Van Puyvelde et al. TWIMS


February 18, 2024


Dataset Description

The data consists of 6.268 PSMs.


  • title: A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
  • dataset tag: ionmobility/VanPuyvelde_TWIMS
  • data publication: Scientific Data
  • machine learning publication:
  • data source identifier: PXD028735
  • data type: ion mobility
  • format: TSV
  • columns: Modified sequence, Charge, CCS, Ion Mobility, Ion Mobility Units, High Energy, Ion Mobility Offset
  • instrument: maXis, timsTOF Pro,
  • organism: Homo sapiens (Human), Saccharomyces cerevisiae (Baker’s yeast), Escherichia coli (E. coli)
  • fixed modifications:
  • variable modification:unmodified & oxidation & acetylation & carbamidomethyl
  • ionmobility type: TWIMS
  • css calibration compounds:

Sample Protocol

From the original paper:

Mass spectrometry-compatible Human K562 (P/N: V6951) and Yeast (P/N: V7461) protein digest extracts were purchased from Promega (Madison, Wisconsin, United States). Lyophilised MassPrep Escherichia.coli digest standard (P/N:186003196) was purchased from Waters Corporation (Milford, Massachusetts, United States). The extracts were reduced with dithiothreitol (DTT), alkylated with iodoacetamide (IAA) and digested with sequencing grade Trypsin(-Lys C) by the respective manufacturers. The digested protein extracts were reconstituted in a mixture of 0.1% Formic acid (FA) in water (Biosolve B.V, Valkenswaard, The Netherlands) and spiked with iRT peptides (Biognosys, Schlieren, Switzerland) at a ratio of 1:20 v/v. Two master samples A and B were created similar to Navarro et al., each in triplicate, as shown in Fig. 1. Sample A was prepared by mixing Human, Yeast and E.coli at 65%, 30% and 5% weight for weight (w/w), respectively. Sample B was prepared by mixing Human, Yeast and E.coli protein digests at 65%, 15%, 20% w/w, respectively. The resulting samples have logarithmic fold changes (log2FCs) of 0, −1 and 2 for respectively Human, Yeast and E.coli. One sixth of each of the triplicate master batches of A and B were mixed to create a QC sample, containing 65% w/w Human, 22.5% w/w Yeast and 12.5% w/w E.coli.

Data Analysis Protocol

From the original paper:

An M-class LC system (Waters Corporation, Milford, MA) was equipped with a 1.7 µm CSH 130 C18 300 µm × 100 mm column, operating at 5 µL/min with a column temperature of 55 °C. Mobile phase A was UPLC-grade water containing 0.1% (v/v) FA and 3% DMSO, mobile phase B was ACN containing 0.1% (v/v) FA. Peptides were separated using a linear gradient of 3−30% mobile phase B over 120 minutes. All experiments were conducted on a Synapt G2-Si mass spectrometer (Waters Corporation, Wilmslow, UK). The ESI Low Flow probe capillary voltage was 3 kV, sampling cone 60 V, source offset 60 V, source temperature 80 °C, desolvation temperature 350 °C, cone gas 80 L/hr, desolvation gas 350 L/hr, and nebulizer pressure 2.5 bar. A lock mass reference signal of GluFibrinopeptide B (m/z 785.8426) was sampled every 30 s.