MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
By Meena Choi, Ching-Yun Chang, Timothy Clough, D. Broudy, Trevor Killeen, Brendan MacLean, Olga Vitek. Bioinform., 2014
944 citations recorded by the source corpus.
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/3e47181109bd158d7de698b961a4d35a4433d0e8
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Alexey I. Nesvizhskii
- Fengchao Yu
- S. Haynes
- R. Aebersold
- B. Searle
- Michael J. MacCoss
- Ludovic C. Gillet
- Brendan MacLean
In Spectroscopy
- Alexey I. Nesvizhskii
- Fengchao Yu
- S. Haynes
- R. Aebersold
- B. Searle
- Michael J. MacCoss
- Ludovic C. Gillet
- Brendan MacLean
Citations in the corpus
- Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial (2018, positive): “…peptides, information such as conservation of the relative fragment ion signal intensities per peptide and the relative peptide intensities per protein can be leveraged across the whole data set, as MSstats (Choi et al , 2014) or mapDIA (Teo et al , 2015) do for fold-change statistics computation.”
- IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs (2020, methodology): “MSstats had errors in processing the file from MaxQuant with MBR.”
- Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues (2015, methodology): “Linear Mixed Effect Model Tests for Differential Abundance—For both DDA and DIA, the log2-intensities of the peptides were summarized across all the samples and runs, and separately for each protein, in a linear mixed model implemented in MSstats (32).”
- The Skyline Ecosystem: Informatics for Quantitative Mass Spectrometry Proteomics (2017, methodology): “The external tool MSstats (Choi et al. 2014) considers these data properties to calculate the relative quantification of proteins and peptides.”
- OpenMS: a flexible open-source software platform for mass spectrometry data analysis (2016, methodology): “Not only does the OpenMS project see high activity from its direct contributors, but several other open-source tools such as MSStats 46 , aLFQ 47 and Skyline 48 have started to integrate their tools with OpenMS.”