MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone-Reference-Cited by-同舟云学术

MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone

Published:2022-05-03 Issue:6 Volume:21 Page:1558-1565
ISSN:1535-3893
Container-title:Journal of Proteome Research
language:en
Short-container-title:J. Proteome Res.

Author:

Pinter Niko¹²,Glätzer Damian³,Fahrner Matthias¹²⁴,Fröhlich Klemens¹²⁴⁵,Johnson James⁶,Grüning Björn Andreas⁷^ORCID,Warscheid Bettina³⁸^ORCID,Drepper Friedel³^ORCID,Schilling Oliver¹²⁹^ORCID,Föll Melanie Christine¹²¹⁰^ORCID

Affiliation:

1. Institute for Surgical Pathology, Medical Center, University of Freiburg, 79106 Freiburg, Germany

2. Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany

3. Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany

4. Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany

5. Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany

6. Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States

7. Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany

8. Faculty of Chemistry and Pharmacy, Department of Biochemistry, Julius Maximilian University of Würzburg, 97074 Würzburg, Germany

9. German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), 79106 Freiburg, Germany

10. Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts 02115, United States

Funder

Bundesministerium f?r Bildung und Forschung

Deutsche Forschungsgemeinschaft

German-Israeli Foundation for Scientific Research and Development

German Consortium for Translational Cancer Research

Publisher

American Chemical Society (ACS)

Subject

General Chemistry,Biochemistry

Link

https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.2c00051

Reference32 articles.

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

2. MaxQuant goes Linux

3. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments

4. MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures

5. Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

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