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MaxQuant goes Linux

MaxQuant goes Linux correspondence 100% To the Editor: We report a Linux version (https://chorusproject.org). We expect that of MaxQuant (http://www.biochem. the number of applications will increase 1,000 mpg.de/5111795/maxquant), our popular with our Linux-compatible MaxQuant software platform for the analysis of shotgun version. We envision that proteomics 61% proteomics data. core facilities, for instance, will benefit Write output tables (52%) LFQ normalization (94%) One of our main intentions in developing from the combination of command-line Protein assembly (118%) MaxQuant was to ‘take the pain out of ’ access and Linux compatibility, which Second peptide search (23%) quantifying large collections of protein enables standardized high-throughput Main search (31%) profiles . However, unlike, for instance, data analysis. The MaxQuant code base is Mass recalibration (41%) First search (61%) the Trans-Proteomic Pipeline , the original identical for Windows and for Linux; thus Feature detection (44%) version of MaxQuant could be run only on .NET on Windows Mono on Linux there is only a single distributable running Microsoft Windows, and thus its use was on both operating systems, which can be Fig. 1 | Benchmarking MaxQuant on Linux and restricted in high-performance computing downloaded from http://www.maxquant. Windows. We analyzed 300 LC-MS runs with environments, which very rarely http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Nature Methods Springer Journals

MaxQuant goes Linux

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MaxQuant goes Linux

Abstract

correspondence 100% To the Editor: We report a Linux version (https://chorusproject.org). We expect that of MaxQuant (http://www.biochem. the number of applications will increase 1,000 mpg.de/5111795/maxquant), our popular with our Linux-compatible MaxQuant software platform for the analysis of shotgun version. We envision that proteomics 61% proteomics data. core facilities, for instance, will benefit Write output tables (52%) LFQ normalization (94%) One of our main intentions in developing...
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Publisher
Springer Journals
Copyright
Copyright © 2018 by The Author(s)
Subject
Life Sciences; Life Sciences, general; Biological Techniques; Biological Microscopy; Biomedical Engineering/Biotechnology; Bioinformatics; Proteomics
ISSN
1548-7091
eISSN
1548-7105
DOI
10.1038/s41592-018-0018-y
Publisher site
See Article on Publisher Site

Abstract

correspondence 100% To the Editor: We report a Linux version (https://chorusproject.org). We expect that of MaxQuant (http://www.biochem. the number of applications will increase 1,000 mpg.de/5111795/maxquant), our popular with our Linux-compatible MaxQuant software platform for the analysis of shotgun version. We envision that proteomics 61% proteomics data. core facilities, for instance, will benefit Write output tables (52%) LFQ normalization (94%) One of our main intentions in developing from the combination of command-line Protein assembly (118%) MaxQuant was to ‘take the pain out of ’ access and Linux compatibility, which Second peptide search (23%) quantifying large collections of protein enables standardized high-throughput Main search (31%) profiles . However, unlike, for instance, data analysis. The MaxQuant code base is Mass recalibration (41%) First search (61%) the Trans-Proteomic Pipeline , the original identical for Windows and for Linux; thus Feature detection (44%) version of MaxQuant could be run only on .NET on Windows Mono on Linux there is only a single distributable running Microsoft Windows, and thus its use was on both operating systems, which can be Fig. 1 | Benchmarking MaxQuant on Linux and restricted in high-performance computing downloaded from http://www.maxquant. Windows. We analyzed 300 LC-MS runs with environments, which very rarely

Journal

Nature Methods – Springer Journals

Published: May 31, 2018

References