MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments

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

(2022) Niko Pinter et al.   JOURNAL OF PROTEOME RESEARCH

amica: an interactive and user-friendly web-platform for the analysis of proteomics data

(2022) Sebastian Didusch et al.   BMC GENOMICS

MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics

(2022) Devon Kohler et al.   MOLECULAR & CELLULAR PROTEOMICS

Genetic inactivation of RIP1 kinase activity in rats protects against ischemic brain injury

(2021) Kimberly Stark et al.   Cell Death & Disease

Multiplexed proteomics of autophagy-deficient murine macrophages reveals enhanced antimicrobial immunity via the oxidative stress response

(2021) Timurs Maculins et al.   eLife

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis

(2020) Yafeng Zhu et al.   MOLECULAR & CELLULAR PROTEOMICS

MSstatsTMT: Statistical detection of differentially abundant proteins in experiments with isobaric labeling and multiple mixtures

(2020) Ting Huang et al.   MOLECULAR & CELLULAR PROTEOMICS

Philosopher: a versatile toolkit for shotgun proteomics data analysis

(2020) Felipe da Veiga Leprevost et al.   NATURE METHODS

MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets

(2020) Meena Choi et al.   NATURE METHODS

LFQ-Analyst: An Easy-To-Use Interactive Web Platform To Analyze and Visualize Label-Free Proteomics Data Preprocessed with MaxQuant

(2019) Anup D. Shah et al.   JOURNAL OF PROTEOME RESEARCH

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics

(2017) Lindsay K. Pino et al.   MASS SPECTROMETRY REVIEWS

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

Quantitative proteomics: challenges and opportunities in basic and applied research

(2017) Olga T Schubert et al.   Nature Protocols

The START App: a web-based RNAseq analysis and visualization resource

(2016) Jonathan W. Nelson et al.   BIOINFORMATICS

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Who qualifies to be a bioinformatician?

(2015) Antony T. Vincent et al.   Frontiers in Genetics

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

(2014) Meena Choi et al.   BIOINFORMATICS

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Bioinformatics analysis of mass spectrometry-based proteomics data sets

(2009) Chanchal Kumar et al.   FEBS LETTERS

MapReduce

(2008) Jeffrey Dean et al.   COMMUNICATIONS OF THE ACM

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

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY