Reprocessed quantitative dataset: Participant- and peptide-resolved analysis of PXD004928 aqueous humor proteomes across glaucoma groups

ABSTRACT: This reprocessed quantitative dataset contains participant-resolvable identification and label-free quantification outputs generated from all 40 public data-dependent acquisition mass spectrometry runs in PXD004928. The source cohort comprises aqueous humor from 27 participants: 9 with primary angle-closure glaucoma, 9 with primary open-angle glaucoma, and 9 with age-related cataract; repeat technical acquisitions are explicitly annotated. The deposit provides per-run and combined peptide-spectrum match, peptide, protein, and ion outputs; the exact search database; search and quantification parameters; and sample-to-run metadata. The 40 source mass spectrometry RAW files are included unchanged under their original filenames and remain linked to the source accession PXD004928. REPROCESSING METHODS: All 40 PXD004928 data-dependent acquisition RAW files were searched jointly with FragPipe 24.0 and MSFragger 4.4.1 against the supplied reviewed-human-plus-isoform, contaminant, and reversed-decoy FASTA. Searches used strict trypsin specificity, up to two missed cleavages, 7-50-residue peptides, +/-20-ppm precursor and +/-0.6-Da fragment tolerances, isotope errors 0/1/2, fixed cysteine carbamidomethylation, and variable methionine oxidation and protein N-terminal acetylation. Percolator 3.7.1 and Philosopher 5.1.3-RC9 controlled peptide-spectrum match, peptide, and protein false-discovery rates at 1%. IonQuant 1.11.20 generated label-free quantities with normalization and MaxLFQ enabled, match-between-runs disabled, and requantification disabled. Technical repeat acquisitions were retained at the search stage and are explicitly linked to participants in the sample-to-run metadata.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Anterior Chamber Of The Eye

DISEASE(S): Primary Open Angle Glaucoma,Primary Angle-closure Glaucoma,Senile Cataract

SUBMITTER: Yuchen Fan  

LAB HEAD: Ziqing Gao

PROVIDER: PXD082879 | Pride | 2026-11-07

REPOSITORIES: Pride