2 SV=1', + 'peptide': {'b_ions': 2, + 'b_score': 8.2, + 'delta': 0.0, + 'end': 14, + 'expect': 1.5e-07, + 'hyperscore': 16.4, + 'id': '11745.2.1', + 'mh': 800.4189, + 'missed_cleavages': 0, + 'nextscore': 16.4, + 'post': 'NFIN', + 'pre': 'AADK', + 'seq': 'YLYVDK', + 'start': 9, + 'y_ions': 3, + 'y_score': 11.8}, + 'sumI': 8.24, + 'uid': '249280'}, + {'expect': -660.7, + 'file': {'URL': '/home/lab006/fasta/uniprot_sprot.fasta', + 'type': 'peptide'}, + 'id': '11745.3', + 'label': 'sp|Q8VDD5|MYH9_MOUSE Myosin-9 OS=Mus musculus GN=Myh9 PE=1 SV=4', + 'note': 'sp|Q8VDD5|MYH9_MOUSE Myosin-9 OS=Mus musculus GN=Myh9 PE=1 SV=4', + 'peptide': {'b_ions': 2, + 'b_score': 8.2, + 'delta': 0.0, + 'end': 14, + 'expect': 1.5e-07, + 'hyperscore': 16.4, + 'id': '11745.3.1', + 'mh': 800.4189, + 'missed_cleavages': 0, + 'nextscore': 16.4, + 'post': 'NFIN', + 'pre': 'AADK', + 'seq': 'YLYVDK', + 'start': 9, + 'y_ions': 3, + 'y_score': 11.8}, + 'sumI': 8.19, + 'uid': '249283'}, + {'expect': -654.3, + 'file': {'URL': '/home/lab006/fasta/uniprot_sprot.fasta', + 'type': 'peptide'}, + 'id': '11745.4', + 'label': 'sp|Q62812|MYH9_RAT Myosin-9 OS=Rattus norvegicus GN=Myh9 PE=1 SV=3', + 'note': 'sp|Q62812|MYH9_RAT Myosin-9 OS=Rattus norvegicus GN=Myh9 PE=1 SV=3', + 'peptide': {'b_ions': 2, + 'b_score': 8.2, + 'delta': 0.0, + 'end': 14, + 'expect': 1.5e-07, + 'hyperscore': 16.4, + 'id': '11745.4.1', + 'mh': 800.4189, + 'missed_cleavages': 0, + 'nextscore': 16.4, + 'post': 'NFIN', + 'pre': 'AADK', + 'seq': 'YLYVDK', + 'start': 9, + 'y_ions': 3, + 'y_score': 11.8}, + 'sumI': 8.15, + 'uid': '249284'}, + {'expect': -463.3, + 'file': {'URL': '/home/lab006/fasta/uniprot_sprot.fasta', + 'type': 'peptide'}, + 'id': '11745.5', + 'label': 'sp|P14105|MYH9_CHICK Myosin-9 OS=Gallus gallus GN=MYH9 PE=2 SV=1', + 'note': 'sp|P14105|MYH9_CHICK Myosin-9 OS=Gallus gallus GN=MYH9 PE=2 SV=1', + 'peptide': {'b_ions': 2, + 'b_score': 8.2, + 'delta': 0.0, + 'end': 14, + 'expect': 1.5e-07, + 'hyperscore': 16.4, + 'id': '11745.5.1', + 'mh': 800.4189, + 'missed_cleavages': 0, + 'nextscore': 16.4, + 'post': 'NIIN', + 'pre': 'DADK', + 'seq': 'YLYVDK', + 'start': 9, + 'y_ions': 3, + 'y_score': 11.8}, + 'sumI': 8.05, + 'uid': '249281'}], + 'rt': 42.0, + 'sumI': 6.93, + 'support': {'fragment ion mass spectrum': {'M+H': 800.419, + 'Xdata': {'units': 'MASSTOCHARGERATIO', + 'values': makeCA(np.array( + [174.759, 249.16, 262.135, 277.155, 361.208, + 378.203, + 401.716, 440.218, 472.624, 495.27, 504.276, + 524.271, + 526.277, 637.355]))}, + 'Ydata': {'units': 'UNKNOWN', + 'values': makeCA(np.array( + [2., 22., 3., 13., 4., 1., 5., 2., 2., + 2., 10., 100., 4., 6.]))}, + 'charge': 2, + 'id': '11745', + 'label': '11745.spectrum', + 'note': 'YLYVDK'}, + 'supporting data': {'b ion histogram': {'Xdata': {'units': 'number of ions', + 'values': makeCA( + np.array([0, 1, 2, 3]))}, + 'Ydata': {'units': 'counts', 'values': makeCA( + np.array([346, 64, 21, 0]))}, + 'label': '11745.b'}, + 'convolution survival function': {'Xdata': {'units': 'score', + 'values': makeCA( + np.array( + [0, 1, 2, 3, 4, + 5, 6, 7, 8, 9, + 10, 11, 12, + 13]))}, + 'Ydata': {'units': 'counts', + 'values': makeCA( + np.array( + [351, 351, 351, + 309, 99, 20, 1, + 0, 0, 0, 80, 0, + 43, 0]))}, + 'label': '11745.convolute'}, + 'hyperscore expectation function': {'Xdata': {'units': 'score', + 'values': makeCA( + np.array( + [0, 1, 2, 3, 4, + 5, 6, 7, 8, 9, + 10, 11, 12, + 13, 14, 15, + 16, + 17]))}, + 'Ydata': {'units': 'counts', + 'values': makeCA( + np.array( + [350, 350, 350, + 308, 98, 19, + 0, 81, 0, 0, + 80, 3, 0, + 47, 4, 0, 10, + 0]))}, + 'a0': 4.84111, + 'a1': -0.712472, + 'label': '11745.hyper'}, + 'y ion histogram': {'Xdata': {'units': 'number of ions', + 'values': makeCA( + np.array([0, 1, 2, 3, 4]))}, + 'Ydata': {'units': 'counts', 'values': makeCA( + np.array([2, 381, 38, 10, 0]))}, + 'label': '11745.y'}}}, + 'z': 2}] features = [{'FWHM': 8.53579425811768, - 'charge': 1, - 'convexhull': [{'nr': 0, - 'pt': [{'x': 4020.447, 'y': 489.778198242188}, - {'x': 4026.53226, 'y': 489.778198242188}, - {'x': 4026.53226, 'y': 489.778747558594}, - {'x': 4020.447, 'y': 489.778747558594}]}, - {'nr': 1, - 'pt': [{'x': 4019.229, 'y': 490.779388427734}, - {'x': 4026.53226, 'y': 490.779388427734}, - {'x': 4026.53226, 'y': 490.780151367188}, - {'x': 4019.229, 'y': 490.780151367188}]}], - 'id': 'f_16832770593554750385', - 'intensity': 666996000.0, - 'label': 0.0, - 'overallquality': 0.791454, - 'position': [{'dim': 0, 'position': 4022.03514673128}, - {'dim': 1, 'position': 489.778444938208}], - 'quality': [{'dim': 0, 'quality': 0}, {'dim': 1, 'quality': 0}], - 'score_correlation': 0.991616770766787, - 'score_fit': 0.631694771390403, - 'spectrum_index': 4, - 'spectrum_native_id': 'controllerType=0 controllerNumber=1 scan=29899'}, - {'FWHM': 7.54492568969727, - 'charge': 3, - 'convexhull': [{'nr': 0, - 'pt': [{'x': 4020.447, 'y': 639.657653808594}, - {'x': 4026.53226, 'y': 639.657653808594}, - {'x': 4026.53226, 'y': 639.658386230469}, - {'x': 4020.447, 'y': 639.658386230469}]}, - {'nr': 1, - 'pt': 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345095000.0, - 'label': 82.0, - 'overallquality': 0.945634, - 'position': [{'dim': 0, 'position': 4022.97774692935}, - {'dim': 1, 'position': 639.656521928634}], - 'quality': [{'dim': 0, 'quality': 0}, {'dim': 1, 'quality': 0}], - 'score_correlation': 0.994121041144976, - 'score_fit': 0.899512445523661, - 'spectrum_index': 5, - 'spectrum_native_id': 'controllerType=0 controllerNumber=1 scan=29910'}] + 'charge': 1, + 'convexhull': [{'nr': 0, + 'pt': [{'x': 4020.447, 'y': 489.778198242188}, + {'x': 4026.53226, 'y': 489.778198242188}, + {'x': 4026.53226, 'y': 489.778747558594}, + {'x': 4020.447, 'y': 489.778747558594}]}, + {'nr': 1, + 'pt': [{'x': 4019.229, 'y': 490.779388427734}, + {'x': 4026.53226, 'y': 490.779388427734}, + {'x': 4026.53226, 'y': 490.780151367188}, + {'x': 4019.229, 'y': 490.780151367188}]}], + 'id': 'f_16832770593554750385', + 'intensity': 666996000.0, + 'label': 0.0, + 'overallquality': 0.791454, + 'position': [{'dim': 0, 'position': 4022.03514673128}, + {'dim': 1, 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B2 at 193 nm RT.RAW'} + 'Extractor version': 'Xcalibur', + 'Extractor': 'ProteoWizard', + 'Source file': 'Set 1. B2 at 193 nm RT.RAW'} -ms2_spectra = [{'intensity array': makeCA([ 73., 44., 67., 291., 54., 49.]), - 'm/z array': makeCA([ 846.6, 846.8, 847.6, 1640.1, 1640.6, 1895.5]), - 'params': {'charge': [2.0], - 'neutral mass': [1966.193], - 'precursor m/z': 983.6, - 'scan': ('0', '0')}}, - {'intensity array': makeCA([ 237., 128., 108., 1007., 974., 79.]), - 'm/z array': makeCA([ 345.1, 370.2, 460.2, 1673.3, 1674. , 1675.3]), - 'params': {'RTime': 25.0, 'precursor m/z': 1084.9, 'scan': ('1', '1')}}] +ms2_spectra = [{'intensity array': makeCA([73., 44., 67., 291., 54., 49.]), + 'm/z array': makeCA([846.6, 846.8, 847.6, 1640.1, 1640.6, 1895.5]), + 'params': {'charge': [2.0], + 'neutral mass': [1966.193], + 'precursor m/z': 983.6, + 'scan': ('0', '0')}}, + {'intensity array': makeCA([237., 128., 108., 1007., 974., 79.]), + 'm/z array': makeCA([345.1, 370.2, 460.2, 1673.3, 1674., 1675.3]), + 'params': {'RTime': 25.0, 'precursor m/z': 1084.9, 'scan': ('1', '1')}}] -ms2_spectra_lists = [{'intensity array': [ 73., 44., 67., 291., 54., 49.], - 'm/z array': [ 846.6, 846.8, 847.6, 1640.1, 1640.6, 1895.5], - 'params': {'charge': [2.0], - 'neutral mass': [1966.193], - 'precursor m/z': 983.6, - 'scan': ('0', '0')}}, - {'intensity array': [ 237., 128., 108., 1007., 974., 79.], - 'm/z array': [ 345.1, 370.2, 460.2, 1673.3, 1674. , 1675.3], - 'params': {'RTime': 25.0, 'precursor m/z': 1084.9, 'scan': ('1', '1')}}] +ms2_spectra_lists = [{'intensity array': [73., 44., 67., 291., 54., 49.], + 'm/z array': [846.6, 846.8, 847.6, 1640.1, 1640.6, 1895.5], + 'params': {'charge': [2.0], + 'neutral mass': [1966.193], + 'precursor m/z': 983.6, + 'scan': ('0', '0')}}, + {'intensity array': [237., 128., 108., 1007., 974., 79.], + 'm/z array': [345.1, 370.2, 460.2, 1673.3, 1674., 1675.3], + 'params': {'RTime': 25.0, 'precursor m/z': 1084.9, 'scan': ('1', '1')}}] ms2_header = {'CreationDate': 'Wed Apr 24 17:06:23 2019', - 'Extractor': 'ProteoWizard', - 'Extractor version': 'pwiz_2.1.2575 (TPP v4.5 RAPTURE rev 2, Build 201208012328 (linux))', - 'Source file': 'test.mgf'} + 'Extractor': 'ProteoWizard', + 'Extractor version': 'pwiz_2.1.2575 (TPP v4.5 RAPTURE rev 2, Build 201208012328 (linux))', + 'Source file': 'test.mgf'} -protxml_results =[{'group_number': 1, - 'probability': 1.0, - 'protein': [{'confidence': 1.0, - 'group_sibling_id': 'a', - 'n_indistinguishable_proteins': 1, - 'pct_spectrum_ids': 0.018, - 'peptide': [{'calc_neutral_pep_mass': 2094.0307, - 'charge': 2, - 'exp_tot_instances': 1.0, - 'fpkm_adjusted_probability': 0.9995, - 'initial_probability': 0.999, - 'is_contributing_evidence': True, - 'is_nondegenerate_evidence': True, - 'n_enzymatic_termini': 2, - 'n_instances': 1, - 'n_sibling_peptides': 4.38, - 'n_sibling_peptides_bin': 3, - 'nsp_adjusted_probability': 0.9995, - 'peptide_group_designator': 'a', - 'peptide_sequence': 'NIPIMSTASVEIDDAIYSR', - 'weight': 1.0}, - {'calc_neutral_pep_mass': 1538.794, - 'charge': 2, - 'exp_tot_instances': 1.0, - 'fpkm_adjusted_probability': 0.9995, - 'initial_probability': 0.999, - 'is_contributing_evidence': True, - 'is_nondegenerate_evidence': True, - 'mod_aminoacid_mass': [{'mass': '111.032030', 'position': '1'}], - 'modified_peptide': 'Q[111]DVIITAIDNVEAR', - 'n_enzymatic_termini': 2, - 'n_instances': 1, - 'n_sibling_peptides': 4.38, - 'n_sibling_peptides_bin': 3, - 'nsp_adjusted_probability': 0.9995, - 'peptide_sequence': 'QDVIITAIDNVEAR', - 'weight': 1.0}, - {'calc_neutral_pep_mass': 2094.0303, - 'charge': 3, - 'exp_tot_instances': 1.0, - 'fpkm_adjusted_probability': 0.9995, - 'initial_probability': 0.999, - 'is_contributing_evidence': True, - 'is_nondegenerate_evidence': True, - 'n_enzymatic_termini': 2, - 'n_instances': 1, - 'n_sibling_peptides': 4.38, - 'n_sibling_peptides_bin': 3, - 'nsp_adjusted_probability': 0.9995, - 'peptide_group_designator': 'a', - 'peptide_sequence': 'NIPIMSTASVEIDDAIYSR', - 'weight': 1.0}, - {'calc_neutral_pep_mass': 2212.2752, - 'charge': 3, - 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- 'is_nondegenerate_evidence': True, - 'n_enzymatic_termini': 2, - 'n_instances': 1, - 'n_sibling_peptides': 4.9, - 'n_sibling_peptides_bin': 4, - 'nsp_adjusted_probability': 0.695, - 'peptide_sequence': 'NAIFQIEK', - 'weight': 1.0}, - {'calc_neutral_pep_mass': 945.5131, - 'charge': 2, - 'exp_tot_instances': 0.25, - 'fpkm_adjusted_probability': 0.249, - 'initial_probability': 0.249, - 'is_contributing_evidence': True, - 'is_nondegenerate_evidence': True, - 'n_enzymatic_termini': 2, - 'n_instances': 1, - 'n_sibling_peptides': 5.13, - 'n_sibling_peptides_bin': 4, - 'nsp_adjusted_probability': 0.249, - 'peptide_sequence': 'AIISNEATK', - 'weight': 1.0}], - 'percent_coverage': 7.7, - 'probability': 1.0, - 'prot_length': 1052, - 'protein_description': 'Ubiquitin-like modifier-activating enzyme 6 OS=Homo sapiens GN=UBA6 PE=1 SV=1', - 'protein_name': 'sp|A0AVT1|UBA6_HUMAN', - 'raw_intensity': '0.000', - 'total_number_distinct_peptides': 7, - 'total_number_peptides': 7, - 'unique_stripped_peptides': ['AIISNEATK', 'IIPAIATTTATVSGIVAIEMIK', 'NAIFQIEK', 'NIPIMSTASVEIDDAIYSR', 'QDVIITAIDNVEAR', 'TVFFESIER']}]}, - {'group_number': 2, - 'probability': 0.999, - 'protein': [{'confidence': 1.0, - 'group_sibling_id': 'a', - 'n_indistinguishable_proteins': 1, - 'pct_spectrum_ids': 0.093, - 'peptide': [{'calc_neutral_pep_mass': 1519.9086, - 'charge': 2, - 'exp_tot_instances': 1.0, - 'fpkm_adjusted_probability': 0.9997, - 'initial_probability': 0.999, - 'is_contributing_evidence': True, - 'is_nondegenerate_evidence': True, - 'n_enzymatic_termini': 2, - 'n_instances': 1, - 'n_sibling_peptides': 24.8, - 'n_sibling_peptides_bin': 8, - 'nsp_adjusted_probability': 0.9997, - 'peptide_group_designator': 'a', - 'peptide_sequence': 'AVPIAIAIISVSNPR', - 'weight': 1.0}, - {'calc_neutral_pep_mass': 1166.5316, - 'charge': 2, - 'exp_tot_instances': 1.0, - 'fpkm_adjusted_probability': 0.9997, - 'initial_probability': 0.999, - 'is_contributing_evidence': True, - 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'n_enzymatic_termini': 2, - 'n_instances': 1, - 'n_sibling_peptides': 24.81, - 'n_sibling_peptides_bin': 8, - 'nsp_adjusted_probability': 0.9992, - 'peptide_sequence': 'SGAIIACGIVNSGVR', - 'weight': 1.0}, - {'calc_neutral_pep_mass': 1279.5972, - 'charge': 2, - 'exp_tot_instances': 1.0, - 'fpkm_adjusted_probability': 0.9988, - 'initial_probability': 0.9959, - 'is_contributing_evidence': True, - 'is_nondegenerate_evidence': True, - 'n_enzymatic_termini': 2, - 'n_instances': 1, - 'n_sibling_peptides': 24.81, - 'n_sibling_peptides_bin': 8, - 'nsp_adjusted_probability': 0.9988, - 'peptide_sequence': 'YIYSSEDYIK', - 'weight': 1.0}, - {'calc_neutral_pep_mass': 2520.3227, - 'charge': 3, - 'exp_tot_instances': 0.99, - 'fpkm_adjusted_probability': 0.9975, - 'initial_probability': 0.9917, - 'is_contributing_evidence': True, - 'is_nondegenerate_evidence': True, - 'mod_aminoacid_mass': [{'mass': '111.032030', 'position': '1'}], - 'modified_peptide': 'E[111]WQEIDDAEKVQREPIITIVK', - 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'n_sibling_peptides_bin': 8, - 'nsp_adjusted_probability': 0.995, - 'peptide_sequence': 'VQREPIITIVK', - 'weight': 1.0}, - {'calc_neutral_pep_mass': 1015.5913, - 'charge': 2, - 'exp_tot_instances': 0.86, - 'fpkm_adjusted_probability': 0.9544, - 'initial_probability': 0.8603, - 'is_contributing_evidence': True, - 'is_nondegenerate_evidence': True, - 'n_enzymatic_termini': 2, - 'n_instances': 1, - 'n_sibling_peptides': 24.94, - 'n_sibling_peptides_bin': 8, - 'nsp_adjusted_probability': 0.9544, - 'peptide_sequence': 'INIIDTISK', - 'weight': 1.0}, - {'calc_neutral_pep_mass': 911.5691, - 'charge': 2, - 'exp_tot_instances': 0.86, - 'fpkm_adjusted_probability': 0.9526, - 'initial_probability': 0.8555, - 'is_contributing_evidence': True, - 'is_nondegenerate_evidence': True, - 'n_enzymatic_termini': 2, - 'n_instances': 1, - 'n_sibling_peptides': 24.95, - 'n_sibling_peptides_bin': 8, - 'nsp_adjusted_probability': 0.9526, - 'peptide_sequence': 'EPIITIVK', - 'weight': 1.0}, - {'calc_neutral_pep_mass': 973.479, - 'charge': 2, - 'exp_tot_instances': 0.8, - 'fpkm_adjusted_probability': 0.9297, - 'initial_probability': 0.7956, - 'is_contributing_evidence': True, - 'is_nondegenerate_evidence': True, - 'n_enzymatic_termini': 2, - 'n_instances': 1, - 'n_sibling_peptides': 25.01, - 'n_sibling_peptides_bin': 8, - 'nsp_adjusted_probability': 0.9297, - 'peptide_sequence': 'EIDIMEPK', - 'weight': 1.0}, - {'calc_neutral_pep_mass': 889.448, - 'charge': 2, - 'exp_tot_instances': 0.65, - 'fpkm_adjusted_probability': 0.8644, - 'initial_probability': 0.6523, - 'is_contributing_evidence': True, - 'is_nondegenerate_evidence': False, - 'mod_aminoacid_mass': [{'mass': '228.056870', 'position': '1'}], - 'modified_peptide': 'CAIGVFR', - 'n_enzymatic_termini': 2, - 'n_instances': 1, - 'n_sibling_peptides': 25.45, - 'n_sibling_peptides_bin': 8, - 'nsp_adjusted_probability': 0.8644, - 'peptide_parent_protein': [{'protein_name': 'DECOY_sp|A0A5B9|TRBC2_HUMAN'}], - 'peptide_sequence': 'CAIGVFR', - 'weight': 0.54}], - 'percent_coverage': 29.3, - 'probability': 1.0, - 'prot_length': 908, - 'protein_description': '26S proteasome non-ATPase regulatory subunit 2 OS=Homo sapiens GN=PSMD2 PE=1 SV=3', - 'protein_name': 'DECOY_sp|Q13200|PSMD2_HUMAN', - 'raw_intensity': '0.000', - 'total_number_distinct_peptides': 29, - 'total_number_peptides': 29, - 'unique_stripped_peptides': ['AEIATEEFIPVTPIIEGFVIIR', 'AEIATEEFIPVTPIIEGFVIIRK', 'APVQPQQSPAAAPGGTDEKPSGK', 'AVPIAIAIISVSNPR', 'CAIGVFR', 'DKAPVQPQQSPAAAPGGTDEKPSGK', 'EIDIMEPK', 'EPIITIVK', 'EWQEIDDAEKVQREPIITIVK', 'FGGSGSQVDSAR', 'GTITICPYHSDR', 'INIIDTISK', 'IVGSQEEIASWGHEYVR', 'MIVTFDEEIRPIPVSVR', 'MNIASSFVNGFVNAAFGQDK', 'SGAIIACGIVNSGVR', 'TITGFQTHTTPVIIAHGER', 'VGQAVDVVGQAGKPK', 'VPDDIYKTHIENNR', 'VQREPIITIVK', 'YGEPTIR', 'YIYSSEDYIK']}]}] +protxml_results = [{'group_number': 1, + 'probability': 1.0, + 'protein': [{'confidence': 1.0, + 'group_sibling_id': 'a', + 'n_indistinguishable_proteins': 1, + 'pct_spectrum_ids': 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0.9544, + 'peptide_sequence': 'INIIDTISK', + 'weight': 1.0}, + {'calc_neutral_pep_mass': 911.5691, + 'charge': 2, + 'exp_tot_instances': 0.86, + 'fpkm_adjusted_probability': 0.9526, + 'initial_probability': 0.8555, + 'is_contributing_evidence': True, + 'is_nondegenerate_evidence': True, + 'n_enzymatic_termini': 2, + 'n_instances': 1, + 'n_sibling_peptides': 24.95, + 'n_sibling_peptides_bin': 8, + 'nsp_adjusted_probability': 0.9526, + 'peptide_sequence': 'EPIITIVK', + 'weight': 1.0}, + {'calc_neutral_pep_mass': 973.479, + 'charge': 2, + 'exp_tot_instances': 0.8, + 'fpkm_adjusted_probability': 0.9297, + 'initial_probability': 0.7956, + 'is_contributing_evidence': True, + 'is_nondegenerate_evidence': True, + 'n_enzymatic_termini': 2, + 'n_instances': 1, + 'n_sibling_peptides': 25.01, + 'n_sibling_peptides_bin': 8, + 'nsp_adjusted_probability': 0.9297, + 'peptide_sequence': 'EIDIMEPK', + 'weight': 1.0}, + {'calc_neutral_pep_mass': 889.448, + 'charge': 2, + 'exp_tot_instances': 0.65, + 'fpkm_adjusted_probability': 0.8644, + 'initial_probability': 0.6523, + 'is_contributing_evidence': True, + 'is_nondegenerate_evidence': False, + 'mod_aminoacid_mass': [{'mass': '228.056870', 'position': '1'}], + 'modified_peptide': 'CAIGVFR', + 'n_enzymatic_termini': 2, + 'n_instances': 1, + 'n_sibling_peptides': 25.45, + 'n_sibling_peptides_bin': 8, + 'nsp_adjusted_probability': 0.8644, + 'peptide_parent_protein': [ + {'protein_name': 'DECOY_sp|A0A5B9|TRBC2_HUMAN'}], + 'peptide_sequence': 'CAIGVFR', + 'weight': 0.54}], + 'percent_coverage': 29.3, + 'probability': 1.0, + 'prot_length': 908, + 'protein_description': '26S proteasome non-ATPase regulatory subunit 2 OS=Homo sapiens GN=PSMD2 PE=1 SV=3', + 'protein_name': 'DECOY_sp|Q13200|PSMD2_HUMAN', + 'raw_intensity': '0.000', + 'total_number_distinct_peptides': 29, + 'total_number_peptides': 29, + 'unique_stripped_peptides': ['AEIATEEFIPVTPIIEGFVIIR', 'AEIATEEFIPVTPIIEGFVIIRK', + 'APVQPQQSPAAAPGGTDEKPSGK', 'AVPIAIAIISVSNPR', 'CAIGVFR', + 'DKAPVQPQQSPAAAPGGTDEKPSGK', 'EIDIMEPK', 'EPIITIVK', + 'EWQEIDDAEKVQREPIITIVK', 'FGGSGSQVDSAR', 'GTITICPYHSDR', + 'INIIDTISK', 'IVGSQEEIASWGHEYVR', 'MIVTFDEEIRPIPVSVR', + 'MNIASSFVNGFVNAAFGQDK', 'SGAIIACGIVNSGVR', + 'TITGFQTHTTPVIIAHGER', 'VGQAVDVVGQAGKPK', + 'VPDDIYKTHIENNR', 'VQREPIITIVK', 'YGEPTIR', + 'YIYSSEDYIK']}]}] transitions = [ - [{'Precursor': {'charge state': 2.0, - 'isolation window target m/z': 862.9467}, - 'Prediction': {'contactRef': 'CS', - 'linear ion trap': '', - 'peak intensity': 10000.0, - 'peak intensity rank': 1.0, - 'peak targeting suitability rank': 1.0, - 'softwareRef': 'MaRiMba', - 'transition purported from an MS/MS spectrum on a different, specified instrument': ''}, - 'Product': {'ConfigurationList': {'Configuration': [{'ValidationStatus': [{'4000 QTRAP': '', - 'peak intensity': 4072.0, - 'peak intensity rank': 2.0, - 'peak targeting suitability rank': 1.0, - 'transition optimized on specified instrument': ''}], - 'collision energy': 26.0, - 'collision gas': 'argon', - 'collision gas pressure': 12.0, - 'cone voltage': 1200.0, - 'contactRef': 'CS', - 'declustering potential': 64.0, - 'dwell time': 0.12, - 'instrumentRef': 'QTRAP', - 'interchannel delay': 0.01, - 'tube lens voltage': 23.0}]}, - 'InterpretationList': {'Interpretation': [{'name': 'frag: y ion', - 'product interpretation rank': 1.0, - 'product ion m/z delta': 0.03, - 'product ion series ordinal': 8.0}, - {'name': 'frag: b ion - H2O', - 'product interpretation rank': 2.0, - 'product ion m/z delta': -0.43, - 'product ion series ordinal': 9.0}]}, - 'charge state': 1.0, - 'isolation window target m/z': 1040.57}, - 'RetentionTime': [{'local retention time': 40.02, - 'retention time window lower offset': 3.0, - 'retention time window upper offset': 3.0, - 'softwareRef': 'Skyline0.5'}], - 'id': 'ADTHFLLNIYDQLR-M1-T1', - 'peptideRef': 'ADTHFLLNIYDQLR-M1'}, - {'IntermediateProduct': [{'ConfigurationList': {'Configuration': [{'collision energy': 26.0, - 'contactRef': 'CS', - 'instrumentRef': 'QTRAP'}]}, - 'InterpretationList': {'Interpretation': [{'name': 'frag: y ion', - 'product interpretation rank': 1.0, - 'product ion m/z delta': 0.03, - 'product ion series ordinal': 8.0}]}, - 'charge state': 1.0, - 'isolation window target m/z': 1040.57}], - 'Precursor': {'charge state': 2.0, - 'isolation window lower offset': 1.0, - 'isolation window target m/z': 862.9467, - 'isolation window upper offset': 1.0}, - 'Product': {'ConfigurationList': {'Configuration': [{'collision energy': 20.4, - 'contactRef': 'CS', - 'dwell time': 0.12, - 'instrumentRef': 'QTRAP'}]}, - 'InterpretationList': {'Interpretation': [{'name': 'frag: y ion', - 'product interpretation rank': 1.0, - 'product ion m/z delta': 0.03, - 'product ion series ordinal': 4.0}]}, - 'charge state': 1.0, - 'isolation window target m/z': 543.2}, - 'RetentionTime': [{'local retention time': 40.02, - 'retention time window lower offset': 3.0, - 'retention time window upper offset': 3.0, - 'softwareRef': 'Skyline0.5'}], - 'id': 'ADTHFLLNIYDQLR-M1-T2', - 'peptideRef': 'ADTHFLLNIYDQLR-M1'}], - [ - {'Precursor': {'charge state': 2.0, - 'isolation window target m/z': 862.9467}, - 'Prediction': {'contact': {'contact URL': 'http://www.systemsbiology.org/', - 'contact address': '1441 NE 34th St, Seattle WA 98103, USA', - 'contact email': 'example@systemsbiology.org', - 'contact name': 'Eric Deutsch', - 'contact organization': 'Institute for Systems Biology', - 'id': 'CS'}, - 'linear ion trap': '', - 'peak intensity': 10000.0, - 'peak intensity rank': 1.0, - 'peak targeting suitability rank': 1.0, - 'software': {'name': 'MaRiMba', 'id': 'MaRiMba', 'version': '1.0'}, - 'transition purported from an MS/MS spectrum on a different, specified instrument': ''}, - 'Product': {'ConfigurationList': {'Configuration': [{'ValidationStatus': [{'4000 QTRAP': '', - 'peak intensity': 4072.0, - 'peak intensity rank': 2.0, - 'peak targeting suitability rank': 1.0, - 'transition optimized on specified instrument': ''}], - 'collision energy': 26.0, - 'collision gas': 'argon', - 'collision gas pressure': 12.0, - 'cone voltage': 1200.0, - 'contact': {'contact URL': 'http://www.systemsbiology.org/', - 'contact address': '1441 NE 34th St, Seattle WA 98103, USA', - 'contact email': 'example@systemsbiology.org', - 'contact name': 'Eric Deutsch', - 'contact organization': 'Institute for Systems Biology', - 'id': 'CS'}, - 'declustering potential': 64.0, - 'dwell time': 0.12, - 'instrument': {'4000 QTRAP': '', 'id': 'QTRAP'}, - 'interchannel delay': 0.01, - 'tube lens voltage': 23.0}]}, - 'InterpretationList': {'Interpretation': [{'name': 'frag: y ion', - 'product interpretation rank': 1.0, - 'product ion m/z delta': 0.03, - 'product ion series ordinal': 8.0}, - {'name': 'frag: b ion - H2O', - 'product interpretation rank': 2.0, - 'product ion m/z delta': -0.43, - 'product ion series ordinal': 9.0}]}, - 'charge state': 1.0, - 'isolation window target m/z': 1040.57}, - 'RetentionTime': [{'local retention time': 40.02, - 'retention time window lower offset': 3.0, - 'retention time window upper offset': 3.0, - 'software': {'name': 'Skyline', 'id': 'Skyline0.5', 'version': '0.5'}}], - 'id': 'ADTHFLLNIYDQLR-M1-T1', - 'peptide': {'Evidence': {'confident peptide': 6.0}, - 'Modification': [{'location': 0, - 'monoisotopicMassDelta': 127.063324, - 'name': 'SMA'}, - {'location': 1, 'monoisotopicMassDelta': 15.994919, 'name': 'Oxidation'}], - 'Protein': [{'Sequence': 'MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKE', - 'id': 'Q12149', - 'protein accession': 'Q00613', - 'protein name': 'Heat shock factor protein 1', - 'protein short name': 'HSF 1', - 'ref': 'Q12149'}, - {'Sequence': 'MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKEELISNSSDALDKI', - 'id': 'ENSP00000332698', - 'protein accession': 'ENSP00000332698', - 'protein name': 'Heat shock factor protein 1', - 'protein short name': 'HSF 1', - 'ref': 'ENSP00000332698'}], - 'RetentionTimeList': [{'RetentionTime': [{'predicted retention time': 44.07, - 'software': {'name': 'SSRCalc', 'id': 'SSRCalc3.0', 'version': '3.0'}}, - {'H-PINS retention time normalization standard': '', - 'normalized retention time': 38.43}]}], - 'heavy labeled peptide': '', - 'id': 'ADTHFLLNIYDQLR-M1', - 'isomerization potential': 0.583, - 'peptide group label': 'G1', - 'predicted isoelectric point': 5.22, - 'sequence': 'ADTHFLLNIYDQLR', - 'theoretical mass': 1189.22}}, - {'IntermediateProduct': [{'ConfigurationList': {'Configuration': [{'collision energy': 26.0, - 'contact': {'contact URL': 'http://www.systemsbiology.org/', - 'contact address': '1441 NE 34th St, Seattle WA 98103, USA', - 'contact email': 'example@systemsbiology.org', - 'contact name': 'Eric Deutsch', - 'contact organization': 'Institute for Systems Biology', - 'id': 'CS'}, - 'instrument': {'4000 QTRAP': '', 'id': 'QTRAP'}}]}, - 'InterpretationList': {'Interpretation': [{'name': 'frag: y ion', - 'product interpretation rank': 1.0, - 'product ion m/z delta': 0.03, - 'product ion series ordinal': 8.0}]}, - 'charge state': 1.0, - 'isolation window target m/z': 1040.57}], - 'Precursor': {'charge state': 2.0, - 'isolation window lower offset': 1.0, - 'isolation window target m/z': 862.9467, - 'isolation window upper offset': 1.0}, - 'Product': {'ConfigurationList': {'Configuration': [{'collision energy': 20.4, - 'contact': {'contact URL': 'http://www.systemsbiology.org/', - 'contact address': '1441 NE 34th St, Seattle WA 98103, USA', - 'contact email': 'example@systemsbiology.org', - 'contact name': 'Eric Deutsch', - 'contact organization': 'Institute for Systems Biology', - 'id': 'CS'}, - 'dwell time': 0.12, - 'instrument': {'4000 QTRAP': '', 'id': 'QTRAP'}}]}, - 'InterpretationList': {'Interpretation': [{'name': 'frag: y ion', - 'product interpretation rank': 1.0, - 'product ion m/z delta': 0.03, - 'product ion series ordinal': 4.0}]}, - 'charge state': 1.0, - 'isolation window target m/z': 543.2}, - 'RetentionTime': [{'local retention time': 40.02, - 'retention time window lower offset': 3.0, - 'retention time window upper offset': 3.0, - 'software': {'name': 'Skyline', 'id': 'Skyline0.5', 'version': '0.5'}}], - 'id': 'ADTHFLLNIYDQLR-M1-T2', - 'peptide': {'Evidence': {'confident peptide': 6.0}, - 'Modification': [{'location': 0, - 'monoisotopicMassDelta': 127.063324, - 'name': 'SMA'}, - {'location': 1, 'monoisotopicMassDelta': 15.994919, 'name': 'Oxidation'}], - 'Protein': [{'Sequence': 'MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKE', - 'id': 'Q12149', - 'protein accession': 'Q00613', - 'protein name': 'Heat shock factor protein 1', - 'protein short name': 'HSF 1', - 'ref': 'Q12149'}, - {'Sequence': 'MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKEELISNSSDALDKI', - 'id': 'ENSP00000332698', - 'protein accession': 'ENSP00000332698', - 'protein name': 'Heat shock factor protein 1', - 'protein short name': 'HSF 1', - 'ref': 'ENSP00000332698'}], - 'RetentionTimeList': [{'RetentionTime': [{'predicted retention time': 44.07, - 'software': {'name': 'SSRCalc', 'id': 'SSRCalc3.0', 'version': '3.0'}}, - {'H-PINS retention time normalization standard': '', - 'normalized retention time': 38.43}]}], - 'heavy labeled peptide': '', - 'id': 'ADTHFLLNIYDQLR-M1', - 'isomerization potential': 0.583, - 'peptide group label': 'G1', - 'predicted isoelectric point': 5.22, - 'sequence': 'ADTHFLLNIYDQLR', - 'theoretical mass': 1189.22}}] + [{'Precursor': {'charge state': 2.0, + 'isolation window target m/z': 862.9467}, + 'Prediction': {'contactRef': 'CS', + 'linear ion trap': '', + 'peak intensity': 10000.0, + 'peak intensity rank': 1.0, + 'peak targeting suitability rank': 1.0, + 'softwareRef': 'MaRiMba', + 'transition purported from an MS/MS spectrum on a different, specified instrument': ''}, + 'Product': {'ConfigurationList': {'Configuration': [{'ValidationStatus': [{'4000 QTRAP': '', + 'peak intensity': 4072.0, + 'peak intensity rank': 2.0, + 'peak targeting suitability rank': 1.0, + 'transition optimized on specified instrument': ''}], + 'collision energy': 26.0, + 'collision gas': 'argon', + 'collision gas pressure': 12.0, + 'cone voltage': 1200.0, + 'contactRef': 'CS', + 'declustering potential': 64.0, + 'dwell time': 0.12, + 'instrumentRef': 'QTRAP', + 'interchannel delay': 0.01, + 'tube lens voltage': 23.0}]}, + 'InterpretationList': {'Interpretation': [{'name': 'frag: y ion', + 'product interpretation rank': 1.0, + 'product ion m/z delta': 0.03, + 'product ion series ordinal': 8.0}, + {'name': 'frag: b ion - H2O', + 'product interpretation rank': 2.0, + 'product ion m/z delta': -0.43, + 'product ion series ordinal': 9.0}]}, + 'charge state': 1.0, + 'isolation window target m/z': 1040.57}, + 'RetentionTime': [{'local retention time': 40.02, + 'retention time window lower offset': 3.0, + 'retention time window upper offset': 3.0, + 'softwareRef': 'Skyline0.5'}], + 'id': 'ADTHFLLNIYDQLR-M1-T1', + 'peptideRef': 'ADTHFLLNIYDQLR-M1'}, + {'IntermediateProduct': [{'ConfigurationList': {'Configuration': [{'collision energy': 26.0, + 'contactRef': 'CS', + 'instrumentRef': 'QTRAP'}]}, + 'InterpretationList': {'Interpretation': [{'name': 'frag: y ion', + 'product interpretation rank': 1.0, + 'product ion m/z delta': 0.03, + 'product ion series ordinal': 8.0}]}, + 'charge state': 1.0, + 'isolation window target m/z': 1040.57}], + 'Precursor': {'charge state': 2.0, + 'isolation window lower offset': 1.0, + 'isolation window target m/z': 862.9467, + 'isolation window upper offset': 1.0}, + 'Product': {'ConfigurationList': {'Configuration': [{'collision energy': 20.4, + 'contactRef': 'CS', + 'dwell time': 0.12, + 'instrumentRef': 'QTRAP'}]}, + 'InterpretationList': {'Interpretation': [{'name': 'frag: y ion', + 'product interpretation rank': 1.0, + 'product ion m/z delta': 0.03, + 'product ion series ordinal': 4.0}]}, + 'charge state': 1.0, + 'isolation window target m/z': 543.2}, + 'RetentionTime': [{'local retention time': 40.02, + 'retention time window lower offset': 3.0, + 'retention time window upper offset': 3.0, + 'softwareRef': 'Skyline0.5'}], + 'id': 'ADTHFLLNIYDQLR-M1-T2', + 'peptideRef': 'ADTHFLLNIYDQLR-M1'}], + [ + {'Precursor': {'charge state': 2.0, + 'isolation window target m/z': 862.9467}, + 'Prediction': {'contact': {'contact URL': 'http://www.systemsbiology.org/', + 'contact address': '1441 NE 34th St, Seattle WA 98103, USA', + 'contact email': 'example@systemsbiology.org', + 'contact name': 'Eric Deutsch', + 'contact organization': 'Institute for Systems Biology', + 'id': 'CS'}, + 'linear ion trap': '', + 'peak intensity': 10000.0, + 'peak intensity rank': 1.0, + 'peak targeting suitability rank': 1.0, + 'software': {'name': 'MaRiMba', 'id': 'MaRiMba', 'version': '1.0'}, + 'transition purported from an MS/MS spectrum on a different, specified instrument': ''}, + 'Product': {'ConfigurationList': {'Configuration': [{'ValidationStatus': [{'4000 QTRAP': '', + 'peak intensity': 4072.0, + 'peak intensity rank': 2.0, + 'peak targeting suitability rank': 1.0, + 'transition optimized on specified instrument': ''}], + 'collision energy': 26.0, + 'collision gas': 'argon', + 'collision gas pressure': 12.0, + 'cone voltage': 1200.0, + 'contact': { + 'contact URL': 'http://www.systemsbiology.org/', + 'contact address': '1441 NE 34th St, Seattle WA 98103, USA', + 'contact email': 'example@systemsbiology.org', + 'contact name': 'Eric Deutsch', + 'contact organization': 'Institute for Systems Biology', + 'id': 'CS'}, + 'declustering potential': 64.0, + 'dwell time': 0.12, + 'instrument': {'4000 QTRAP': '', 'id': 'QTRAP'}, + 'interchannel delay': 0.01, + 'tube lens voltage': 23.0}]}, + 'InterpretationList': {'Interpretation': [{'name': 'frag: y ion', + 'product interpretation rank': 1.0, + 'product ion m/z delta': 0.03, + 'product ion series ordinal': 8.0}, + {'name': 'frag: b ion - H2O', + 'product interpretation rank': 2.0, + 'product ion m/z delta': -0.43, + 'product ion series ordinal': 9.0}]}, + 'charge state': 1.0, + 'isolation window target m/z': 1040.57}, + 'RetentionTime': [{'local retention time': 40.02, + 'retention time window lower offset': 3.0, + 'retention time window upper offset': 3.0, + 'software': {'name': 'Skyline', 'id': 'Skyline0.5', 'version': '0.5'}}], + 'id': 'ADTHFLLNIYDQLR-M1-T1', + 'peptide': {'Evidence': {'confident peptide': 6.0}, + 'Modification': [{'location': 0, + 'monoisotopicMassDelta': 127.063324, + 'name': 'SMA'}, + {'location': 1, 'monoisotopicMassDelta': 15.994919, 'name': 'Oxidation'}], + 'Protein': [{'Sequence': 'MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKE', + 'id': 'Q12149', + 'protein accession': 'Q00613', + 'protein name': 'Heat shock factor protein 1', + 'protein short name': 'HSF 1', + 'ref': 'Q12149'}, + { + 'Sequence': 'MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKEELISNSSDALDKI', + 'id': 'ENSP00000332698', + 'protein accession': 'ENSP00000332698', + 'protein name': 'Heat shock factor protein 1', + 'protein short name': 'HSF 1', + 'ref': 'ENSP00000332698'}], + 'RetentionTimeList': [{'RetentionTime': [{'predicted retention time': 44.07, + 'software': {'name': 'SSRCalc', 'id': 'SSRCalc3.0', + 'version': '3.0'}}, + {'H-PINS retention time normalization standard': '', + 'normalized retention time': 38.43}]}], + 'heavy labeled peptide': '', + 'id': 'ADTHFLLNIYDQLR-M1', + 'isomerization potential': 0.583, + 'peptide group label': 'G1', + 'predicted isoelectric point': 5.22, + 'sequence': 'ADTHFLLNIYDQLR', + 'theoretical mass': 1189.22}}, + {'IntermediateProduct': [{'ConfigurationList': {'Configuration': [{'collision energy': 26.0, + 'contact': { + 'contact URL': 'http://www.systemsbiology.org/', + 'contact address': '1441 NE 34th St, Seattle WA 98103, USA', + 'contact email': 'example@systemsbiology.org', + 'contact name': 'Eric Deutsch', + 'contact organization': 'Institute for Systems Biology', + 'id': 'CS'}, + 'instrument': {'4000 QTRAP': '', + 'id': 'QTRAP'}}]}, + 'InterpretationList': {'Interpretation': [{'name': 'frag: y ion', + 'product interpretation rank': 1.0, + 'product ion m/z delta': 0.03, + 'product ion series ordinal': 8.0}]}, + 'charge state': 1.0, + 'isolation window target m/z': 1040.57}], + 'Precursor': {'charge state': 2.0, + 'isolation window lower offset': 1.0, + 'isolation window target m/z': 862.9467, + 'isolation window upper offset': 1.0}, + 'Product': {'ConfigurationList': {'Configuration': [{'collision energy': 20.4, + 'contact': { + 'contact URL': 'http://www.systemsbiology.org/', + 'contact address': '1441 NE 34th St, Seattle WA 98103, USA', + 'contact email': 'example@systemsbiology.org', + 'contact name': 'Eric Deutsch', + 'contact organization': 'Institute for Systems Biology', + 'id': 'CS'}, + 'dwell time': 0.12, + 'instrument': {'4000 QTRAP': '', 'id': 'QTRAP'}}]}, + 'InterpretationList': {'Interpretation': [{'name': 'frag: y ion', + 'product interpretation rank': 1.0, + 'product ion m/z delta': 0.03, + 'product ion series ordinal': 4.0}]}, + 'charge state': 1.0, + 'isolation window target m/z': 543.2}, + 'RetentionTime': [{'local retention time': 40.02, + 'retention time window lower offset': 3.0, + 'retention time window upper offset': 3.0, + 'software': {'name': 'Skyline', 'id': 'Skyline0.5', 'version': '0.5'}}], + 'id': 'ADTHFLLNIYDQLR-M1-T2', + 'peptide': {'Evidence': {'confident peptide': 6.0}, + 'Modification': [{'location': 0, + 'monoisotopicMassDelta': 127.063324, + 'name': 'SMA'}, + {'location': 1, 'monoisotopicMassDelta': 15.994919, 'name': 'Oxidation'}], + 'Protein': [{'Sequence': 'MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKE', + 'id': 'Q12149', + 'protein accession': 'Q00613', + 'protein name': 'Heat shock factor protein 1', + 'protein short name': 'HSF 1', + 'ref': 'Q12149'}, + { + 'Sequence': 'MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKEELISNSSDALDKI', + 'id': 'ENSP00000332698', + 'protein accession': 'ENSP00000332698', + 'protein name': 'Heat shock factor protein 1', + 'protein short name': 'HSF 1', + 'ref': 'ENSP00000332698'}], + 'RetentionTimeList': [{'RetentionTime': [{'predicted retention time': 44.07, + 'software': {'name': 'SSRCalc', 'id': 'SSRCalc3.0', + 'version': '3.0'}}, + {'H-PINS retention time normalization standard': '', + 'normalized retention time': 38.43}]}], + 'heavy labeled peptide': '', + 'id': 'ADTHFLLNIYDQLR-M1', + 'isomerization potential': 0.583, + 'peptide group label': 'G1', + 'predicted isoelectric point': 5.22, + 'sequence': 'ADTHFLLNIYDQLR', + 'theoretical mass': 1189.22}}] ] idxml_data = {(0, - 0): [{'score_type': 'q-value', - 'higher_score_better': False, - 'significance_threshold': 0.0, - 'MZ': 368.832366943359, - 'RT': 1517.88525390625}, {'score_type': 'q-value', - 'higher_score_better': False, - 'significance_threshold': 0.0, - 'MZ': 552.744079589844, - 'RT': 1520.14294433594}], - (0, - 1): [{'score_type': 'q-value', - 'higher_score_better': False, - 'significance_threshold': 0.0, - 'MZ': 368.832366943359, - 'RT': 1517.88525390625}, {'score_type': 'q-value', - 'higher_score_better': False, - 'significance_threshold': 0.0, - 'MZ': 552.744079589844, - 'RT': 1520.14294433594}], - (1, - 0): [{'score_type': 'q-value', - 'higher_score_better': False, - 'significance_threshold': 0.0, - 'MZ': 368.832366943359, - 'RT': 1517.88525390625, - 'PeptideHit': [{'score': 0.0, - 'sequence': 'DGDIEAEISR', - 'charge': 3, - 'aa_before': ['K'], - 'aa_after': ['E'], - 'protein_refs': 'PH_0', - 'OMSSA_score': 0.000846175003530426, - 'target_decoy': 'target'}]}, {'score_type': 'q-value', - 'higher_score_better': False, - 'significance_threshold': 0.0, - 'MZ': 552.744079589844, - 'RT': 1520.14294433594, - 'PeptideHit': [{'score': 0.0, - 'sequence': 'LAMTLAEAER', - 'charge': 2, - 'aa_before': ['R'], - 'aa_after': ['A'], - 'protein_refs': 'PH_6', - 'OMSSA_score': 0.0384710999326793, - 'target_decoy': 'target'}]}], - (1, - 1): [{'score_type': 'q-value', - 'higher_score_better': False, - 'significance_threshold': 0.0, - 'MZ': 368.832366943359, - 'RT': 1517.88525390625, - 'PeptideHit': [{'score': 0.0, - 'sequence': 'DGDIEAEISR', - 'charge': 3, - 'aa_before': ['K'], - 'aa_after': ['E'], - 'OMSSA_score': 0.000846175003530426, - 'target_decoy': 'target', - 'protein': [{'accession': 'tr|A9EY18|A9EY18_SORC5', - 'score': 0.0, - 'sequence': '', - 'OMSSA_score': 0.0}]}]}, {'score_type': 'q-value', - 'higher_score_better': False, - 'significance_threshold': 0.0, - 'MZ': 552.744079589844, - 'RT': 1520.14294433594, - 'PeptideHit': [{'score': 0.0, - 'sequence': 'LAMTLAEAER', - 'charge': 2, - 'aa_before': ['R'], - 'aa_after': ['A'], - 'OMSSA_score': 0.0384710999326793, - 'target_decoy': 'target', - 'protein': [{'accession': 'tr|A9GID7|A9GID7_SORC5', - 'score': 0.0, - 'sequence': '', - 'OMSSA_score': 0.0}]}]}]} + 0): [{'score_type': 'q-value', + 'higher_score_better': False, + 'significance_threshold': 0.0, + 'MZ': 368.832366943359, + 'RT': 1517.88525390625}, {'score_type': 'q-value', + 'higher_score_better': False, + 'significance_threshold': 0.0, + 'MZ': 552.744079589844, + 'RT': 1520.14294433594}], + (0, + 1): [{'score_type': 'q-value', + 'higher_score_better': False, + 'significance_threshold': 0.0, + 'MZ': 368.832366943359, + 'RT': 1517.88525390625}, {'score_type': 'q-value', + 'higher_score_better': False, + 'significance_threshold': 0.0, + 'MZ': 552.744079589844, + 'RT': 1520.14294433594}], + (1, + 0): [{'score_type': 'q-value', + 'higher_score_better': False, + 'significance_threshold': 0.0, + 'MZ': 368.832366943359, + 'RT': 1517.88525390625, + 'PeptideHit': [{'score': 0.0, + 'sequence': 'DGDIEAEISR', + 'charge': 3, + 'aa_before': ['K'], + 'aa_after': ['E'], + 'protein_refs': 'PH_0', + 'OMSSA_score': 0.000846175003530426, + 'target_decoy': 'target'}]}, {'score_type': 'q-value', + 'higher_score_better': False, + 'significance_threshold': 0.0, + 'MZ': 552.744079589844, + 'RT': 1520.14294433594, + 'PeptideHit': [{'score': 0.0, + 'sequence': 'LAMTLAEAER', + 'charge': 2, + 'aa_before': ['R'], + 'aa_after': ['A'], + 'protein_refs': 'PH_6', + 'OMSSA_score': 0.0384710999326793, + 'target_decoy': 'target'}]}], + (1, + 1): [{'score_type': 'q-value', + 'higher_score_better': False, + 'significance_threshold': 0.0, + 'MZ': 368.832366943359, + 'RT': 1517.88525390625, + 'PeptideHit': [{'score': 0.0, + 'sequence': 'DGDIEAEISR', + 'charge': 3, + 'aa_before': ['K'], + 'aa_after': ['E'], + 'OMSSA_score': 0.000846175003530426, + 'target_decoy': 'target', + 'protein': [{'accession': 'tr|A9EY18|A9EY18_SORC5', + 'score': 0.0, + 'sequence': '', + 'OMSSA_score': 0.0}]}]}, {'score_type': 'q-value', + 'higher_score_better': False, + 'significance_threshold': 0.0, + 'MZ': 552.744079589844, + 'RT': 1520.14294433594, + 'PeptideHit': [{'score': 0.0, + 'sequence': 'LAMTLAEAER', + 'charge': 2, + 'aa_before': ['R'], + 'aa_after': ['A'], + 'OMSSA_score': 0.0384710999326793, + 'target_decoy': 'target', + 'protein': [{ + 'accession': 'tr|A9GID7|A9GID7_SORC5', + 'score': 0.0, + 'sequence': '', + 'OMSSA_score': 0.0}]}]}]} diff --git a/tests/test_annotated.mgf b/tests/test_annotated.mgf new file mode 100644 index 00000000..2d0b7330 --- /dev/null +++ b/tests/test_annotated.mgf @@ -0,0 +1,31 @@ +MIN_MZ=69.5367320 +MAX_MZ=1395.63277 +BEGIN IONS +TITLE=HAPPYNEWYEAR||2 +CHARGE=2 +PEPMASS=766.84948 +138.0 0.013 b1+1 +153.5 0.049 b3+2 +375.1 0.059 y3+1 +484.2 0.012 y7+2 +662.8 0.454 y10+2 +698.3 0.002 y11+2 +1130.2 0.956 y8+1 +1395.4 0.098 y11+1 +END IONS +BEGIN IONS +TITLE=RAEYWENYPPAH||3 +CHARGE=3 +PEPMASS=511.56875 +156.0 0.597 y1+1 +157.1 0.091 b1+1 +162.5 0.063 y3+2 +211.1 0.177 y4+2 +227.1 0.165 y2+1 +228.1 0.038 b2+1 +418.1 0.043 b6+2 +698.3 0.026 y6+1 +835.3 0.213 b6+1 +949.4 0.288 b7+1 +1112.7 0.177 b8+1 +END IONS diff --git a/tests/test_mgf.py b/tests/test_mgf.py old mode 100644 new mode 100755 index a98602f8..33f8396b --- a/tests/test_mgf.py +++ b/tests/test_mgf.py @@ -1,7 +1,9 @@ import os import numpy as np import pyteomics + pyteomics.__path__ = [os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, 'pyteomics'))] + import tempfile import unittest import pickle @@ -11,9 +13,11 @@ from pyteomics import mgf, auxiliary as aux import data + class MGFTest(unittest.TestCase): maxDiff = None _encoding = 'utf-8' + def setUp(self): self.path = 'test.mgf' self.header = mgf.read_header(self.path) @@ -27,6 +31,8 @@ def setUp(self): self.spectra2 = list(tmpreader) self.ns = len(self.spectra) self.tmpfile.close() + self.path_annotated = 'test_annotated.mgf' + self.header_annotated = mgf.read_header(self.path_annotated) def test_read(self): for func in [mgf.read, mgf.MGF, mgf.IndexedMGF]: @@ -45,9 +51,9 @@ def test_read_source_kw(self): def test_read_decoding(self): for func in [mgf.read, mgf.MGF, mgf.IndexedMGF]: self.assertEqual(data.mgf_spectra_long_decoded, - list(func(self.path, encoding=self._encoding))) + list(func(self.path, encoding=self._encoding))) self.assertEqual(data.mgf_spectra_short_decoded, - list(func(self.path, False, encoding=self._encoding))) + list(func(self.path, False, encoding=self._encoding))) with func(self.path, encoding=self._encoding) as reader: self.assertEqual(data.mgf_spectra_long_decoded, list(reader)) with func(self.path, False, encoding=self._encoding) as reader: @@ -60,6 +66,17 @@ def test_read_no_charges(self): with mgf.read(self.path, False, read_charges=False) as reader: self.assertEqual(data.mgf_spectra_short_no_charges, list(reader)) + def test_read_with_ions(self): + with mgf.read(self.path_annotated, read_ions=True) as reader: + for spec_data, spec_read in zip(data.mgf_spectra_annotated_long, list(reader)): + # Check that the spectra have the same dict keys + self.assertEqual(spec_data.keys(), spec_read.keys()) + for key in spec_data.keys(): + if type(spec_data[key]) == dict: + self.assertDictEqual(spec_data[key], spec_read[key]) + else: + np.testing.assert_array_equal(spec_data[key], spec_read[key]) + def test_read_array_conversion(self): with mgf.read(self.path, convert_arrays=0) as reader: self.assertEqual(data.mgf_spectra_lists, list(reader)) @@ -82,7 +99,7 @@ def test_readwrite_keys(self): for s, s2 in zip(self.spectra, self.spectra2): self.assertEqual(set(s), set(s2)) self.assertEqual(set(s), - {'intensity array', 'm/z array', 'params', 'charge array'}) + {'intensity array', 'm/z array', 'params', 'charge array'}) def test_readwrite_params(self): for s, s2 in zip(self.spectra, self.spectra2): @@ -96,18 +113,18 @@ def test_readwrite_msms_len(self): self.assertEqual(al, len(self.spectra2[i]['intensity array'])) for j in range(al): self.assertEqual(self.spectra[i]['m/z array'][j], - self.spectra2[i]['m/z array'][j]) + self.spectra2[i]['m/z array'][j]) self.assertEqual(self.spectra[i]['intensity array'][j], - self.spectra2[i]['intensity array'][j]) + self.spectra2[i]['intensity array'][j]) def test_readwrite_msms(self): for i in range(self.ns): al = len(self.spectra[i]['m/z array']) for j in range(al): self.assertEqual(self.spectra[i]['m/z array'][j], - self.spectra2[i]['m/z array'][j]) + self.spectra2[i]['m/z array'][j]) self.assertEqual(self.spectra[i]['intensity array'][j], - self.spectra2[i]['intensity array'][j]) + self.spectra2[i]['intensity array'][j]) def test_read_dtype(self): dtypes = {'m/z array': np.float32, 'intensity array': np.int32} From d3538dd47fe44952633179dac5d9cad879a3d2a0 Mon Sep 17 00:00:00 2001 From: Lev Levitsky Date: Fri, 9 Oct 2020 19:27:06 +0300 Subject: [PATCH 4/8] Fix mgf.write with write_ions, add a read-write mgf test with ions --- pyteomics/auxiliary/structures.py | 15 +++++--- pyteomics/mgf.py | 58 +++++++++++++++++-------------- tests/test_mgf.py | 25 +++++++++++-- 3 files changed, 65 insertions(+), 33 deletions(-) diff --git a/pyteomics/auxiliary/structures.py b/pyteomics/auxiliary/structures.py index c6f801f5..44fa491b 100644 --- a/pyteomics/auxiliary/structures.py +++ b/pyteomics/auxiliary/structures.py @@ -1,5 +1,6 @@ import re from collections import defaultdict, Counter +import warnings try: basestring @@ -82,15 +83,19 @@ def __new__(cls, *args, **kwargs): def __str__(self): return str(abs(self)) + '+-'[self < 0] + class Ion(str): """Represents an Ion, right now just a subclass of String. """ + _pattern = r'([abcxyz]\d+(\-H2O|\-NH3)?)([\+|-]\d+)' # "y2-H2O+1" + def __init__(self, *args, **kwargs): if args and isinstance(args[0], basestring): try: - self.ion_type, self.neutral_loss, self.charge = re.match(r'([abcxyz]\d+(\-H2O|\-NH3)?)([\+|-]\d+)', args[0]).groups() #"y2-H2O+1" - except Exception as e: - raise PyteomicsError("Malformed ion string, must match the regex r'([abcxyz]\d+(\-H2O|\-NH3)?)([\+|-]\d+)'") + self.ion_type, self.neutral_loss, self.charge = re.match(self._pattern, args[0]).groups() + except Exception: + raise PyteomicsError("Malformed ion string, must match the regex {!r}".format(self._pattern)) + class ChargeList(list): """Just a list of :py:class:`Charge`s. When printed, looks like an @@ -126,11 +131,13 @@ def _parse_charge(s, list_only=False): pass return ChargeList(s) + def _parse_ion(ion_text): try: return Ion(ion_text) except Exception as e: - print(e) + warnings.warn('Could not parse ion string: {} ({})'.format(ion_text, e.args[0])) + class BasicComposition(defaultdict, Counter): """A generic dictionary for compositions. diff --git a/pyteomics/mgf.py b/pyteomics/mgf.py index a76f7c75..835c2f48 100755 --- a/pyteomics/mgf.py +++ b/pyteomics/mgf.py @@ -75,6 +75,7 @@ import sys from . import auxiliary as aux + class MGFBase(object): """Abstract mixin class representing an MGF file. Subclasses implement different approaches to parsing.""" _comments = set('#;!/') @@ -91,7 +92,6 @@ class MGFBase(object): _array_keys_unicode = [u'm/z array', u'intensity array', u'charge array', u'ion array'] encoding = None - def __init__(self, source=None, **kwargs): """Create an MGF file object, set MGF-specific parameters. @@ -135,7 +135,7 @@ def __init__(self, source=None, **kwargs): raise aux.PyteomicsError('numpy is required for array conversion') self._read_charges = kwargs.pop('read_charges', True) self._read_ions = kwargs.pop('read_ions', False) - #Make sure no charges are read if ions are read + # Make sure no charges are read if ions are read if self._read_ions: self._read_charges = False dtype = kwargs.pop('dtype', None) @@ -145,7 +145,6 @@ def __init__(self, source=None, **kwargs): else: self._header = None - def parse_precursor_charge(self, charge_text, list_only=False): return aux._parse_charge(charge_text, list_only=list_only) @@ -227,10 +226,10 @@ def _read_spectrum_lines(self, lines): return out else: - if '=' in sline: # spectrum-specific parameters! + if '=' in sline: # spectrum-specific parameters! l = sline.split('=', 1) params[l[0].lower()] = l[1].strip() - else: # this must be a peak list + else: # this must be a peak list l = sline.split() try: masses.append(float(l[0])) @@ -274,11 +273,9 @@ class IndexedMGF(MGFBase, aux.TaskMappingMixin, aux.TimeOrderedIndexedReaderMixi A property used for accessing spectra by retention time. """ delimiter = 'BEGIN IONS' - - - def __init__(self, source=None, use_header=True, convert_arrays=2, read_charges=True, - read_ions=False, dtype=None, encoding='utf-8', index_by_scans=False, _skip_index=False, **kwargs): + def __init__(self, source=None, use_header=True, convert_arrays=2, read_charges=True, + read_ions=False, dtype=None, encoding='utf-8', index_by_scans=False, _skip_index=False, **kwargs): self.label = r'SCANS=(\d+)\s*' if index_by_scans else r'TITLE=([^\n]*\S)\s*' super(IndexedMGF, self).__init__(source, parser_func=self._read, pass_file=False, args=(), kwargs={}, use_header=use_header, convert_arrays=convert_arrays, read_charges=read_charges, @@ -305,7 +302,7 @@ def __setstate__(self, state): def _read_header(self): try: first = next(v for v in self._offset_index.values())[0] - except StopIteration: # the index is empty, no spectra in file + except StopIteration: # the index is empty, no spectra in file first = -1 header_lines = self.read(first).decode(self.encoding).split('\n') return self._read_header_lines(header_lines) @@ -355,9 +352,9 @@ class MGF(MGFBase, aux.FileReader): """ def __init__(self, source=None, use_header=True, convert_arrays=2, read_charges=True, - read_ions=False, dtype=None, encoding=None): + read_ions=False, dtype=None, encoding=None): super(MGF, self).__init__(source, mode='r', parser_func=self._read, pass_file=False, args=(), kwargs={}, - encoding=encoding, use_header=use_header, convert_arrays=convert_arrays, read_charges=read_charges, + encoding=encoding, use_header=use_header, convert_arrays=convert_arrays, read_charges=read_charges, read_ions=read_ions, dtype=dtype) # self.encoding = encoding @@ -516,30 +513,33 @@ def read_header(source): _default_key_order = ['title', 'pepmass', 'rtinseconds', 'charge'] + def _pepmass_repr(k, pepmass): outstr = k.upper() + '=' - if not isinstance(pepmass, (str, int, float)): # assume iterable + if not isinstance(pepmass, (str, int, float)): # assume iterable try: outstr += ' '.join(str(x) for x in pepmass if x is not None) except TypeError: - raise aux.PyteomicsError( - 'Cannot handle parameter: PEPMASS = {}'.format(pepmass)) + raise aux.PyteomicsError('Cannot handle parameter: PEPMASS = {}'.format(pepmass)) else: outstr += str(pepmass) return outstr + def _charge_repr(k, charge): return '{}={}'.format(k.upper(), aux._parse_charge(str(charge))) + def _default_repr(key, val): return '{}={}'.format(key.upper(), val) + _default_value_formatters = {'pepmass': _pepmass_repr, 'charge': _charge_repr} + @aux._file_writer() -def write(spectra, output=None, header='', key_order=_default_key_order, - fragment_format=None, write_charges=True, write_ions=False, use_numpy=None, - param_formatters=_default_value_formatters): +def write(spectra, output=None, header='', key_order=_default_key_order, fragment_format=None, + write_charges=True, write_ions=False, use_numpy=None, param_formatters=_default_value_formatters): """ Create a file in MGF format. @@ -577,10 +577,11 @@ def write(spectra, output=None, header='', key_order=_default_key_order, write_ions : bool, optional If :py:const:`False`, fragment ions from 'ion array' will not be written. + If :py:const:`True`, then `write_charges` is set to :py:const:`False`. Default is :py:const:`False`. fragment_format : str, optional - Format string for m/z, intensity and charge of a fragment. Useful to set + Format string for m/z, intensity and charge (or ion annotation) of a fragment. Useful to set the number of decimal places, e.g.: ``fragment_format='%.4f %.0f'``. Default is ``'{} {} {}'``. @@ -639,10 +640,13 @@ def key_value_line(key, val): fragment_format = '{} {} {}' np_format_2 = '%.5f %.1f' np_format_3 = '%.5f %.1f %d' + np_format_i = '%.5f %.1f %s' else: - np_format_2 = np_format_3 = fragment_format + np_format_2 = np_format_3 = np_format_i = fragment_format format_str = fragment_format + '\n' + if write_ions: + write_charges = False if use_numpy is None: use_numpy = not write_charges @@ -659,9 +663,8 @@ def key_value_line(key, val): head_str = '\n'.join(header) head_dict = {} for line in head_lines: - if not line.strip() or any( - line.startswith(c) for c in MGF._comments): - continue + if not line.strip() or any(line.startswith(c) for c in MGF._comments): + continue l = line.split('=') if len(l) == 2: head_dict[l[0].lower()] = l[1].strip() @@ -697,7 +700,7 @@ def key_value_line(key, val): X[:, 0] = spectrum['m/z array'] X[:, 1] = spectrum['intensity array'] X[:, 2] = spectrum['ion array'] - np.savetxt(output, X, fmt=np_format_3) + np.savetxt(output, X, fmt=np_format_i) else: success = False else: @@ -706,7 +709,9 @@ def key_value_line(key, val): if not success: for m, i, c in zip(spectrum['m/z array'], spectrum['intensity array'], - spectrum.get('charge array', it.cycle((None,)))): + spectrum.get('charge array', it.cycle((None,))) if write_charges else + spectrum.get('ion array', it.cycle((None,))) if write_ions else + it.cycle((None,))): output.write(format_str.format( m, i, (c if c not in nones else ''))) @@ -715,4 +720,5 @@ def key_value_line(key, val): output.write('END IONS\n\n') return output -chain = aux._make_chain(read, 'read') \ No newline at end of file + +chain = aux._make_chain(read, 'read') diff --git a/tests/test_mgf.py b/tests/test_mgf.py index 33f8396b..aad335c2 100755 --- a/tests/test_mgf.py +++ b/tests/test_mgf.py @@ -21,7 +21,8 @@ class MGFTest(unittest.TestCase): def setUp(self): self.path = 'test.mgf' self.header = mgf.read_header(self.path) - self.spectra = list(mgf.read(self.path)) + with mgf.read(self.path) as f: + self.spectra = list(f) self.tmpfile = tempfile.TemporaryFile(mode='r+') mgf.write(header=self.header, spectra=self.spectra, output=self.tmpfile) self.tmpfile.seek(0) @@ -33,6 +34,8 @@ def setUp(self): self.tmpfile.close() self.path_annotated = 'test_annotated.mgf' self.header_annotated = mgf.read_header(self.path_annotated) + with mgf.read(self.path_annotated, read_ions=True) as f: + self.spectra_annotated = list(f) def test_read(self): for func in [mgf.read, mgf.MGF, mgf.IndexedMGF]: @@ -67,8 +70,24 @@ def test_read_no_charges(self): self.assertEqual(data.mgf_spectra_short_no_charges, list(reader)) def test_read_with_ions(self): - with mgf.read(self.path_annotated, read_ions=True) as reader: - for spec_data, spec_read in zip(data.mgf_spectra_annotated_long, list(reader)): + for spec_data, spec_read in zip(data.mgf_spectra_annotated_long, list(self.spectra_annotated)): + # Check that the spectra have the same dict keys + self.assertEqual(spec_data.keys(), spec_read.keys()) + for key in spec_data.keys(): + if type(spec_data[key]) == dict: + self.assertDictEqual(spec_data[key], spec_read[key]) + else: + np.testing.assert_array_equal(spec_data[key], spec_read[key]) + + def test_read_write_with_ions(self): + formats = ['{:.6f} {:.6f} {}', '%.6f %.6f %s'] + for use_numpy in range(2): + with tempfile.TemporaryFile(mode='r+') as f: + mgf.write(self.spectra_annotated, f, write_ions=True, use_numpy=use_numpy, + fragment_format=formats[use_numpy]) + f.seek(0) + spectra = list(mgf.read(f, read_ions=True)) + for spec_data, spec_read in zip(data.mgf_spectra_annotated_long, spectra): # Check that the spectra have the same dict keys self.assertEqual(spec_data.keys(), spec_read.keys()) for key in spec_data.keys(): From 87897584bb85f631b5cbef306b114c2eb316dc26 Mon Sep 17 00:00:00 2001 From: Julian Mueller Date: Mon, 12 Oct 2020 18:30:25 +0200 Subject: [PATCH 5/8] Reset changes in auxiliary/file_helpers.py --- pyteomics/auxiliary/file_helpers.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) mode change 100644 => 100755 pyteomics/auxiliary/file_helpers.py diff --git a/pyteomics/auxiliary/file_helpers.py b/pyteomics/auxiliary/file_helpers.py old mode 100644 new mode 100755 index b5e42656..5f28a634 --- a/pyteomics/auxiliary/file_helpers.py +++ b/pyteomics/auxiliary/file_helpers.py @@ -244,11 +244,11 @@ def get_by_id(self, elem_id): index = self.default_index if index is None: raise PyteomicsError('Access by ID requires building an offset index.') - offsets = index[str(elem_id)] + offsets = index[elem_id] return self._item_from_offsets(offsets) def get_by_ids(self, ids): - return [self.get_by_id(str(key)) for key in ids] + return [self.get_by_id(key) for key in ids] def get_by_index(self, i): try: From 07020e5583289ec4281293d3b46156ba7c70a8d0 Mon Sep 17 00:00:00 2001 From: Julian Mueller Date: Mon, 12 Oct 2020 18:51:16 +0200 Subject: [PATCH 6/8] Moved read_ions parameter to end of function in mgf.py --- pyteomics/mgf.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/pyteomics/mgf.py b/pyteomics/mgf.py index 835c2f48..f1076ded 100755 --- a/pyteomics/mgf.py +++ b/pyteomics/mgf.py @@ -275,28 +275,32 @@ class IndexedMGF(MGFBase, aux.TaskMappingMixin, aux.TimeOrderedIndexedReaderMixi delimiter = 'BEGIN IONS' def __init__(self, source=None, use_header=True, convert_arrays=2, read_charges=True, - read_ions=False, dtype=None, encoding='utf-8', index_by_scans=False, _skip_index=False, **kwargs): + dtype=None, encoding='utf-8', index_by_scans=False, read_ions=False, _skip_index=False, **kwargs): self.label = r'SCANS=(\d+)\s*' if index_by_scans else r'TITLE=([^\n]*\S)\s*' super(IndexedMGF, self).__init__(source, parser_func=self._read, pass_file=False, args=(), kwargs={}, - use_header=use_header, convert_arrays=convert_arrays, read_charges=read_charges, - read_ions=read_ions, dtype=dtype, encoding=encoding, _skip_index=_skip_index, **kwargs) + use_header=use_header, convert_arrays=convert_arrays, + read_charges=read_charges, + dtype=dtype, encoding=encoding, read_ions=read_ions, _skip_index=_skip_index, + **kwargs) def __reduce_ex__(self, protocol): return (self.__class__, - (self._source_init, False, self._convert_arrays, self._read_charges, - self._read_ions, self._dtype_dict, self.encoding, True), - self.__getstate__()) + (self._source_init, False, self._convert_arrays, self._read_charges, + self._dtype_dict, self.encoding, True), + self.__getstate__()) def __getstate__(self): state = super(IndexedMGF, self).__getstate__() state['use_header'] = self._use_header state['header'] = self._header + state['read_ions'] = self._read_ions return state def __setstate__(self, state): super(IndexedMGF, self).__setstate__(state) self._header = state['header'] self._use_header = state['use_header'] + self._read_ions = state['read_ions'] @aux._keepstate_method def _read_header(self): From b55601f86cb9ee515b88491d1eeeac20783fba06 Mon Sep 17 00:00:00 2001 From: Lev Levitsky Date: Tue, 13 Oct 2020 22:30:31 +0300 Subject: [PATCH 7/8] Undo str conversion of MGF ID --- pyteomics/mgf.py | 2 +- tests/data.py | 0 tests/test_mgf.py | 0 3 files changed, 1 insertion(+), 1 deletion(-) mode change 100755 => 100644 tests/data.py mode change 100755 => 100644 tests/test_mgf.py diff --git a/pyteomics/mgf.py b/pyteomics/mgf.py index f1076ded..7c62cf6c 100755 --- a/pyteomics/mgf.py +++ b/pyteomics/mgf.py @@ -322,7 +322,7 @@ def _read(self, **kwargs): yield spectrum def get_spectrum(self, key): - return self.get_by_id(str(key)) + return self.get_by_id(key) def _get_time(self, spectrum): try: diff --git a/tests/data.py b/tests/data.py old mode 100755 new mode 100644 diff --git a/tests/test_mgf.py b/tests/test_mgf.py old mode 100755 new mode 100644 From 4898a25135ad0bb6314d693bc1b41ff57d70789e Mon Sep 17 00:00:00 2001 From: Lev Levitsky Date: Tue, 13 Oct 2020 23:50:35 +0300 Subject: [PATCH 8/8] Add an extra test for index access and ions --- tests/test_mgf.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/test_mgf.py b/tests/test_mgf.py index aad335c2..c3b537e8 100644 --- a/tests/test_mgf.py +++ b/tests/test_mgf.py @@ -160,6 +160,10 @@ def test_get_spectrum(self): self.assertEqual(data.mgf_spectra_long[1], f.get_spectrum(key)) self.assertEqual(data.mgf_spectra_long[1], mgf.get_spectrum(self.path, key)) + def test_key_access_ions(self): + with mgf.IndexedMGF(self.path_annotated, read_ions=True) as f: + np.testing.assert_array_equal(f['RAEYWENYPPAH||3']['ion array'], self.spectra_annotated[1]['ion array']) + def test_read_list(self): key = ['Spectrum 2', 'Spectrum 1'] with mgf.IndexedMGF(self.path) as f: