MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics.

Molecular & Cellular Proteomics : MCP
N. PrianichnikovJürgen Cox

Abstract

Ion mobility can add a dimension to LC-MS based shotgun proteomics which has the potential to boost proteome coverage, quantification accuracy and dynamic range. Required for this is suitable software that extracts the information contained in the four-dimensional (4D) data space spanned by m/z, retention time, ion mobility and signal intensity. Here we describe the ion mobility enhanced MaxQuant software, which utilizes the added data dimension. It offers an end to end computational workflow for the identification and quantification of peptides and proteins in LC-IMS-MS/MS shotgun proteomics data. We apply it to trapped ion mobility spectrometry (TIMS) coupled to a quadrupole time-of-flight (QTOF) analyzer. A highly parallelizable 4D feature detection algorithm extracts peaks which are assembled to isotope patterns. Masses are recalibrated with a non-linear m/z, retention time, ion mobility and signal intensity dependent model, based on peptides from the sample. A new matching between runs (MBR) algorithm that utilizes collisional cross section (CCS) values of MS1 features in the matching process significantly gains specificity from the extra dimension. Prerequisite for using CCS values in MBR is a relative alignment of the io...Continue Reading

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Citations

Jul 4, 2020·Molecular & Cellular Proteomics : MCP·Fengchao YuAlexey I Nesvizhskii
Oct 21, 2020·Biochemical Society Transactions·Lindsay K PinoBirgit Schilling
Jan 17, 2021·Molecular & Cellular Proteomics : MCP·Fengchao YuAlexey I Nesvizhskii

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Datasets Mentioned

BETA
PXD014777

Methods Mentioned

BETA
Peptide assay
acetylation

Software Mentioned

Windows
Jupyter
Linux
Evosep
Linux Ubuntu
MaxQuant
Andromeda
Perseus
PASEF
timsTOF

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The American Society for Biochemistry and Molecular Biology (ASBMB) includes the Journal of Biological Chemistry, Molecular & Cellular Proteomics, and the Journal of Lipid Research. Discover the latest research from ASBMB here.