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

Status: Open.

#111 In bzhanglab/PepQuery;

· abatool110 opened on Mar 12, 2026

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

Status: Open.

#109 In bzhanglab/PepQuery;

· anuC opened on Nov 6, 2025

Questions about using HBV PDC000198 dataset

Status: Open.

#108 In bzhanglab/PepQuery;

· 2390735351-byte opened on Nov 4, 2025

spectrum matched to a wrong peptide

Status: Open.

#105 In bzhanglab/PepQuery;

· treko90 opened on Oct 14, 2025

No output of peptide with low score in validation model

Status: Open.

#104 In bzhanglab/PepQuery;

· YongchaoDou opened on Jul 24, 2025

Comparing Wild-Type and Mutant Protein Expression

Status: Open.

#102 In bzhanglab/PepQuery;

· anuC opened on Jul 18, 2025

ms files in dataset Deep_29_healthy_human_tissues_PXD010154

Status: Open.

#99 In bzhanglab/PepQuery;

· sophiachen1 opened on Jun 1, 2025

MS/MS index file retrieving error through AWS

Status: Open.

#98 In bzhanglab/PepQuery;

· qqwang-berkeley opened on May 29, 2025

Meaning of n_db and n_ptm values

Status: Open.

#93 In bzhanglab/PepQuery;

· katherine-d21 opened on Apr 17, 2025

Testing different intensity thresholds

Status: Open.

#92 In bzhanglab/PepQuery;

· Francis-B opened on Apr 9, 2025

no matched spectrum on ab sciex

help wanted

V2

Status: Open.

#91 In bzhanglab/PepQuery;

· treko90 opened on Apr 8, 2025

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

Status: Open.

#90 In bzhanglab/PepQuery;

· xiaodfeng opened on Apr 1, 2025