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Fix peptidoform modification offset and mass (fixes #100)
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@RalfG
RalfG committed Oct 31, 2024
1 parent b0fb411 commit 407a8f3
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Showing 2 changed files with 100 additions and 3 deletions.
90 changes: 90 additions & 0 deletions example_files/PXD053286-G1_PTMiprophet.slice.pep.xml
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<?xml version="1.0" encoding="UTF-8"?>
<msms_pipeline_analysis date="2022-05-17T22:37:25"
xmlns="http://regis-web.systemsbiology.net/pepXML"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v122.xsd"
summary_xml="/mnt/nfs/DataPool/Projects/Lumos/2022/22_2_Apr_Jun/20220510_VC/Pipe_Mferi_M/G1_iprophet.pep.xml">
<analysis_summary analysis="ptmprophet" time="2022-05-17T23:41:43">
<ptmprophet_summary version="TPP v5.1.0 Syzygy, Build 202012091755-8315 (Linux-x86_64)"
options="M:15.994915,n:42.010565 MZTOL=0.4 G1_iprophet.pep.xml G1_PTMiprophet.pep.xml">
<inputfile name="G1_iprophet.pep.xml" />
<inputfile name="20220511_M1_Mferi_0535_VC_i01_comet.pep.xml"
directory="/mnt/nfs/DataPool/Projects/Lumos/2022/22_2_Apr_Jun/20220510_VC/Data" />
<inputfile name="20220511_M1_Mferi_0535_VC_i02_comet.pep.xml"
directory="/mnt/nfs/DataPool/Projects/Lumos/2022/22_2_Apr_Jun/20220510_VC/Data" />
</ptmprophet_summary>
</analysis_summary>
<msms_run_summary
base_name="/mnt/nfs/DataPool/Projects/Lumos/2022/22_2_Apr_Jun/20220510_VC/Data/20220511_M1_Mferi_0535_VC_i01"
msManufacturer="UNKNOWN" msModel="UNKNOWN" raw_data_type="raw" raw_data=".mzXML">
<sample_enzyme name="trypsin">
<specificity cut="KR" no_cut="P" sense="C" />
</sample_enzyme>
<search_summary
base_name="/mnt/nfs/DataPool/Projects/Lumos/2022/22_2_Apr_Jun/20220510_VC/Data/20220511_M1_Mferi_0535_VC_i01"
search_engine="Comet" search_engine_version="2019.01 rev. 5"
precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1">
<search_database
local_path="/mnt/nfs/DataPool/FastaDataBases/Mferi_G5847_GCF_000327395.faa_REV.fasta"
type="AA" />
<enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="3"
min_number_termini="2" />
<aminoacid_modification aminoacid="M" massdiff="15.994900" mass="147.035385"
variable="Y" symbol="*" />
<terminal_modification terminus="N" massdiff="42.010565" mass="43.018390" variable="Y"
protein_terminus="Y" symbol="#" />
<aminoacid_modification aminoacid="C" massdiff="57.021464" mass="160.030649"
variable="N" />
</search_summary>
<spectrum_query spectrum="20220511_M1_Mferi_0535_VC_i01.05387.05387.2" start_scan="5387"
end_scan="5387" precursor_neutral_mass="1006.560276" assumed_charge="2" index="143"
retention_time_sec="1413.1" experiment_label="Mferi_M1">
<search_result>
<search_hit hit_rank="1" peptide="SNLFLMLK" peptide_prev_aa="M" peptide_next_aa="Q"
protein="WP_008364460.1" num_tot_proteins="1" num_matched_ions="11"
tot_num_ions="14" calc_neutral_pep_mass="1006.552139" massdiff="0.008137"
num_tol_term="2" num_missed_cleavages="0" num_matched_peptides="55"
protein_descr="ABC transporter permease [Mycoplasma feriruminatoris]">
<modification_info modified_peptide="n[43]SNLFLMLK" mod_nterm_mass="43.01839"></modification_info>
<search_score name="xcorr" value="1.214" />
<search_score name="deltacn" value="1.000" />
<search_score name="deltacnstar" value="0.000" />
<search_score name="spscore" value="453.5" />
<search_score name="sprank" value="1" />
<search_score name="expect" value="1.17E+00" />
<analysis_result analysis="peptideprophet">
<peptideprophet_result probability="0.5131"
all_ntt_prob="(0.0000,0.0000,0.5131)">
<search_score_summary>
<parameter name="fval" value="-0.3767" />
<parameter name="ntt" value="2" />
<parameter name="nmc" value="0" />
<parameter name="massd" value="8.084" />
<parameter name="isomassd" value="0" />
</search_score_summary>
</peptideprophet_result>
</analysis_result>
<analysis_result analysis="interprophet">
<interprophet_result probability="0.00133535"
all_ntt_prob="(0,0,0.00133535)">
<search_score_summary>
<parameter name="nss" value="0.1289" />
<parameter name="nrs" value="-0.7221" />
<parameter name="nse" value="-0.5741" />
<parameter name="nsi" value="0" />
<parameter name="nsm" value="0.9838" />
<parameter name="nsp" value="20" />
</search_score_summary>
</interprophet_result>
</analysis_result>
<analysis_result analysis="ptmprophet">
<ptmprophet_result prior="1" ptm="PTMProphet_n42.0106"
ptm_peptide="n(1.000)SNLFLMLK">
<mod_terminal_probability terminus="n" probability="1.000" />
</ptmprophet_result>
</analysis_result>
</search_hit>
</search_result>
</spectrum_query>
</msms_run_summary>
</msms_pipeline_analysis>
13 changes: 10 additions & 3 deletions psm_utils/io/pepxml.py
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Expand Up @@ -7,7 +7,7 @@
from pathlib import Path
from typing import List, Optional, Union

from pyteomics import pepxml, proforma
from pyteomics import mass, pepxml, proforma

from psm_utils.io._base_classes import ReaderBase
from psm_utils.peptidoform import Peptidoform
Expand Down Expand Up @@ -81,13 +81,20 @@ def _parse_peptidoform(peptide: str, modifications: List[dict], charge: Optional
n_term = []
c_term = []
for mod in modifications:
mod_tag = proforma.process_tag_tokens(f"{mod['mass']:+}")
# Round mass modification to 6 decimal places, precision from UniMod
if mod["position"] == 0:
mod_tag = proforma.process_tag_tokens(f"{mod['mass']:+.6f}")
n_term.append(mod_tag)
elif mod["position"] == len(peptide) + 1:
mod_tag = proforma.process_tag_tokens(f"{mod['mass']:+.6f}")
c_term.append(mod_tag)
else:
modifications_dict[mod["position"]].append(mod_tag)
# Convert 1-based to 0-based position
position = mod["position"] - 1
# Sequence modifications are written as residue mass + modification mass
mod_mass = mod["mass"] - mass.std_aa_mass[peptide[position]]
mod_tag = proforma.process_tag_tokens(f"{mod_mass:+.6f}")
modifications_dict[position].append(mod_tag)

sequence = [(aa, modifications_dict[i] or None) for i, aa in enumerate(peptide)]
properties = {
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