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

The structural context of posttranslational modifications at a proteome-wide scale

(2022) Isabell Bludau et al.   PLOS BIOLOGY

PTMViz: a tool for analyzing and visualizing histone post translational modification data

(2021) Kevin Chappell et al.   BMC BIOINFORMATICS

Shigella ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection

(2021) Giovanni Luchetti et al.   Cell Host & Microbe

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

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

(2020) Meena Choi et al.   NATURE METHODS

A practical guide for analysis of histone post-translational modifications by mass spectrometry: Best practices and pitfalls

(2019) Sydney P. Thomas et al.   METHODS

Post-translational modifications of FDA-approved plasma biomarkers in glioblastoma samples

(2017) Natalia A. Petushkova et al.   PLoS One

Common errors in mass spectrometry-based analysis of post-translational modifications

(2016) Min-Sik Kim et al.   PROTEOMICS

Computational and statistical methods for high-throughput analysis of post-translational modifications of proteins

(2015) Veit Schwämmle et al.   Journal of Proteomics

USP30 and parkin homeostatically regulate atypical ubiquitin chains on mitochondria

(2015) Christian N. Cunningham et al.   NATURE CELL BIOLOGY

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

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

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

(2014) Meena Choi et al.   BIOINFORMATICS

Enrichment and separation techniques for large-scale proteomics analysis of the protein post-translational modifications

(2014) Junfeng Huang et al.   JOURNAL OF CHROMATOGRAPHY A

IsobarPTM: A software tool for the quantitative analysis of post-translationally modified proteins

(2013) Florian P. Breitwieser et al.   Journal of Proteomics

Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry

(2013) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Integrated proteomic analysis of post-translational modifications by serial enrichment

(2013) Philipp Mertins et al.   NATURE METHODS

Phosphoproteomic characterization of DNA damage response in melanoma cells following MEK/PI3K dual inhibition

(2013) D. S. Kirkpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correct Interpretation of Comprehensive Phosphorylation Dynamics Requires Normalization by Protein Expression Changes

(2011) Ronghu Wu et al.   MOLECULAR & CELLULAR PROTEOMICS

Computational Mass Spectrometry–Based Proteomics

(2011) Lukas Käll et al.   PLoS Computational Biology

Post-translational modifications in signal integration

(2010) Yonathan Lissanu Deribe et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Statistical Design of Quantitative Mass Spectrometry-Based Proteomic Experiments

(2009) Ann L. Oberg et al.   JOURNAL OF PROTEOME RESEARCH

Generalized linear mixed models: a practical guide for ecology and evolution

(2009) Benjamin M. Bolker et al.   TRENDS IN ECOLOGY & EVOLUTION

The Impact of Peptide Abundance and Dynamic Range on Stable-Isotope-Based Quantitative Proteomic Analyses

(2008) Corey E. Bakalarski et al.   JOURNAL OF PROTEOME RESEARCH