Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

Development and validation of a mass spectrometry-based assay for quantification of insulin-like factor 3 in human serum

(2018) Jakob Albrethsen et al.   CLINICAL CHEMISTRY AND LABORATORY MEDICINE

Proteome analysis of an Escherichia coli ptsN -null strain under different nitrogen regimes

(2018) Fernanda Gravina et al.   Journal of Proteomics

Thermal proteome profiling in bacteria: probing protein state in vivo

(2018) André Mateus et al.   Molecular Systems Biology

Comprehensive Peptide Analysis of Mouse Brain Striatum Identifies Novel sORF-Encoded Polypeptides

(2018) Harshavardhan Budamgunta et al.   PROTEOMICS

Spectral Library Search Improves Assignment of TMT Labeled MS/MS Spectra

(2018) Jianqiao Shen et al.   JOURNAL OF PROTEOME RESEARCH

Assembling the Community-Scale Discoverable Human Proteome

(2018) Mingxun Wang et al.   Cell Systems

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana

(2017) Patrick Willems et al.   MOLECULAR & CELLULAR PROTEOMICS

Building ProteomeTools based on a complete synthetic human proteome

(2017) Daniel P Zolg et al.   NATURE METHODS

Temporal quantitative phosphoproteomics of ADP stimulation reveals novel central nodes in platelet activation and inhibition

(2016) Florian Beck et al.   BLOOD

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

(2016) Matthew The et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

The unique peptidome: Taxon-specific tryptic peptides as biomarkers for targeted metaproteomics

(2016) Bart Mesuere et al.   PROTEOMICS

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

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

MS2PIP prediction server: compute and visualize MS2peak intensity predictions for CID and HCD fragmentation

(2015) Sven Degroeve et al.   NUCLEIC ACIDS RESEARCH

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

A repository of assays to quantify 10,000 human proteins by SWATH-MS

(2014) George Rosenberger et al.   Scientific Data

MS2PIP: a tool for MS/MS peak intensity prediction

(2013) Sven Degroeve et al.   BIOINFORMATICS

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors

(2008) Sheila J. Barton et al.   MASS SPECTROMETRY REVIEWS