alphabase.psm_reader.psm_reader¶

The base class for all PSM readers and the provider for all readers.

Classes:

`PSMReaderBase`(*[, column_mapping, ...])	The Base class for all PSMReaders.
`PSMReaderProvider`()	A factory class to register and get readers for different PSM types.

Data:

`psm_reader_provider`	A factory `PSMReaderProvider` object to register and get readers for different PSM types.
`psm_reader_yaml`	See psm_reader.yaml

class alphabase.psm_reader.psm_reader.PSMReaderBase(*, column_mapping: dict | None = None, modification_mapping: dict | None = None, fdr: float = 0.01, keep_decoy: bool = False, rt_unit: str | None = None, mod_seq_columns: List[str] | None = None, **kwargs)[source][source]¶

Bases: ABC

The Base class for all PSMReaders.

Methods:

`__init__`(*[, column_mapping, ...])	The Base class for all PSMReaders.
`add_column_mapping`(column_mapping)	Add additional column mappings for the search engine.
`add_modification_mapping`(modification_mapping)	Append additional modification mappings for the search engine.
`filter_psm_by_modifications`([include_mod_set])	Only keeps peptides with modifications in include_mod_list.
`import_file`(_file)	Main entry function of PSM readers.
`import_files`(file_list)	Import multiple files.
`load`(_file)	Import a single file or multiple files.
`normalize_rt_by_raw_name`()	Normalize RT by raw name.
`set_modification_mapping`([modification_mapping])	Set the modification mapping for the search engine.

Attributes:

`modification_mapping`	Get the modification mapping dictionary.
`psm_df`	Get the PSM DataFrame.

__init__(*, column_mapping: dict | None = None, modification_mapping: dict | None = None, fdr: float = 0.01, keep_decoy: bool = False, rt_unit: str | None = None, mod_seq_columns: List[str] | None = None, **kwargs)[source][source]¶

The Base class for all PSMReaders.

The key of the sub-classes for different search engine format is to re-define column_mapping and modification_mapping.

Parameters:

column_mapping (dict, optional) –
A dict that maps alphabase’s columns to those of other search engines’. If it is None, this dict will be read from psm_reader.yaml key column_mapping.

The key of the column_mapping is alphabase’s column name, and the value could be the column name or a list of column names in other engine’s result, for example:
```
columns_mapping = {
    'sequence': 'NakedSequence',
    'charge': 'Charge',
    'proteins':['Proteins','UniprotIDs'] # list, this reader will automatically detect all of them.
}
```
The first column name in the list will be mapped to the harmonized column names, the rest will be ignored. Defaults to None.
modification_mapping (dict, optional) –
A dict that maps alphabase’s modifications to other engine’s. If it is None, this dict will be init by default modification mapping for each search engine (see psm_reader_yaml). The dict values can be either str or list, for exaplme:
```
modification_mapping = {
    'Oxidation@M': 'Oxidation (M)', # str
    'Phospho@S': ['S(Phospho (STY))','S(ph)','pS'], # list, this reader will automatically detect all of them.
}
```
Defaults to None.
fdr (float, optional) – FDR level to keep PSMs. Defaults to 0.01.
keep_decoy (bool, optional) – If keep decoy PSMs in self.psm_df. Defaults to False.
rt_unit (str, optional) – The unit of RT in the search engine result, “minute”, “second” or “irt”. If None, it is read from psm_reader_yaml key “rt_unit”.
mod_seq_columns (list, optional) – The columns to find modified sequences. The first column name in the list will be used, the rest will be ignored. By default read from psm_reader_yaml key “mod_seq_columns”. If it is not found there, an empty list is used.
**kwargs (dict) – deprecated

column_mapping¶

Dict structure same as column_mapping in Args.

Type:: dict

modification_mapping¶

Dict structure same as modification_mapping in Args. We must use self.set_modification_mapping(new_mapping) to update it.

Type:: dict

psm_df¶

the PSM DataFrame after loading from search engines.

Type:: pd.DataFrame

add_column_mapping(column_mapping: Dict) → None[source][source]¶: Add additional column mappings for the search engine.

add_modification_mapping(modification_mapping: Dict) → None[source][source]¶

Append additional modification mappings for the search engine.

See ModificationMapper.add_modification_mapping for more details.

filter_psm_by_modifications(include_mod_set: Set | None = None) → None[source][source]¶: Only keeps peptides with modifications in include_mod_list.

import_file(_file: str) → DataFrame[source][source]¶

Main entry function of PSM readers.

Imports a file and processes it.

Parameters:: _file (str) – file path or file stream (io).

import_files(file_list: List[str]) → DataFrame[source][source]¶: Import multiple files.

load(_file: List[str] | str) → DataFrame[source][source]¶: Import a single file or multiple files.

property modification_mapping: Dict¶: Get the modification mapping dictionary.

normalize_rt_by_raw_name() → None[source][source]¶: Normalize RT by raw name.

property psm_df: DataFrame¶: Get the PSM DataFrame.

set_modification_mapping(modification_mapping: Dict | None = None) → None[source][source]¶

Set the modification mapping for the search engine.

See ModificationMapper.set_modification_mapping for more details.

class alphabase.psm_reader.psm_reader.PSMReaderProvider[source][source]¶

Bases: object

A factory class to register and get readers for different PSM types.

Methods:

`__init__`()	Initialize PSMReaderProvider.
`get_reader`(reader_type, *[, column_mapping, ...])	Get a reader by reader_type.
`get_reader_by_yaml`(yaml_dict)	Get a reader by a yaml dict.
`register_reader`(reader_type, reader_class)	Register a reader by reader_type.

__init__()[source][source]¶: Initialize PSMReaderProvider.

get_reader(reader_type: str, *, column_mapping: dict | None = None, modification_mapping: dict | None = None, fdr: float = 0.01, keep_decoy: bool = False, **kwargs) → PSMReaderBase[source][source]¶: Get a reader by reader_type.

get_reader_by_yaml(yaml_dict: dict) → PSMReaderBase[source][source]¶: Get a reader by a yaml dict.

register_reader(reader_type: str, reader_class: Type[PSMReaderBase]) → None[source][source]¶: Register a reader by reader_type.

alphabase.psm_reader.psm_reader.psm_reader_provider = <alphabase.psm_reader.psm_reader.PSMReaderProvider object>¶: A factory PSMReaderProvider object to register and get readers for different PSM types.

alphabase.psm_reader.psm_reader.psm_reader_yaml = {'alphadia': {'column_mapping': {'ccs': 'ccs', 'charge': ['charge', 'precursor.charge'], 'fdr': 'fdr', 'genes': ['genes', 'pg.genes'], 'intensity': ['intensity', 'pg.intensity'], 'mobility': 'mobility', 'mods': ['mods', 'precursor.mods'], 'peptide_intensity': ['peptide.intensity'], 'precursor_id': ['precursor_idx', 'precursor.idx'], 'precursor_intensity': ['precursor.intensity'], 'proteins': ['proteins', 'pg.proteins'], 'raw_name': ['run', 'raw.name'], 'rt': ['rt_observed', 'precursor.rt.observed'], 'rt_start': 'rt_start', 'rt_stop': 'rt_stop', 'score': ['score', 'precursor.score'], 'sequence': ['sequence', 'precursor.sequence'], 'uniprot_ids': 'uniprot_ids'}, 'fixed_C57': False, 'modification_mapping_type': 'maxquant', 'reader_type': 'alphadia', 'rt_unit': 'minute'}, 'alphapept': {'column_mapping': {'charge': 'charge', 'decoy': 'decoy', 'fdr': 'q_value', 'mobility': 'mobility', 'precursor_mz': 'mz', 'query_id': 'query_idx', 'raw_name': 'raw_name', 'rt': 'rt', 'scan_num': 'scan_no', 'score': 'score', 'spec_idx': 'raw_idx'}, 'modification_mapping_type': 'alphapept', 'reader_type': 'alphapept', 'rt_unit': 'minute'}, 'diann': {'column_mapping': {'ccs': 'CCS', 'charge': 'Precursor.Charge', 'fdr': 'Q.Value', 'fdr1_search1': 'Global.Q.Value', 'fdr1_search2': 'Lib.Q.Value', 'fdr2_search1': 'Global.PG.Q.Value', 'fdr2_search2': 'Lib.PG.Q.Value', 'gene_intensity': 'Genes.MaxLFQ', 'genes': 'Genes', 'intensity': 'PG.MaxLFQ', 'mobility': ['IM', 'IonMobility'], 'precursor_id': 'Precursor.Id', 'precursor_intensity': 'Precursor.Normalised', 'proteins': 'Protein.Group', 'raw_name': 'Run', 'rt': 'RT', 'rt_start': 'RT.Start', 'rt_stop': 'RT.Stop', 'scan_num': 'MS2.Scan', 'score': 'CScore', 'sequence': 'Stripped.Sequence', 'uniprot_ids': 'Protein.Ids'}, 'fixed_C57': False, 'mod_seq_columns': ['Modified.Sequence'], 'modification_mapping_type': 'maxquant', 'reader_type': 'diann', 'rt_unit': 'minute'}, 'library_reader_base': {'column_mapping': {'ccs': 'CCS', 'charge': 'PrecursorCharge', 'fragment_charge': ['FragmentCharge', 'FragmentIonCharge', 'ProductCharge', 'ProductIonCharge'], 'fragment_intensity': ['LibraryIntensity', 'RelativeIntensity', 'RelativeFragmentIntensity', 'RelativeFragmentIonIntensity'], 'fragment_loss_type': ['FragmentLossType', 'FragmentIonLossType', 'ProductLossType', 'ProductIonLossType'], 'fragment_mz': ['ProductMz'], 'fragment_series': ['FragmentSeriesNumber', 'FragmentNumber'], 'fragment_type': ['FragmentType', 'FragmentIonType', 'ProductType', 'ProductIonType'], 'genes': ['GeneName', 'Genes', 'Gene'], 'mobility': ['Mobility', 'IonMobility', 'PrecursorIonMobility'], 'modified_sequence': ['ModifiedPeptideSequence', 'ModifiedPeptide'], 'precursor_mz': 'PrecursorMz', 'proteins': ['ProteinId', 'ProteinID', 'ProteinName', 'Protein Name'], 'raw_name': 'ReferenceRun', 'rt': ['RT', 'iRT', 'Tr_recalibrated', 'RetentionTime', 'NormalizedRetentionTime'], 'sequence': ['PeptideSequence', 'StrippedPeptide'], 'uniprot_ids': ['UniProtIds', 'UniProtID', 'UniprotId']}, 'fixed_C57': False, 'mod_seq_columns': ['ModifiedPeptideSequence', 'ModifiedPeptide', 'ModifiedSequence', 'FullUniModPeptideName', 'LabeledSequence', 'FullUniModPeptideName'], 'modification_mapping_type': 'maxquant', 'reader_type': 'library_reader_base', 'rt_unit': 'irt'}, 'maxquant': {'column_mapping': {'ccs': 'CCS', 'charge': 'Charge', 'decoy': 'Reverse', 'genes': ['Gene Names', 'Gene names'], 'intensity': 'Intensity', 'mobility': ['Mobility', 'IonMobility', 'K0', '1/K0'], 'precursor_mz': 'm/z', 'proteins': 'Proteins', 'raw_name': 'Raw file', 'rt': 'Retention time', 'scan_num': ['Scan number', 'MS/MS scan number', 'MS/MS Scan Number', 'Scan index'], 'score': 'Score', 'sequence': 'Sequence'}, 'fixed_C57': True, 'mod_seq_columns': ['Modified sequence'], 'modification_mapping_type': 'maxquant', 'reader_type': 'maxquant', 'rt_unit': 'minute'}, 'modification_mappings': {'alphapept': {'Acetyl@Protein_N-term': 'a', 'Carbamidomethyl@C': 'cC', 'Oxidation@M': 'oxM', 'Phospho@S': 'pS', 'Phospho@T': 'pT', 'Phospho@Y': 'pY'}, 'maxquant': {'Acetyl@K': ['K(ac)'], 'Acetyl@Protein_N-term': ['_(Acetyl (Protein N-term))', '_(ac)'], 'Carbamidomethyl@C': ['C(Carbamidomethyl (C))', 'C(Carbamidomethyl)'], 'Crotonyl@K': ['K(cr)'], 'Deamidated@N': ['N(Deamidation (NQ))', 'N(de)'], 'Deamidated@Q': ['Q(Deamidation (NQ))', 'Q(de)'], 'Dimethyl@Any_N-term': ['(Dimethyl)'], 'Dimethyl@K': ['K(Dimethyl)'], 'Dimethyl@R': ['R(Dimethyl)'], 'GG@K': ['K(GlyGly (K))', 'K(gl)'], 'Lactylation@K': ['K(la)'], 'Oxidation@M': ['M(Oxidation)', 'M(Oxidation (M))', 'M(ox)'], 'Phospho@D': ['D(Phospho (STYDH))', 'pD'], 'Phospho@H': ['H(Phospho (STYDH))', 'pH'], 'Phospho@S': ['S(Phospho (S))', 'S(Phospho (ST))', 'S(Phospho (STY))', 'S(Phospho (STYDH))', 'S(ph)', 'pS'], 'Phospho@T': ['T(Phospho (T))', 'T(Phospho (ST))', 'T(Phospho (STY))', 'T(Phospho (STYDH))', 'T(ph)', 'pT'], 'Phospho@Y': ['Y(Phospho (Y))', 'Y(Phospho (STY))', 'Y(Phospho (STYDH))', 'pY'], 'Succinyl@K': ['K(su)'], 'hydroxyisobutyryl@K': 'K(2-)', 'mTRAQ@Any_N-term': ['(mTRAQ)'], 'mTRAQ@K': ['K(mTRAQ)']}, 'msfragger': {'Acetyl@Any_N-term': ['N-term(42.0105)'], 'Acetyl@K': ['K(42.0105)'], 'Acetyl@Protein_N-term': ['N-term(42.0105)'], 'Amidated@Any_C-term': ['C-term(-0.9840)'], 'Ammonia-loss@C^Any_N-term': ['C(-17.0265)'], 'Benzyl-TA-Succinamide@Any_N-term': ['N-term(295.0514)'], 'Benzyl-TA-Succinamide@K': ['K(295.0514)'], 'Benzyl-TA@Any_N-term': ['N-term(164.0295)'], 'Benzyl-TA@K': ['K(164.0295)'], 'Benzyl@Any_N-term': ['N-term(90.0469)'], 'Benzyl@K': ['K(90.0469)'], 'Biotin@Any_N-term': ['N-term(226.0775)'], 'Butyryl@K': ['K(70.0418)'], 'Carbamidomethyl@C': ['C(57.0214)'], 'Carbamidomethyl@M': ['M(57.0214)'], 'Carbamyl@Any_N-term': ['N-term(43.0058)'], 'Crotonyl@K': ['K(68.0262)'], 'Cysteinyl@C': ['C(119.0040)'], 'Deamidated@N': ['N(0.9840)'], 'Deamidated@Q': ['Q(0.9840)'], 'DiLeu4plex115@Any_N-term': ['N-term(145.1199)'], 'DiLeu4plex115@K': ['K(145.1199)'], 'DiLeu4plex115@S': ['S(145.1199)'], 'DiLeu4plex115@T': ['T(145.1199)'], 'DiLeu4plex115@Y': ['Y(145.1199)'], 'DiLeu4plex117@Any_N-term': ['N-term(145.1283)'], 'DiLeu4plex117@K': ['K(145.1283)'], 'DiLeu4plex117@S': ['S(145.1283)'], 'DiLeu4plex117@T': ['T(145.1283)'], 'DiLeu4plex117@Y': ['Y(145.1283)'], 'DiLeu4plex118@Any_N-term': ['N-term(145.1404)'], 'DiLeu4plex118@K': ['K(145.1404)'], 'DiLeu4plex118@S': ['S(145.1404)'], 'DiLeu4plex118@T': ['T(145.1404)'], 'DiLeu4plex118@Y': ['Y(145.1404)'], 'DiLeu4plex@Any_N-term': ['N-term(145.1321)'], 'DiLeu4plex@K': ['K(145.1321)'], 'DiLeu4plex@S': ['S(145.1321)'], 'DiLeu4plex@T': ['T(145.1321)'], 'DiLeu4plex@Y': ['Y(145.1321)'], 'Dimethyl:2H(4)13C(2)@Any_N-term': ['N-term(34.0631)'], 'Dimethyl:2H(4)13C(2)@K': ['K(34.0631)'], 'Dimethyl:2H(4)@Any_N-term': ['N-term(32.0564)'], 'Dimethyl:2H(4)@K': ['K(32.0564)'], 'Dimethyl:2H(6)13C(2)@Any_N-term': ['N-term(36.0756)'], 'Dimethyl:2H(6)13C(2)@K': ['K(36.0756)'], 'Dimethyl:2H(6)@Any_N-term': ['N-term(34.0689)'], 'Dimethyl:2H(6)@K': ['K(34.0689)'], 'Dimethyl@Any_N-term': ['N-term(28.0313)'], 'Dimethyl@K': ['K(28.0313)'], 'Formyl@Any_N-term': ['N-term(27.9949)'], 'Formyl@K': ['K(27.9949)'], 'Formyl@S': ['S(27.9949)'], 'Formyl@T': ['T(27.9949)'], 'GG@Any_N-term': ['N-term(114.0429)'], 'GG@C': ['C(114.0429)'], 'GG@K': ['K(114.0429)'], 'GG@S': ['S(114.0429)'], 'GG@T': ['T(114.0429)'], 'Gal-b14-Glc-TA-Succinamide@Any_N-term': ['N-term(513.1152)'], 'Gal-b14-Glc-TA-Succinamide@K': ['K(513.1152)'], 'Gal-b14-Glc-TA@Any_N-term': ['N-term(398.0882)'], 'Gal-b14-Glc-TA@K': ['K(398.0882)'], 'Glc-TA-Succinamide@Any_N-term': ['N-term(351.0624)'], 'Glc-TA-Succinamide@K': ['K(351.0624)'], 'Glc-TA@Any_N-term': ['N-term(236.0354)'], 'Glc-TA@K': ['K(236.0354)'], 'Gln->pyro-Glu@Q^Any_N-term': ['Q(-17.0265)'], 'Glu->pyro-Glu@E^Any_N-term': ['E(-18.0105)'], 'Lactyl@Any_N-term': ['N-term(72.0211)'], 'Lactyl@K': ['K(72.0211)'], 'Malonyl@K': ['K(86.0003)'], 'Met->Hse@M^Any_C-term': ['M(-29.9928)'], 'Methyl@Any_N-term': ['N-term(14.0156)'], 'Methyl@H': ['H(14.0156)'], 'Methylthio@C': ['C(45.9877)'], 'Nethylmaleimide@C': ['C(125.0476)'], 'Nitro@Y': ['Y(44.9850)'], 'Oxidation@M': ['M(15.9949)'], 'PSMtag@Any_N-term': ['N-term(308.1160)'], 'PSMtag@K': ['K(308.1160)'], 'PSMtag@S': ['S(308.1160)'], 'PSMtag@T': ['T(308.1160)'], 'PSMtag@Y': ['Y(308.1160)'], 'Phospho@D': ['D(79.9663)'], 'Phospho@H': ['H(79.9663)'], 'Phospho@S': ['S(79.9663)'], 'Phospho@T': ['T(79.9663)'], 'Phospho@Y': ['Y(79.9663)'], 'Pro->(2S,3aS,7aS)-Octahydro-1H-indole-2-carboxylic_acid@P': ['P(54.0469)'], 'Pro->(2S,4R)-4-hydroxyproline@P': ['P(15.9949)'], 'Pro->(DL)-5-trifluoromethylproline@P': ['P(67.9873)'], 'Pro->(DL)-pipecolic_acid@P': ['P(14.0156)'], 'Pro->3,4-Dehydro-L-proline@P': ['P(-2.0156)'], 'Propionyl@Any_N-term': ['N-term(56.0262)'], 'Propionyl@K': ['K(56.0262)'], 'Pyridylethyl@C': ['C(105.0578)'], 'SATA-Succinamide@Any_N-term': ['N-term(247.0150)'], 'SATA-Succinamide@K': ['K(247.0150)'], 'SATA@Any_N-term': ['N-term(115.9932)'], 'SATA@K': ['K(115.9932)'], 'SATP-Succinamide@Any_N-term': ['N-term(261.0307)'], 'SATP-Succinamide@K': ['K(261.0307)'], 'SATP@Any_N-term': ['N-term(130.0088)'], 'SATP@K': ['K(130.0088)'], 'Sia-a23-Gal-b14-Glc-TA-Succinamide@Any_N-term': ['N-term(820.2055)'], 'Sia-a23-Gal-b14-Glc-TA-Succinamide@K': ['K(820.2055)'], 'Sia-a23-Gal-b14-Glc-TA@Any_N-term': ['N-term(689.1836)'], 'Sia-a23-Gal-b14-Glc-TA@K': ['K(689.1836)'], 'Succinyl@K': ['K(100.0160)'], 'TMT6plex@Any_N-term': ['N-term(229.1629)'], 'TMT6plex@H': ['H(229.1629)'], 'TMT6plex@K': ['K(229.1629)'], 'TMT6plex@S': ['S(229.1629)'], 'TMT6plex@T': ['T(229.1629)'], 'TMT6plex@Y': ['Y(229.1629)'], 'TMTpro@Any_N-term': ['N-term(304.2071)'], 'TMTpro@K': ['K(304.2071)'], 'YnLactyl@Any_N-term': ['N-term(239.1269)'], 'YnLactyl@K': ['K(239.1269)'], 'hydroxyisobutyryl@K': ['K(86.0367)'], 'iTRAQ4plex@Any_N-term': ['N-term(144.1020)'], 'iTRAQ4plex@C': ['C(144.1020)'], 'iTRAQ4plex@H': ['H(144.1020)'], 'iTRAQ4plex@K': ['K(144.1020)'], 'iTRAQ4plex@S': ['S(144.1020)'], 'iTRAQ4plex@T': ['T(144.1020)'], 'iTRAQ4plex@Y': ['Y(144.1020)'], 'mTRAQ:13C(3)15N(1)@Any_N-term': ['N-term(144.1020)'], 'mTRAQ:13C(3)15N(1)@K': ['K(144.1020)'], 'mTRAQ:13C(6)15N(2)@Any_N-term': ['N-term(148.1091)'], 'mTRAQ:13C(6)15N(2)@H': ['H(148.1091)'], 'mTRAQ:13C(6)15N(2)@K': ['K(148.1091)'], 'mTRAQ:13C(6)15N(2)@S': ['S(148.1091)'], 'mTRAQ:13C(6)15N(2)@T': ['T(148.1091)'], 'mTRAQ:13C(6)15N(2)@Y': ['Y(148.1091)'], 'mTRAQ@Any_N-term': ['N-term(140.0949)'], 'mTRAQ@H': ['H(140.0949)'], 'mTRAQ@K': ['K(140.0949)'], 'mTRAQ@S': ['S(140.0949)'], 'mTRAQ@T': ['T(140.0949)'], 'mTRAQ@Y': ['Y(140.0949)']}}, 'msfragger_pepxml': {'column_mapping': {'charge': 'assumed_charge', 'mobility': 'ion_mobility', 'proteins': 'protein', 'query_id': 'spectrum', 'raw_name': 'raw_name', 'rt': 'retention_time_sec', 'scan_num': 'start_scan', 'score': 'expect', 'sequence': 'peptide'}, 'mass_mapped_mods': ['Oxidation@M', 'Carbamidomethyl@C', 'Phospho@S', 'GG@K', 'Cysteinyl@C', 'Acetyl@Any_N-term', 'Glu->pyro-Glu@E^Any_N-term', 'Gln->pyro-Glu@Q^Any_N-term', 'Dimethyl@K', 'Methyl@E'], 'mod_mass_tol': 0.1, 'modification_mapping_type': 'maxquant', 'reader_type': 'msfragger_pepxml', 'rt_unit': 'second'}, 'msfragger_psm_tsv': {'column_mapping': {'_tmp_mods': 'Assigned Modifications', 'charge': 'Charge', 'decoy': 'Is Decoy', 'intensity': 'Intensity', 'mobility': 'Ion Mobility', 'precursor_mz': 'Observed M/Z', 'proteins': 'Protein', 'raw_name': 'raw_name', 'rt': 'Retention', 'scan_num': 'scan_num', 'score': 'Hyperscore', 'sequence': 'Peptide'}, 'mass_mapped_mods': ['Oxidation@M', 'Carbamidomethyl@C', 'Carbamidomethyl@M', 'Phospho@S', 'Phospho@T', 'Phospho@Y', 'Phospho@H', 'Phospho@D', 'GG@K', 'GG@Any_N-term', 'GG@C', 'GG@S', 'GG@T', 'Acetyl@K', 'Acetyl@Any_N-term', 'Lactyl@K', 'Lactyl@Any_N-term', 'YnLactyl@K', 'YnLactyl@Any_N-term', 'Formyl@K', 'Formyl@Any_N-term', 'Formyl@T', 'Formyl@S', 'Glu->pyro-Glu@E^Any_N-term', 'Gln->pyro-Glu@Q^Any_N-term', 'Ammonia-loss@C^Any_N-term', 'TMT6plex@K', 'TMT6plex@Any_N-term', 'TMT6plex@S', 'TMT6plex@T', 'TMT6plex@H', 'TMT6plex@Y', 'TMTpro@K', 'TMTpro@Any_N-term', 'PSMtag@K', 'PSMtag@S', 'PSMtag@T', 'PSMtag@Y', 'PSMtag@Any_N-term', 'Dimethyl@K', 'Dimethyl@Any_N-term', 'Dimethyl:2H(4)@K', 'Dimethyl:2H(4)@Any_N-term', 'Dimethyl:2H(4)13C(2)@K', 'Dimethyl:2H(4)13C(2)@Any_N-term', 'Dimethyl:2H(6)13C(2)@K', 'Dimethyl:2H(6)13C(2)@Any_N-term', 'Dimethyl:2H(6)@K', 'Dimethyl:2H(6)@Any_N-term', 'Nethylmaleimide@C', 'Deamidated@N', 'Deamidated@Q', 'Methyl@H', 'Methyl@Any_N-term', 'Methylthio@C', 'Propionyl@K', 'Propionyl@Any_N-term', 'Butyryl@K', 'Crotonyl@K', 'Succinyl@K', 'Malonyl@K', 'hydroxyisobutyryl@K', 'Nitro@Y', 'Cysteinyl@C', 'Pyridylethyl@C', 'Carbamyl@Any_N-term', 'Biotin@Any_N-term', 'Amidated@Any_C-term', 'Met->Hse@M^Any_C-term', 'iTRAQ4plex@K', 'iTRAQ4plex@Any_N-term', 'iTRAQ4plex@Y', 'iTRAQ4plex@C', 'iTRAQ4plex@S', 'iTRAQ4plex@T', 'iTRAQ4plex@H', 'mTRAQ@K', 'mTRAQ@Any_N-term', 'mTRAQ@Y', 'mTRAQ@H', 'mTRAQ@S', 'mTRAQ@T', 'mTRAQ:13C(6)15N(2)@K', 'mTRAQ:13C(6)15N(2)@Any_N-term', 'mTRAQ:13C(6)15N(2)@Y', 'mTRAQ:13C(6)15N(2)@H', 'mTRAQ:13C(6)15N(2)@S', 'mTRAQ:13C(6)15N(2)@T', 'DiLeu4plex@K', 'DiLeu4plex@Any_N-term', 'DiLeu4plex@Y', 'DiLeu4plex@S', 'DiLeu4plex@T', 'DiLeu4plex115@K', 'DiLeu4plex115@Any_N-term', 'DiLeu4plex117@K', 'DiLeu4plex117@Any_N-term', 'DiLeu4plex118@K', 'DiLeu4plex118@Any_N-term', 'Glc-TA@K', 'Glc-TA@Any_N-term', 'Glc-TA-Succinamide@K', 'Glc-TA-Succinamide@Any_N-term', 'Gal-b14-Glc-TA@K', 'Gal-b14-Glc-TA@Any_N-term', 'Gal-b14-Glc-TA-Succinamide@K', 'Gal-b14-Glc-TA-Succinamide@Any_N-term', 'Sia-a23-Gal-b14-Glc-TA@K', 'Sia-a23-Gal-b14-Glc-TA@Any_N-term', 'Sia-a23-Gal-b14-Glc-TA-Succinamide@K', 'Sia-a23-Gal-b14-Glc-TA-Succinamide@Any_N-term', 'Benzyl-TA-Succinamide@K', 'Benzyl-TA-Succinamide@Any_N-term', 'Benzyl-TA@K', 'Benzyl-TA@Any_N-term', 'Benzyl@Any_N-term', 'Benzyl@K', 'DiLeu4plex115@S', 'DiLeu4plex115@T', 'DiLeu4plex115@Y', 'DiLeu4plex117@S', 'DiLeu4plex117@T', 'DiLeu4plex117@Y', 'DiLeu4plex118@S', 'DiLeu4plex118@T', 'DiLeu4plex118@Y'], 'mod_mass_tol': 0.1, 'modification_mapping_type': 'msfragger', 'reader_type': 'msfragger_psm_tsv', 'rt_unit': 'second'}, 'pfind': {'column_mapping': {'charge': 'Charge', 'decoy': ['Target/Decoy', 'Targe/Decoy'], 'fdr': 'Q-value', 'proteins': 'Proteins', 'query_id': 'File_Name', 'raw_name': 'raw_name', 'rt': 'RT', 'scan_num': 'Scan_No', 'score': 'Final_Score', 'sequence': 'Sequence', 'uniprot_ids': 'Proteins'}, 'modification_mapping_type': None, 'reader_type': 'pfind', 'rt_unit': 'minute'}, 'sage': {'column_mapping': {'charge': 'charge', 'decoy': 'is_decoy', 'fdr': 'spectrum_q', 'mobility': 'mobility', 'modified_sequence': 'peptide', 'peptide_fdr': 'peptide_q', 'protein_fdr': 'protein_q', 'proteins': 'proteins', 'raw_name': 'filename', 'rt': 'rt', 'scannr': 'scannr', 'score': 'sage_discriminant_score', 'sequence': 'stripped_peptide'}, 'modification_mapping_type': None, 'reader_type': 'sage', 'rt_unit': 'second'}, 'spectronaut': {'column_mapping': {'ccs': 'CCS', 'charge': 'PrecursorCharge', 'genes': ['Genes', 'Gene', 'GeneName', 'GeneNames'], 'mobility': ['Mobility', 'IonMobility', 'PrecursorIonMobility'], 'precursor_mz': 'PrecursorMz', 'proteins': ['Protein Name', 'ProteinId', 'ProteinID', 'ProteinName', 'ProteinGroup', 'ProteinGroups'], 'raw_name': 'ReferenceRun', 'rt': ['RT', 'iRT', 'Tr_recalibrated', 'RetentionTime', 'NormalizedRetentionTime'], 'sequence': ['StrippedPeptide', 'PeptideSequence'], 'uniprot_ids': ['UniProtIds', 'UniProtID', 'UniprotId']}, 'fixed_C57': False, 'mod_seq_columns': ['ModifiedPeptide', 'ModifiedSequence', 'FullUniModPeptideName', 'ModifiedPeptideSequence', 'LabeledSequence', 'FullUniModPeptideName'], 'modification_mapping_type': 'maxquant', 'precursor_id_columns': ['EG.PrecursorId'], 'reader_type': 'spectronaut', 'rt_unit': 'irt'}, 'spectronaut_report': {'column_mapping': {'charge': 'charge', 'genes': 'PG.Genes', 'mobility': ['FG.ApexIonMobility'], 'proteins': ['PG.ProteinNames', 'PG.ProteinGroups'], 'raw_name': 'R.FileName', 'rt': ['EG.ApexRT', 'EG.MeanApexRT'], 'uniprot_ids': 'PG.UniProtIds'}, 'fixed_C57': False, 'mod_seq_columns': ['ModifiedSequence'], 'modification_mapping_type': 'maxquant', 'precursor_id_columns': ['EG.PrecursorId'], 'reader_type': 'spectronaut_report', 'rt_unit': 'minute'}}¶: See psm_reader.yaml