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psm_reader.yaml
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psm_reader.yaml
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alphapept:
reader_type: alphapept
rt_unit: minute
column_mapping:
'rt': 'rt'
'scan_num': 'scan_no'
'spec_idx': 'raw_idx'
'query_id': 'query_idx'
'mobility': 'mobility'
'score': 'score'
'precursor_mz': 'mz'
'charge': 'charge'
'raw_name': 'raw_name' #parse from `ms_data.hdf`` file
'fdr': 'q_value'
'decoy': 'decoy'
modification_mapping:
'Carbamidomethyl@C': 'cC'
'Oxidation@M': 'oxM'
'Phospho@S': 'pS'
'Phospho@T': 'pT'
'Phospho@Y': 'pY'
'Acetyl@Protein N-term': 'a'
maxquant:
reader_type: maxquant
rt_unit: minute
fixed_C57: True
column_mapping:
'sequence': 'Sequence'
'charge': 'Charge'
'rt': 'Retention time'
'ccs': 'CCS'
'mobility':
- 'Mobility'
- 'IonMobility'
- 'K0' # Bug in MaxQuant? It should be 1/K0
- '1/K0'
'scan_num':
- 'Scan number'
- 'MS/MS scan number'
- 'Scan index'
'raw_name': 'Raw file'
'precursor_mz': 'm/z'
'score': 'Score'
'proteins': 'Proteins'
'genes': ['Gene Names','Gene names']
'decoy': 'Reverse'
'intensity': 'Intensity'
modification_mapping:
'Dimethyl@K':
- 'K(Dimethyl)'
'Dimethyl@R':
- 'R(Dimethyl)'
'Dimethyl@Any N-term':
- '(Dimethyl)'
'Acetyl@Protein N-term':
- '_(Acetyl (Protein N-term))'
- '_(ac)'
'Carbamidomethyl@C':
- 'C(Carbamidomethyl (C))'
- 'C(Carbamidomethyl)'
'Oxidation@M':
- 'M(Oxidation)'
- 'M(Oxidation (M))'
- 'M(ox)'
'Phospho@S':
- 'S(Phospho (S))'
- 'S(Phospho (ST))'
- 'S(Phospho (STY))'
- 'S(ph)'
- 'pS'
'Phospho@T':
- 'T(Phospho (T))'
- 'T(Phospho (ST))'
- 'T(Phospho (STY))'
- 'T(ph)'
- 'pT'
'Phospho@Y':
- 'Y(Phospho (Y))'
- 'Y(Phospho (STY))'
- 'Y(ph)'
- 'pY'
'Deamidated@N': ['N(Deamidation (NQ))','N(de)']
'Deamidated@Q': ['Q(Deamidation (NQ))','Q(de)']
'GlyGly@K': ['K(GlyGly (K))', 'K(gl)']
pfind:
reader_type: pfind
rt_unit: minute
column_mapping:
'sequence': 'Sequence'
'charge': 'Charge'
'rt': 'RT'
'raw_name': 'raw_name'
'query_id': 'File_Name'
'scan_num': 'Scan_No'
'score': 'Final_Score'
'proteins': 'Proteins'
'uniprot_ids': 'Proteins'
'fdr': 'Q-value'
'decoy': ['Target/Decoy', 'Targe/Decoy']
modification_mapping:
'': ''
msfragger_pepxml:
reader_type: msfragger_pepxml
rt_unit: second
column_mapping:
'sequence': 'peptide'
'charge': 'assumed_charge'
'rt': 'retention_time_sec'
'query_id': 'spectrum'
'scan_num': 'start_scan'
'score': 'expect'
'fdr': 'expect'
'proteins': 'protein'
'raw_name': 'raw_name'
'mobility': 'ion_mobility'
modification_mapping:
'': ''
mass_mapped_mods:
- 'Oxidation@M' #other Oxidation@X are not needed here
- 'Carbamidomethyl@C'
- 'Phospho@S' #TY are not needed here
- 'GlyGly@K'
- 'Cysteinyl@C'
- 'Acetyl@Any N-term'
- 'Glu->pyro-Glu@E^Any N-term'
- 'Gln->pyro-Glu@Q^Any N-term'
- 'Dimethyl@K' # Any N-term is not needed here as it will be infered in-the-fly
- 'Methyl@E' #an example of a PTM that can be C-term
mod_mass_tol: 0.1 # Da
diann:
reader_type: diann
rt_unit: minute
fixed_C57: False
column_mapping:
'raw_name': 'Run'
'sequence': 'Stripped.Sequence'
'charge': 'Precursor.Charge'
'rt': 'RT'
'rt_start': 'RT.Start'
'rt_stop': 'RT.Stop'
'ccs': 'CCS'
'mobility': ['IM','IonMobility']
'proteins': 'Protein.Names'
'uniprot_ids': 'Protein.Ids'
'genes': 'Genes'
'scan_num': 'MS2.Scan'
'score': 'CScore'
'fdr': 'Q.Value'
modification_mapping: 'maxquant'
spectronaut_report:
reader_type: spectronaut_report
rt_unit: minute
fixed_C57: False
column_mapping:
'raw_name': 'R.FileName'
'rt': ['EG.ApexRT','EG.MeanApexRT']
'proteins': ['PG.ProteinNames','PG.ProteinGroups']
'genes': 'PG.Genes'
'uniprot_ids': 'PG.UniProtIds'
'charge': 'charge'
modification_mapping: 'maxquant'
spectronaut:
reader_type: spectronaut
rt_unit: irt
fixed_C57: False
mod_seq_columns:
- 'ModifiedPeptide'
- 'ModifiedSequence'
- 'FullUniModPeptideName'
- 'ModifiedPeptideSequence'
- 'LabeledSequence'
- 'FullUniModPeptideName'
column_mapping:
'raw_name': 'ReferenceRun'
'sequence': ['StrippedPeptide','PeptideSequence']
'charge': 'PrecursorCharge'
'rt': ['RT','iRT','Tr_recalibrated','RetentionTime','NormalizedRetentionTime']
'ccs': 'CCS'
'precursor_mz': 'PrecursorMz'
'mobility': ['Mobility','IonMobility','PrecursorIonMobility']
'proteins': ['Protein Name','ProteinId','ProteinID','ProteinName','ProteinGroup','ProteinGroups']
'uniprot_ids': ['UniProtIds','UniProtID','UniprotId']
'genes': ['Genes','Gene','GeneName','GeneNames']
modification_mapping: 'maxquant'
library_reader_base:
reader_type: library_reader_base
rt_unit: irt
fixed_C57: False
csv_sep: "\t"
mod_seq_columns:
- 'ModifiedPeptideSequence'
- 'ModifiedPeptide'
- 'ModifiedSequence'
- 'FullUniModPeptideName'
- 'LabeledSequence'
- 'FullUniModPeptideName'
column_mapping:
'raw_name': 'ReferenceRun'
'sequence': ['PeptideSequence', 'StrippedPeptide']
'modified_sequence': ['ModifiedPeptideSequence','ModifiedPeptide']
'charge': 'PrecursorCharge'
'rt': ['RT','iRT','Tr_recalibrated','RetentionTime','NormalizedRetentionTime']
'ccs': 'CCS'
'precursor_mz': 'PrecursorMz'
'mobility': ['Mobility','IonMobility','PrecursorIonMobility']
'proteins': ['ProteinId','ProteinID','ProteinName','Protein Name',]
'uniprot_ids': ['UniProtIds','UniProtID','UniprotId']
'genes': ['GeneName','Genes','Gene',]
'fragment_intensity': ['LibraryIntensity','RelativeIntensity', 'RelativeFragmentIntensity', 'RelativeFragmentIonIntensity']
'fragment_mz': ['ProductMz']
'fragment_type': ['FragmentType', 'FragmentIonType', 'ProductType', 'ProductIonType']
'fragment_charge' : ['FragmentCharge', 'FragmentIonCharge', 'ProductCharge', 'ProductIonCharge']
'fragment_series': ['FragmentSeriesNumber','FragmentNumber']
'fragment_loss_type': ['FragmentLossType', 'FragmentIonLossType', 'ProductLossType', 'ProductIonLossType']
modification_mapping: 'maxquant'
sage:
reader_type: sage
rt_unit: minute
column_mapping:
'modified_sequence': 'peptide'
'sequence': 'stripped_peptide'
'charge': 'charge'
'rt': 'rt'
'mobility': 'mobility'
'raw_name': 'filename'
'scannr': 'scannr'
'score': 'sage_discriminant_score'
'proteins': 'proteins'
'fdr': 'spectrum_q'
'peptide_fdr': 'peptide_q'
'protein_fdr': 'protein_q'
'decoy': 'is_decoy'