Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling

Automated peptide mapping and protein-topographical annotation of proteomics data

(2014) Pavankumar Videm et al.   BMC BIOINFORMATICS

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

(2014) Gloria M Sheynkman et al.   BMC GENOMICS

qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments

(2014) Mathias Walzer et al.   MOLECULAR & CELLULAR PROTEOMICS

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience

(2014) Johannes Griss et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

(2014) Katharina Kramer et al.   NATURE METHODS

A standardized framing for reporting protein identifications in mzIdentML 1.2

(2014) Sean L. Seymour et al.   PROTEOMICS

Data processing methods and quality control strategies for label-free LC–MS protein quantification

(2013) Marianne Sandin et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Double deficiency of cathepsins B and L results in massive secretome alterations and suggests a degradative cathepsin-MMP axis

(2013) Stefan Tholen et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Drug Discovery Applications for KNIME: An Open Source Data Mining Platform

(2013) Michael P. Mazanetz et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Fast and Accurate Database Searches with MS-GF+Percolator

(2013) Viktor Granholm et al.   JOURNAL OF PROTEOME RESEARCH

An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics

(2013) Hendrik Weisser et al.   JOURNAL OF PROTEOME RESEARCH

The mzQuantML Data Standard for Mass Spectrometry–based Quantitative Studies in Proteomics

(2013) Mathias Walzer et al.   MOLECULAR & CELLULAR PROTEOMICS

Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML

(2013) Fawaz Ghali et al.   MOLECULAR & CELLULAR PROTEOMICS

A Defined Methodology for Reliable Quantification of Western Blot Data

(2013) Sean C. Taylor et al.   MOLECULAR BIOTECHNOLOGY

Secretome and degradome profiling shows that Kallikrein-related peptidases 4, 5, 6, and 7 induce TGFβ-1 signaling in ovarian cancer cells

(2013) Hasmik Shahinian et al.   Molecular Oncology

QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis

(2013) Dmitry N. Ivankov et al.   NUCLEIC ACIDS RESEARCH

pyOpenMS: A Python-based interface to the OpenMS mass-spectrometry algorithm library

(2013) Hannes L. Röst et al.   PROTEOMICS

Deletion of Cysteine Cathepsins B or L Yields Differential Impacts on Murine Skin Proteome and Degradome

(2012) Stefan Tholen et al.   MOLECULAR & CELLULAR PROTEOMICS

Tools for Label-free Peptide Quantification

(2012) Sven Nahnsen et al.   MOLECULAR & CELLULAR PROTEOMICS

TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists

(2011) Eric W. Deutsch et al.   MOLECULAR & CELLULAR PROTEOMICS

Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates

(2011) Oded Kleifeld et al.   Nature Protocols

CPFP: a central proteomics facilities pipeline

(2010) D. C. Trudgian et al.   BIOINFORMATICS

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

TOPPView: An Open-Source Viewer for Mass Spectrometry Data

(2009) Marc Sturm et al.   JOURNAL OF PROTEOME RESEARCH

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

(2009) Terri A Addona et al.   NATURE BIOTECHNOLOGY

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics

(2009) Jürgen Cox et al.   Nature Protocols

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS

Global Mapping of the Topography and Magnitude of Proteolytic Events in Apoptosis

(2008) Melissa M. Dix et al.   CELL

Pharmacoproteomics of a Metalloproteinase Hydroxamate Inhibitor in Breast Cancer Cells: Dynamics of Membrane Type 1 Matrix Metalloproteinase-Mediated Membrane Protein Shedding

(2008) G. S. Butler et al.   MOLECULAR AND CELLULAR BIOLOGY