Output

mzTab output

ANN-SoLo exports its identification results in mzTab files. mzTab is a data standard developed by the HUPO-PSI to store mass spectrometry data in a simple tabular format.

Example

MTD	mzTab-version	1.0.0
MTD	mzTab-mode	Summary
MTD	mzTab-type	Identification
MTD	mzTab-ID	ANN-SoLo_ann_oms_shifted.mztab
MTD	title	ANN-SoLo identification file "ann_oms_shifted.mztab"
MTD	description	Identification results of file "/tmp/59994839.1.noble-long.q/iPRG2012.mgf" against spectral library file "/tmp/59994839.1.noble-long.q/human_yeast_targetdecoy.splib"
MTD	software[1]	[MS, MS:1001456, ANN-SoLo, 0.1.3]
MTD	psm_search_engine_score[1]	[MS, MS:1001143, search engine specific score for PSMs,]
MTD	psm_search_engine_score[2]	[MS, MS:1002354, PSM-level q-value,]
MTD	ms_run[1]-location	file:///tmp/59994839.1.noble-long.q/iPRG2012.mgf
MTD	fixed_mod[1]	[MS, MS:1002453, No fixed modifications searched,]
MTD	variable_mod[1]	[MS, MS:1002454, No variable modifications searched,]
MTD	software[1]-setting[0]	resolution = 3
MTD	software[1]-setting[1]	min_mz = 101
MTD	software[1]-setting[2]	max_mz = 1500
MTD	software[1]-setting[3]	remove_precursor = True
MTD	software[1]-setting[4]	remove_precursor_tolerance = 0.02
MTD	software[1]-setting[5]	min_intensity = 0.01
MTD	software[1]-setting[6]	min_peaks = 10
MTD	software[1]-setting[7]	min_mz_range = 250.0
MTD	software[1]-setting[8]	max_peaks_used = 50
MTD	software[1]-setting[9]	scaling = rank
MTD	software[1]-setting[10]	precursor_tolerance_mass = 20.0
MTD	software[1]-setting[11]	precursor_tolerance_mode = ppm
MTD	software[1]-setting[12]	precursor_tolerance_mass_open = 300.0
MTD	software[1]-setting[13]	precursor_tolerance_mode_open = Da
MTD	software[1]-setting[14]	fragment_mz_tolerance = 0.02
MTD	software[1]-setting[15]	allow_peak_shifts = True
MTD	software[1]-setting[16]	fdr = 0.01
MTD	software[1]-setting[17]	mode = ann
MTD	software[1]-setting[18]	bin_size = 0.04
MTD	software[1]-setting[19]	hash_len = 800
MTD	software[1]-setting[20]	num_candidates = 1024
MTD	software[1]-setting[21]	num_list = 256
MTD	software[1]-setting[22]	num_probe = 128
PSH	sequence	PSM_ID	accession	unique	database	database_version	search_engine	search_engine_score[1]	search_engine_score[2]	modifications	retention_time	charge	exp_mass_to_charge	calc_mass_to_charge	spectra_ref	pre	post	start	end	opt_ms_run[1]_cv_MS:1002217_decoy_peptide	opt_ms_run[1]_num_candidates
PSM	TKDAEVNNGSSAR	25	191876	null	file:///tmp/59994839.1.noble-long.q/human_yeast_targetdecoy.splib	null	[MS, MS:1001456, ANN SoLo,]	0.5678355861455202	0.0	null	338.002	3	450.55278590975814	450.21990323333335	ms_run[1]:spectrum=25	null	null	null	null	0	580
PSM	YGSTNTRGDNEGQR	26	352476	null	file:///tmp/59994839.1.noble-long.q/human_yeast_targetdecoy.splib	null	[MS, MS:1001456, ANN SoLo,]	0.46325867623090744	0.00040257648953301127	null	338.502	3	518.9029172533499	518.9012339	ms_run[1]:spectrum=26	null	null	null	null	0	44
PSM	LQEEERER	28	413738	null	file:///tmp/59994839.1.noble-long.q/human_yeast_targetdecoy.splib	null	[MS, MS:1001456, ANN SoLo,]	0.5970180913573131	0.0	null	339.959	2	544.7703392007506	544.7701803500001	ms_run[1]:spectrum=28	null	null	null	null	0	133
PSM	DEALETEK	33	228464	null	file:///tmp/59994839.1.noble-long.q/human_yeast_targetdecoy.splib	null	[MS, MS:1001456, ANN SoLo,]	0.2820901330560446	0.006941001487357461	null	342.409	2	467.72719642625515	467.72183335000005	ms_run[1]:spectrum=33	null	null	null	null	0	111
PSM	FTDTRKDEQER	34	247372	null	file:///tmp/59994839.1.noble-long.q/human_yeast_targetdecoy.splib	null	[MS, MS:1001456, ANN SoLo,]	0.5776693965308368	0.0	null	342.659	3	475.56270967340816	475.56367056666664	ms_run[1]:spectrum=34	null	null	null	null	0	74
PSM	SSKPTDGLEK	45	382994	null	file:///tmp/59994839.1.noble-long.q/human_yeast_targetdecoy.splib	null	[MS, MS:1001456, ANN SoLo,]	0.31843859888613224	0.0	null	347.128	2	523.2728311293068	531.2773068500001	ms_run[1]:spectrum=45	null	null	null	null	0	723
PSM	SRGESDDSLNR	48	114680	null	file:///tmp/59994839.1.noble-long.q/human_yeast_targetdecoy.splib	null	[MS, MS:1001456, ANN SoLo,]	0.6166725260554813	0.0	null	350.615	3	412.1969459118437	412.52521490000004	ms_run[1]:spectrum=48	null	null	null	null	0	335
...

The top rows of the mzTab output contain metadata about the search results. Notably, the following information is available:

• Which version of ANN-SoLo was used to perform the search.
• The input spectral library and experimental spectra files.
• The search settings that were used.

The PSM section is present after the metadata section. This section starts with a header line, followed by each PSM on a separate line. Only target PSMs that have passed the specified FDR threshold are included. Notable information recorded for each PSM is:

• The corresponding peptide sequence. This is the exact peptide sequence as it is present in the spectral library; ANN-SoLo does not try to interpret this sequence.
• The accession of the library spectrum in the spectral library.
• The (shifted) dot product score (search_engine_score[1]) and the q-value (search_engine_score[1]). The order of these scores is defined in the metadata above.
• The mass of the query spectrum (exp_mass_to_charge) and the mass of the library spectrum (calc_mass_to_charge). The presence of modification(s) can be derived from the difference between these two masses. ANN-SoLo does not try to interpret the mass difference to map it to a specific modification at this point.