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  Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification.

Yu, S.-H., Kyriakidou, P., & Cox, J. (2020). Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification. Journal of Proteome Research. doi:10.1021/acs.jproteome.0c00209.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0007-1BB4-0 Version Permalink: http://hdl.handle.net/21.11116/0000-0007-1BB5-F
Genre: Journal Article

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 Creators:
Yu, Sung-Huan1, Author              
Kyriakidou, Pelagia1, Author              
Cox, Jürgen1, Author              
Affiliations:
1Cox, Jürgen / Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Max Planck Society, ou_2063284              

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Free keywords: MaxQuant; Perseus; batch effects; isobaric labeling; match between runs; missing values; multiplexed quantification; normalization; tandem mass tag
 Abstract: Isobaric labeling has the promise of combining high sample multiplexing with precise quantification. However, normalization issues and the missing value problem of complete n-plexes hamper quantification across more than one n-plex. Here, we introduce two novel algorithms implemented in MaxQuant that substantially improve the data analysis with multiple n-plexes. First, isobaric matching between runs makes use of the three-dimensional MS1 features to transfer identifications from identified to unidentified MS/MS spectra between liquid chromatography-mass spectrometry runs in order to utilize reporter ion intensities in unidentified spectra for quantification. On typical datasets, we observe a significant gain in MS/MS spectra that can be used for quantification. Second, we introduce a novel PSM-level normalization, applicable to data with and without the common reference channel. It is a weighted median-based method, in which the weights reflect the number of ions that were used for fragmentation. On a typical dataset, we observe complete removal of batch effects and dominance of the biological sample grouping after normalization. Furthermore, we provide many novel processing and normalization options in Perseus, the companion software for the downstream analysis of quantitative proteomics results. All novel tools and algorithms are available with the regular MaxQuant and Perseus releases, which are downloadable at http://maxquant.org.

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Language(s): eng - English
 Dates: 2020
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: Notes
The MS proteomics data have been deposited to the ProteomeXchange consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD019880 and PXD019881.
 Rev. Type: -
 Identifiers: ISI: 32892627
DOI: 10.1021/acs.jproteome.0c00209
 Degree: -

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Project name : grant number 2019-202671
Grant ID : 2019-202671
Funding program : -
Funding organization : Chan Zuckerberg Foundation

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Title: Journal of Proteome Research
  Other : J. Proteome Res.
Source Genre: Journal
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Publ. Info: Washington, D.C. : American Chemical Society
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: - Identifier: ISSN: 1535-3893
CoNE: https://pure.mpg.de/cone/journals/resource/111019664290000