Update exclusion list (45 new entries)

[proteomics-developers]

Automated update from crosslinking-maintainer validation pipeline.

New entries:

• PXD001593 (83NWI-US_1apr2010undigestedF059907.mzid.gz): No MS:1002511 CV param found
• PXD001677 (result_NormalMode.mzid.gz): Validating file result_NormalMode.mzid. | Sorry, we're only supporting 1.2.0 and 1.3.0 (the ones that contain crosslinks). Rejected schema file: mzIdentML1.1.0.xsd | File result_NormalMode.mzid is schema invalid.
• PXD003532 (Experimentmaxquantresults_20_3K4fromQEPlus2_12172015_20_3K4.mzid.gz): No MS:1002511 CV param found
• PXD003718 (Baits_ORF4259Nter_ORF4259Cterandwildtype_scaffold_mascot_giardia.mzid.gz): No MS:1002511 CV param found
• PXD004473 (CW2176_mzIdentML.mzid): No MS:1002511 CV param found
• PXD004583 (20140718_sr_6335_5785_3F204047.mzid.gz): No MS:1002511 CV param found
• PXD004722 (srpensrpen_F029370_kontrola.mzid): No MS:1002511 CV param found
• PXD005461 (OBJ7325_F057990.mzid.gz): No MS:1002511 CV param found
• PXD006574 (dimerResultsToPRIDE.mzid.gz): Validating file dimerResultsToPRIDE.mzid. | Sorry, we're only supporting 1.2.0 and 1.3.0 (the ones that contain crosslinks). Rejected schema file: mzIdentML1.1.0.xsd | File dimerResultsToPRIDE.mzid is schema invalid.
• PXD006938 (2_NFS1-Fxn-IscU_MarkleyF016506.mzid.gz): No MS:1002511 CV param found
• PXD007716 (F074077.mzid.gz): No MS:1002511 CV param found
• PXD007836 (peptides_1_1_0.mzid.gz): No MS:1002511 CV param found
• PXD009641 (ID16364_01_E749_3008_030315F056134.mzid.gz): No MS:1002511 CV param found
• PXD012466 (mapeixiang-NSSO-3.mzid.gz): No MS:1002511 CV param found
• PXD014523 (xQuest_BSA_DSS_CID.mzid): XML is invalid. First 20 errors: | Error: Element '{http://psidev.info/psi/pi/mzIdentML/1.2}cvParam': No match found for key-sequence ['MS'] of keyref '{http://psidev.info/psi/pi/mzIdentML/1.2}FK_CVlist5'., Line: 11710 | File xQuest_BSA_DSS_CID.mzid is schema invalid.
• PXD017290 (Mudpit_MassSpectrumF001689.mzid.gz): No MS:1002511 CV param found
• PXD017792 (XLG729RE1aE2o.mzid.gz): No MS:1002511 CV param found
• PXD017873 (20200302_072815_PBS_X02_02.raw.mzid.gz): No MS:1002511 CV param found
• PXD018600 (CSL9686A14RW2_E2_105_peptides_1_1_0.mzid.gz): No MS:1002511 CV param found
• PXD018687 (SHR72_4_DC18.mzid.gz): No MS:1002511 CV param found
• PXD018935 (Ribosome_3A.mzid): No MS:1002511 CV param found
• PXD019017 (TRY_AMPK_DSSO_XL-MS.mzid): No MS:1002511 CV param found
• PXD019713 (mapx_Xlink_17-SIM.mzid.gz): No MS:1002511 CV param found
• PXD019944 (mapx_xlink_13-4.mzid.gz): No MS:1002511 CV param found
• PXD023525 (E1oE2oCDI.mzid.gz): No MS:1002511 CV param found
• PXD026622 (Anish_iTRAQ_3h_SPSMS3_fraction1_12.mzid.gz): No MS:1002511 CV param found
• PXD027655 (F271205.mzid): No MS:1002511 CV param found
• PXD028685 (20201231_006_ZR_Smirnova_M7.mzid.gz): No MS:1002511 CV param found
• PXD028919 (20191007_nst9054_20-1917_Troyanovsky_01__F025136_.mzid.gz): No MS:1002511 CV param found
• PXD030048 (export_Mzidentml_F004245.mzid.gz): No MS:1002511 CV param found
• PXD031159 (20210923_SUMO2_49TAG_INCUBATE_CELL_LYSATE_TWICEHISIP_TRYPSIN_REP1.mzid.gz): No MS:1002511 CV param found
• PXD031385 (MSB51072A__F172198_.mzid.gz): No MS:1002511 CV param found
• PXD033004 (Closed-search-Amanda_DTB-PT_500ug.mzid): No MS:1002511 CV param found
• PXD037894 (PD1280_SuTex_FBDD_Soto_bio1_run2.raw__F003497_.mzid.gz): No MS:1002511 CV param found
• PXD038128 (190627_VLopez_Khavari_9923_PR1_VLP_Glc_m3.raw_20190702_Byonic.mzid.gz): No MS:1002511 CV param found
• PXD048297 (peptides_1_1_0.mzid.gz): No MS:1002511 CV param found
• PXD051688 (2023-1215_Ecoli-TMT18plex-TotalPeptideAmount.mzid.gz): No MS:1002511 CV param found
• PXD053415 (Experiment_RA912_8MAM_from_RA912_68MAM.mzid.gz): No MS:1002511 CV param found
• PXD055077 (SUMOylation_PhoX_TBDSPP_FAIMS_140823.mzid.gz): File SUMOylation_PhoX_TBDSPP_FAIMS_140823.mzid is schema valid. | Error parsing SUMOylation_PhoX_TBDSPP_FAIMS_140823.mzid | list index out of range
• PXD056510 (E240411_AMC_Mart_LDLandLDLR_SulfoSDA_007and013Ratios_AllData_Xi1.8_filtered_searches_4CCFrags_5TotFrags.mzid.gz): Error: Element '{http://psidev.info/psi/pi/mzIdentML/1.2}cvParam': The attribute 'cvRef' is required but missing., Line: 10152 | Error: Element '{http://psidev.info/psi/pi/mzIdentML/1.2}cvParam': The attribute 'accession' is required but missing., Line: 10152 | File E240411_AMC_Mart_LDLandLDLR_Sulfo...
• PXD065365 (peptides_1_1_0.mzid): No MS:1002511 CV param found
• PXD065858 (E250221_AMC_rpn1_IP_C1_IV_Dose_pepSEC_A3toB6_ReSearchWithPeaks_Xi1.8_filt_PSU_OR_5SU_BTWNS.mzid): Error: Element '{http://psidev.info/psi/pi/mzIdentML/1.2}cvParam': The attribute 'cvRef' is required but missing., Line: 1523 | Error: Element '{http://psidev.info/psi/pi/mzIdentML/1.2}cvParam': The attribute 'accession' is required but missing., Line: 1523 | File E250221_AMC_rpn1_IP_C1_IV_Dose_pepS...
• PXD065869 (20250422_HSA_C1_HCD_Dose_BothBioReps_ReSearch_Xi1.8_PSU_ONLY.mzid): Error: Element '{http://psidev.info/psi/pi/mzIdentML/1.2}cvParam': The attribute 'cvRef' is required but missing., Line: 1857 | Error: Element '{http://psidev.info/psi/pi/mzIdentML/1.2}cvParam': The attribute 'accession' is required but missing., Line: 1857 | File 20250422_HSA_C1_HCD_Dose_BothBioRep...
• PXD065956 (E241202_AMC_HeLa_C1_IS_Sol_Enriched_pepSEC_Uncleaved_A3toB6_Xi1.8_comb_filt_1CC_3Tot.mzid): Error: Element '{http://psidev.info/psi/pi/mzIdentML/1.2}cvParam': The attribute 'cvRef' is required but missing., Line: 13818 | Error: Element '{http://psidev.info/psi/pi/mzIdentML/1.2}cvParam': The attribute 'accession' is required but missing., Line: 13818 | File E241202_AMC_HeLa_C1_IS_Sol_Enrich...
• PXD065958 (E240905_AMC_Ecoli_C1_InSitu_Enriched_pepSEC_A5toB6_Xi1.8_3CCFrags.mzid): Error: Element '{http://psidev.info/psi/pi/mzIdentML/1.2}cvParam': The attribute 'cvRef' is required but missing., Line: 344 | Error: Element '{http://psidev.info/psi/pi/mzIdentML/1.2}cvParam': The attribute 'accession' is required but missing., Line: 344 | File E240905_AMC_Ecoli_C1_InSitu_Enriched_...

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• mzidentml_data_inclusions/exclusion_list.csv is excluded by !**/*.csv

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[qodo-code-review]

Review Summary by Qodo

Update exclusion list with 45 new validation failures

📦 Other

Walkthroughs

Description

• Automated update to the exclusion list with 45 new entries from the crosslinking-maintainer
  validation pipeline
• New entries added for datasets that fail validation due to:
  - Missing MS:1002511 CV parameter (majority of entries)
  - Unsupported mzIdentML schema versions (only 1.2.0 and 1.3.0 with crosslinks are supported)
  - XML schema validation errors
• Entries span multiple PXD projects with various file format issues

Diagram

flowchart LR
  A["Validation Pipeline"] -- "Identifies invalid files" --> B["Exclusion List"]
  B -- "45 new entries" --> C["Updated Configuration"]

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[qodo-code-review]

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