pyQms enables universal and accurate quantification of mass spectrometry data

Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis

(2016) Lukas P. M. Kremer et al.   JOURNAL OF PROTEOME RESEARCH

PyQuant: A Versatile Framework for Analysis of Quantitative Mass Spectrometry Data

(2016) Christopher J. Mitchell et al.   MOLECULAR & CELLULAR PROTEOMICS

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

(2016) Andrew Palmer et al.   NATURE METHODS

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

(2015) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

STATE TRANSITION7-Dependent Phosphorylation Is Modulated by Changing Environmental Conditions, and Its Absence Triggers Remodeling of Photosynthetic Protein Complexes

(2015) Sonja Verena Bergner et al.   PLANT PHYSIOLOGY

Ion Coalescence of Neutron Encoded TMT 10-Plex Reporter Ions

(2014) Thilo Werner et al.   ANALYTICAL CHEMISTRY

MetaProSIP: Automated Inference of Stable Isotope Incorporation Rates in Proteins for Functional Metaproteomics

(2014) Timo Sachsenberg et al.   JOURNAL OF PROTEOME RESEARCH

Global Metabolomic and Isobaric Tagging Capillary Liquid Chromatography–Tandem Mass Spectrometry Approaches for Uncovering Pathway Dysfunction in Diabetic Mouse Aorta

(2014) Laura A. Filla et al.   JOURNAL OF PROTEOME RESEARCH

The Interplay of Light and Oxygen in the Reactive Oxygen Stress Response ofChlamydomonas reinhardtiiDissected by Quantitative Mass Spectrometry

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

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

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective

(2013) Yasset Perez-Riverol et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

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

(2013) Patrick Kiefer et al.   BIOINFORMATICS

Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics

(2013) Anton A. Goloborodko et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

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

(2013) Hannes L. Röst et al.   PROTEOMICS

pymzML--Python module for high-throughput bioinformatics on mass spectrometry data

(2012) T. Bald et al.   BIOINFORMATICS

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

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

Mass spectrometry in high-throughput proteomics: ready for the big time

(2010) Tommy Nilsson et al.   NATURE METHODS

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

(2009) John R. Yates et al.   Annual Review of Biomedical Engineering

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry

(2008) L. Kall et al.   BIOINFORMATICS

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

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

A quantitative analysis software tool for mass spectrometry–based proteomics

(2008) Sung Kyu Park et al.   NATURE METHODS

mzML: A single, unifying data format for mass spectrometer output

(2008) Eric Deutsch   PROTEOMICS