Literature DB >> 35612753

MaxQuant Module for the Identification of Genomic Variants Propagated into Peptides.

Pavel Sinitcyn1, Maximilian Gerwien1, Jürgen Cox2.   

Abstract

Standard shotgun proteomics data analysis pipelines usually only identify peptides that are encoded in the reference genome. In many situations, it is desirable to identify peptides resulting from non-synonymous variations as well. Here, we present a new module in the MaxQuant software that takes both DNA and RNA based next-generation sequencing (NGS) data as well as raw proteomics data as input. This allows for the identification of variant peptides that are otherwise missed.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Immunopeptidomics; MaxQuant; NGS; Proteogenomics; Proteomics; Sequence variations

Mesh：

Substances：

Year:  2022        PMID： 35612753     DOI： 10.1007/978-1-0716-2124-0_23

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  17 in total

1.  Proteogenomic mapping as a complementary method to perform genome annotation.

Authors:  Jacob D Jaffe; Howard C Berg; George M Church
Journal:  Proteomics       Date:  2004-01       Impact factor: 3.984

2.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

Authors:  Jürgen Cox; Matthias Mann
Journal:  Nat Biotechnol       Date:  2008-11-30       Impact factor: 54.908

3.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.

Authors:  J K Eng; A L McCormack; J R Yates
Journal:  J Am Soc Mass Spectrom       Date:  1994-11       Impact factor: 3.109

4.  Andromeda: a peptide search engine integrated into the MaxQuant environment.

Authors:  Jürgen Cox; Nadin Neuhauser; Annette Michalski; Richard A Scheltema; Jesper V Olsen; Matthias Mann
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Journal:  Cell       Date:  2016-06-29       Impact factor: 41.582

9.  Breast cancer quantitative proteome and proteogenomic landscape.

Authors:  Henrik J Johansson; Fabio Socciarelli; Nathaniel M Vacanti; Mads H Haugen; Yafeng Zhu; Ioannis Siavelis; Alejandro Fernandez-Woodbridge; Miriam R Aure; Bengt Sennblad; Mattias Vesterlund; Rui M Branca; Lukas M Orre; Mikael Huss; Erik Fredlund; Elsa Beraki; Øystein Garred; Jorrit Boekel; Torill Sauer; Wei Zhao; Silje Nord; Elen K Höglander; Daniel C Jans; Hjalmar Brismar; Tonje H Haukaas; Tone F Bathen; Ellen Schlichting; Bjørn Naume; Torben Luders; Elin Borgen; Vessela N Kristensen; Hege G Russnes; Ole Christian Lingjærde; Gordon B Mills; Kristine K Sahlberg; Anne-Lise Børresen-Dale; Janne Lehtiö
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10.  Proteogenomics connects somatic mutations to signalling in breast cancer.

Authors:  Philipp Mertins; D R Mani; Kelly V Ruggles; Michael A Gillette; Karl R Clauser; Pei Wang; Xianlong Wang; Jana W Qiao; Song Cao; Francesca Petralia; Emily Kawaler; Filip Mundt; Karsten Krug; Zhidong Tu; Jonathan T Lei; Michael L Gatza; Matthew Wilkerson; Charles M Perou; Venkata Yellapantula; Kuan-lin Huang; Chenwei Lin; Michael D McLellan; Ping Yan; Sherri R Davies; R Reid Townsend; Steven J Skates; Jing Wang; Bing Zhang; Christopher R Kinsinger; Mehdi Mesri; Henry Rodriguez; Li Ding; Amanda G Paulovich; David Fenyö; Matthew J Ellis; Steven A Carr
Journal:  Nature       Date:  2016-05-25       Impact factor: 49.962
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