Issues

• [ERROR] main.java.pg.StatisticScoreWorker[run:60] - There is no random peptide!

  bzhanglab/PepQuery#113 · Filter by author sophiachen1 opened on Oct 5, 2026

• Novel-peptide validation (-s 1) against a downloaded reference DB aborts: FMIndex rejects '*' in GENCODE translations

  bzhanglab/PepQuery#112 · Filter by author afgane opened on Sep 17, 2026
  2

  

• [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!

  bzhanglab/PepQuery#111 · Filter by author abatool110 opened on Mar 12, 2026

• main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!

  bzhanglab/PepQuery#109 · Filter by author anuC opened on Nov 6, 2025
  1

• Questions about using HBV PDC000198 dataset

  bzhanglab/PepQuery#108 · Filter by author 2390735351-byte opened on Nov 4, 2025
  4

• spectrum matched to a wrong peptide

  bzhanglab/PepQuery#105 · Filter by author treko90 opened on Oct 14, 2025
  3

• No output of peptide with low score in validation model

  bzhanglab/PepQuery#104 · Filter by author YongchaoDou opened on Jul 24, 2025
  4

• Comparing Wild-Type and Mutant Protein Expression

  bzhanglab/PepQuery#102 · Filter by author anuC opened on Jul 18, 2025
  3

• ms files in dataset Deep_29_healthy_human_tissues_PXD010154

  bzhanglab/PepQuery#99 · Filter by author sophiachen1 opened on Jun 1, 2025
  3

• MS/MS index file retrieving error through AWS

  bzhanglab/PepQuery#98 · Filter by author qqwang-berkeley opened on May 29, 2025
  7

• Meaning of n_db and n_ptm values

  bzhanglab/PepQuery#93 · Filter by author katherine-d21 opened on Apr 17, 2025
  4

• Testing different intensity thresholds

  bzhanglab/PepQuery#92 · Filter by author Francis-B opened on Apr 9, 2025
  5

  

• no matched spectrum on ab sciex

  help wantedV2
  bzhanglab/PepQuery#91 · Filter by author treko90 opened on Apr 8, 2025
  13

  

• Cannot open the link https://github.com/wenbostar/pepquery2_manuscript

  bzhanglab/PepQuery#90 · Filter by author xiaodfeng opened on Apr 1, 2025
  

• Does the current standalone version work with public datasets in PRIDE, MassIVE, jPOSTrepo and iProX, or Universal Spectrum Identifiers (USIs) from ProteomeXchange?

  bugV2
  bzhanglab/PepQuery#89 · Filter by author zxseason opened on Mar 18, 2025
  8

  

• PepQuery indexing - spectrum title vs spectrum index

  V2
  bzhanglab/PepQuery#88 · Filter by author treko90 opened on Feb 19, 2025
  29

  

• problem with analysis in linux

  bzhanglab/PepQuery#87 · Filter by author ofleitas opened on Jan 17, 2025
  1

• Validating PepQuery identified PSMs

  bzhanglab/PepQuery#85 · Filter by author anuC opened on Dec 19, 2024
  9

• Issue related to AWS access error

  PepQuery cloud MS/MS indexWeb server
  bzhanglab/PepQuery#84 · Filter by author EmaEtch opened on Dec 18, 2024
  13

• Inquiry about Sample Composition and Patient Information in HBV_Related_Hepatocellular_Carcinoma_Proteome_PDC000198 Dataset

  bzhanglab/PepQuery#82 · Filter by author bioyangyang opened on Dec 2, 2024
  1

• Custom modification search

  enhancement
  bzhanglab/PepQuery#80 · Filter by author treko90 opened on Nov 13, 2024
  5

• Exception in thread "main" java.lang.NumberFormatException: For input string: "peptide"

  bzhanglab/PepQuery#77 · Filter by author Seb-Leb opened on Oct 15, 2024
  5

• CPTAC MS dataset files in s3 bucket are not found

  bzhanglab/PepQuery#75 · Filter by author pixuenan opened on Sep 20, 2024
  7

• Using PepQuerry for identification of protein-protein interaction

  bzhanglab/PepQuery#74 · Filter by author anuC opened on Sep 18, 2024
  3

• Modification search in web version

  bzhanglab/PepQuery#70 · Filter by author icheeseman opened on Aug 26, 2024
  3