MetaMSD: meta analysis for mass spectrometry data

Choosing between methods of combining $p$-values

(2018) N A Heard et al.   BIOMETRIKA

Changes in plasma protein levels as an early indication of a bloodstream infection

(2017) Pentti Kuusela et al.   PLoS One

Mining the human urine proteome for monitoring renal transplant injury

(2016) Tara K. Sigdel et al.   KIDNEY INTERNATIONAL

Combining Untargeted and Targeted Proteomic Strategies for Discrimination and Quantification of Cashmere Fibers

(2016) Shanshan Li et al.   PLoS One

Combined Label-Free Quantitative Proteomics and microRNA Expression Analysis of Breast Cancer Unravel Molecular Differences with Clinical Implications

(2015) Angelo Gámez-Pozo et al.   CANCER RESEARCH

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

(2014) Meena Choi et al.   BIOINFORMATICS

Detecting differential protein expression in large-scale population proteomics

(2014) So Young Ryu et al.   BIOINFORMATICS

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

The Identification of Novel Potential Injury Mechanisms and Candidate Biomarkers in Renal Allograft Rejection by Quantitative Proteomics

(2013) Tara K. Sigdel et al.   MOLECULAR & CELLULAR PROTEOMICS

Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs

(2012) Timothy Clough et al.   BMC BIOINFORMATICS

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

(2008) A. M. Mayampurath et al.   BIOINFORMATICS

Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics

(2008) Hyungwon Choi et al.   MOLECULAR & CELLULAR PROTEOMICS

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