U of Leipzig AG Bioanalytics - seMSE

Improving peptide fragment ion detection using travelling wave ion mobility spectrometry with signal enhancement MSE (seMSE)
Data License: CC BY 4.0 | ProteomeXchange: PXD030431 | doi: https://doi.org/10.6069/exmj-d650
  • Organism: Escherichia coli, Bos taurus, Saccharomyces cerevisiae, Oryctolagus cuniculus
  • Instrument: SYNAPT G2-Si
  • SpikeIn: No
  • Keywords: DDA, DIA, MSE, travelling wave ion mobility spectrometry (TWIMS), LC-TWIMS-MS/MS
  • Lab head: Ralf Hoffmann Submitter: Juan Camilo Rojas Echeverri
Recently, a solution to inherent poor ion beam sampling of time-of-flight (TOF) mass analyzers was proposed by restricting detection to ions expected at specific arrival times after being separated in a travelling wave ion mobility spectrometry (TWIMS) cell. Here, we show that this approach can be applied to data independent acquisition (DIA) using a so-called signal enhancement MSE (seMSE) experiment, which was compared to two different TWIMS-DDA and three different TWIMS-MSE methods with respect to the number of peptide identifications, the spectral quality of supporting peptide spec-tra matches, and, more importantly, fragment ion sensitivity. Comparison of fragment ion summed areas showed that seM-SE showed 6.8 to 11.5-fold improvement in fragment ion detection when compared to other MSE methods and although co-fragmentation of co-eluting peptides limited the seMSE peptide identifications it was possible to consistently detect peptides of interest by integrating DDA and MSE results within Skyline.
Experiment Description
A set of commercial peptide mixtures of increasing complexity, i.e., digests of first four proteins and then mixed with cytosolic proteins of Escherichia coli were analyzed by LC-TWIMS-MS/MS with a Q-IMS-TOF instrument (Synapt G2-Si) using reported two TWIMS-DDA methods, three (TWIMS)-MSE acquisition methods, and a novel MSE DIA method where TWIMS was used to separate fragment ions and use their ion mobility to improve the TOF duty cycle to increase sensitivity in fragment ion detection, as reported previously in a TWIMS-DA method. All six methods were compared in terms of the quality of spectral libraries, number of peptide/protein identifications, and relative peptide quantitation that each method could provide.
Created on 12/15/21, 6:24 PM
Clustergrammer Heatmap
seMSE_EColi_MPDS_2021-09-13_15-58-40.sky.zip2021-12-15 18:18:525882,1512,21216,36418
seMSE_MPDS_2021-09-13_12-06-55.sky.zip2021-12-15 18:18:5241872111,64118
seMSE_MPDS_copy_2021-09-13_12-02-59.sky.zip2021-12-15 18:18:5241872111,64118

Raw files description in attached Samples_description.csv

Instrumental Setup

Instrumental Setup


Abbreviation definitions and MS experiment notes:

MPDS: MassPREP™ Protein Digestion Standard (Waters; PN: 186002866-1)

E.Coli: MassPREP™ E.coli Digestion Standard (Waters; PN: 186003196-1)

HD-DDA: "high definition data dependent acquisition"; tandem mass spectrometry couples to precursor ion mobility (transfer cell fragmentation) or fragment ion mobility (trap cell fragmentation)

WbE: "wide band enhancement"; the HD-DDA (Trap) samples were acquired with an improved TOF duty cycle achieved by synchronizing fragment ion ion mobility to orthogonal pusher and TOF mass analyzer; implemented as described by Helm et al. (DOI: 10.1074/mcp.M114.041038)

MSE: data independent acquisition mass spectrometry method using all-ion-fragmentation with alternating low and high collision energies

HDMSE: "high definition MSE"; MSE coupled to travelling wave ion mobility spectrometry with a focus on precursor ion mobility separation and alignment of corresponding fragment ions to precursor's arrival time distribution

UDMSE: "ultra definition MSE"; HDMSE with drift time-specific collision energies; implemented similarly as described by Distler et al. (DOI: 10.1038/nmeth.2767) following Waters "look-up tables" generation SOP procedure

seMSE: "signal enhancement MSE"; MSE coupled to travelling wave ion mobility spectrometry with a focus on fragment ion mobility spectrometry applying the improved TOF duty cycle achieved by synchronizing fragment ion ion mobility to orthogonal pusher and TOF mass analyzer used previously in the HD-DDA (Trap) + WbE methods

  Attached Files