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

Formalin-Fixed, Paraffin-Embedded Tissues (FFPE) as a Robust Source for the Profiling of Native and Protease-Generated Protein Amino Termini

(2016) Zon Weng Lai et al.   MOLECULAR & CELLULAR PROTEOMICS

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

(2016) James C. Wright et al.   Nature Communications

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR: Fig. 1.

(2015) Hannes L. Röst et al.   BIOINFORMATICS

Quantitative variability of 342 plasma proteins in a human twin population

(2015) Y. Liu et al.   Molecular Systems Biology

PeptideShaker enables reanalysis of MS-derived proteomics data sets

(2015) Marc Vaudel et al.   NATURE BIOTECHNOLOGY

Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

(2015) Robert Petryszak et al.   NUCLEIC ACIDS RESEARCH

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry

(2015) Hannes L. Röst et al.   PLoS One

Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry

(2015) Stephan Aiche et al.   PROTEOMICS

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

(2015) Lars Nilse et al.   Proteomics Clinical Applications

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data

(2014) George Rosenberger et al.   BIOINFORMATICS

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

(2014) Meena Choi et al.   BIOINFORMATICS

iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations

(2014) Peter Kunszt et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

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

Code share

(2014)   NATURE

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

eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows

(2013) Patrick Kiefer et al.   BIOINFORMATICS

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

Automated Label-free Quantification of Metabolites from Liquid Chromatography–Mass Spectrometry Data

(2013) Erhan Kenar et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2013) Hannes L. Röst et al.   PROTEOMICS

TOPPAS: A Graphical Workflow Editor for the Analysis of High-Throughput Proteomics Data

(2012) Johannes Junker et al.   JOURNAL OF PROTEOME RESEARCH

File Formats Commonly Used in Mass Spectrometry Proteomics

(2012) Eric W. Deutsch   MOLECULAR & CELLULAR PROTEOMICS

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

(2012) Andrew R. Jones et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

PRIDE Inspector: a tool to visualize and validate MS proteomics data

(2012) Rui Wang et al.   NATURE BIOTECHNOLOGY

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Contribution of cathepsin L to secretome composition and cleavage pattern of mouse embryonic fibroblasts

(2011) Stefan Tholen et al.   BIOLOGICAL CHEMISTRY

Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification

(2011) Sven Nahnsen et al.   JOURNAL OF PROTEOME RESEARCH

MSSimulator: Simulation of Mass Spectrometry Data

(2011) Chris Bielow et al.   JOURNAL OF PROTEOME RESEARCH

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Efficient Marginalization to Compute Protein Posterior Probabilities from Shotgun Mass Spectrometry Data

(2010) Oliver Serang et al.   JOURNAL OF PROTEOME RESEARCH

The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search

(2010) Sangtae Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

mzML—a Community Standard for Mass Spectrometry Data

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

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

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

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS