February 18, 2024


Dataset Description

The dataset contains 1.056.808 PSMs from 441 MaxQuant evidence files filtered at PEP < 0.001 (Contains only pre-selected columns).


  • title: PXD028248
  • dataset tag: retentiontime/PXD028248_RT
  • data publication: Clinical and Translational Medicine
  • machine learning publication:
  • data source identifier: PXD028248
  • data type: retention time
  • format: CSV
  • columns: Raw file, Sequence, Modifications, Modified sequence, Retention time, Calibrated retention time, PEP
  • instrument: Q. Exactive HF
  • organism: Homo sapiens (human)
  • fixed modifications:
  • variable modification: unmodified, methionine oxidation, N-terminal acetylation, and carbamidomethyl
  • chromatography separation: RP
  • peak measurement:

Sample Protocol

Ascites and greater omentum tissue with metastatic lesions were collected from patients with ovarian HGSC undergoing primary surgery at the University Hospital in Marburg. Clinical courses were evaluated by RECIST criteria33 in patients with measurable disease or profiles of serum CA125 levels according to the recommendations by the Gynecologic Cancer InterGroup (GCIG). Only patients with observations periods ≥12 months after first line surgery were included in the survival.

Peptides were separated using an UHPLC (EASY-nLC 1000, ThermoFisher Scientific) and 20 cm, in-house packed C18 silica columns (1.9 μm C18 beads, Dr. Maisch GmbH, Ammerbuch, Germany) coupled in line to a QExactive HF orbitrap mass spectrometer (ThermoFisher Scientific) using an electrospray ionization source.

Data Analysis Protocol

Analysis by liquid chromatography/tandem mass spectrometry (LC/MS2) was performed and peptide/spectrum matching as well as label free quantitation used the MaxQuant suite of algorithms against the human Uniprot database (canonical and isoforms; downloaded on 2020/02/05; 1888349 entries).