English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics

Prianichnikov, N., Koch, H., Koch, S., Lubeck, M., Heilig, R., Brehmer, S., et al. (2020). MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics. MOLECULAR & CELLULAR PROTEOMICS, 19(6), 1058-1069. doi:10.1074/mcp.TIR119.001720.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/21.11116/0000-0006-A39E-0 Version Permalink: http://hdl.handle.net/21.11116/0000-0006-A39F-F
Genre: Journal Article

Files

show Files

Locators

show

Creators

show
hide
 Creators:
Prianichnikov, Nikita1, Author              
Koch, Heiner2, Author
Koch, Scarlet2, Author
Lubeck, Markus2, Author
Heilig, Raphael2, Author
Brehmer, Sven2, Author
Fischer, Roman2, Author
Cox, Jürgen1, Author              
Affiliations:
1Cox, Jürgen / Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Max Planck Society, ou_2063284              
2external, ou_persistent22              

Content

show
hide
Free keywords: COMPUTATIONAL PLATFORM; MASS; PRECISION; ACCURACY; PERSEUS; RANGE
 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 ion mobility values between the runs. The missing value problem in protein quantification over many samples is greatly reduced by CCS aware MBR.MS1 level label-free quantification is also implemented which proves to be highly precise and accurate on a benchmark dataset with known ground truth. MaxQuant for LC-IMS-MS/MS is part of the basic MaxQuant release and can be downloaded from http://maxquant.org.

Details

show
hide
Language(s): eng - English
 Dates: 2020
 Publication Status: Published in print
 Pages: 12
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: ISI: 000538037600012
DOI: 10.1074/mcp.TIR119.001720
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: MOLECULAR & CELLULAR PROTEOMICS
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: 11200 ROCKVILLE PIKE, SUITE 302, ROCKVILLE, MD, UNITED STATES : AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
Pages: - Volume / Issue: 19 (6) Sequence Number: - Start / End Page: 1058 - 1069 Identifier: ISSN: 1535-9476