calc_precursor_mz leads to unexpected behavior

[GeorgWa]

Hi Feng, I observed the following bug when using AB to create multiplexed DIA libraries. It's technically not a bug but more of a incompatible behavior between functions which might confuse users. Let me know what you think, I'm happy to make a PR.

Describe the bug
When calling calc_precursor_mz on a spectral library, clip_by_precursor_mz_ is always invoked, which messes up the precursor fragment mapping.

To Reproduce

1. Create a library with a preecursor just below the upper mz limit:

precursor_df = pd.DataFrame([
    {'sequence': 'AGHCEWQMKPERGWWWWWPPWWWWGGGGAGGAG', 'mods': 'Dimethyl@Any N-term;Dimethyl@K', 'mod_sites': '0;8', 'charge': 2},
    {'sequence': 'AGHCEWQMKPE', 'mods': 'Dimethyl@Any N-term;Dimethyl@K', 'mod_sites': '0;8', 'charge': 3},
    {'sequence': 'AGHCEWQMKPERGWWWWWPPWWWWGGGGAGGAGG', 'mods': '', 'mod_sites': '', 'charge': 2},
])

spec_lib = SpecLibBase(
    ['b_z1','b_z2','y_z1','y_z2'],
    decoy='pseudo_reverse',
    precursor_mz_max=2000,
)
spec_lib._precursor_df = precursor_df
spec_lib.calc_precursor_mz()
spec_lib.calc_fragment_mz_df()

spec_lib.precursor_df

sequence	mods	mod_sites	charge	nAA	precursor_mz	frag_start_idx	frag_stop_idx
AGHCEWQMKPE	Dimethyl@Any N-term;Dimethyl@K	0;8	3	11	457.877652	0	10
AGHCEWQMKPERGWWWWWPPWWWWGGGGAGGAG	Dimethyl@Any N-term;Dimethyl@K	0;8	2	33	1997.896037	10	42
AGHCEWQMKPERGWWWWWPPWWWWGGGGAGGAGG			2	34	1998.375468	42	75

2. Modify the sequence or modification which will change the m/z of some precursors, recalculate the precursor mz:

spec_lib._precursor_df['mods'] = spec_lib._precursor_df['mods'].str.replace('Dimethyl', 'Dimethyl:2H(6)13C(2)')
spec_lib.calc_precursor_mz()

sequence	mods	mod_sites	charge	nAA	precursor_mz	frag_start_idx	frag_stop_idx
AGHCEWQMKPE	Dimethyl:2H(6)13C(2)@Any N-term;Dimethyl:2H(6)...	0;8	3	11	463.240566	0	10
AGHCEWQMKPERGWWWWWPPWWWWGGGGAGGAGG			2	34	1998.375468	42	75

3. recalculate the fragment masses:
   spec_lib.calc_fragment_mz_df()

File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/IPython/core/interactiveshell.py", line 3378, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "/var/folders/lc/9594t94d5b5_gn0y04w1jh980000gn/T/ipykernel_6587/3999293303.py", line 1, in <module>
    spec_lib.calc_fragment_mz_df()
  File "/Users/georgwallmann/Documents/git/alphabase/alphabase/spectral_library/base.py", line 361, in calc_fragment_mz_df
    )
  File "/Users/georgwallmann/Documents/git/alphabase/alphabase/peptide/fragment.py", line 818, in create_fragment_mz_dataframe
  File "/Users/georgwallmann/Documents/git/alphabase/alphabase/peptide/fragment.py", line 876, in create_fragment_mz_dataframe
    '''
  File "/Users/georgwallmann/Documents/git/alphabase/alphabase/peptide/fragment.py", line 435, in mask_fragments_for_charge_greater_than_precursor_charge
    elif frag_type == 'y':
  File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexing.py", line 815, in __setitem__
    indexer = self._get_setitem_indexer(key)
  File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexing.py", line 698, in _get_setitem_indexer
    return self._convert_tuple(key)
  File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexing.py", line 897, in _convert_tuple
    keyidx = [self._convert_to_indexer(k, axis=i) for i, k in enumerate(key)]
  File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexing.py", line 897, in <listcomp>
    keyidx = [self._convert_to_indexer(k, axis=i) for i, k in enumerate(key)]
  File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexing.py", line 1394, in _convert_to_indexer
    key = check_bool_indexer(labels, key)
  File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexing.py", line 2567, in check_bool_indexer
    return check_array_indexer(index, result)
  File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexers/utils.py", line 553, in check_array_indexer
    raise IndexError(
IndexError: Boolean index has wrong length: 43 instead of 75

Expected behavior
calc_fragment_mz_df requires a continous frag_start_idx, frag_stop_idx, which is not compatible with the way clip_by_precursor_mz_ works. It is also not immediatley clear thatclip_by_precursor_mz_ has been called and precursors were removed.

Possible Solutions

• don't call clip_by_precursor_mz_ by default within calc_precursor_mz
• issue a warning: n precursors were remove because they were outside the mz limits
• call spec_lib.remove_unused_fragments() right after clip_by_precursor_mz_

[jalew188]

Good catch! And good suggestions!

[GeorgWa]

Thanks, will open a PR later!