Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery

Application of Machine Learning to Proteomics Data: Classification and Biomarker Identification in Postgenomics Biology

(2013) Anna Louise Swan et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Speeding up the screening of steroids in urine: Development of a user-friendly library

(2013) M. Galesio et al.   STEROIDS

MALDIquant: a versatile R package for the analysis of mass spectrometry data

(2012) S. Gibb et al.   BIOINFORMATICS

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats

(2012) Johannes Griss et al.   PROTEOMICS

Fast human serum profiling through chemical depletion coupled to gold-nanoparticle-assisted protein separation

(2012) Rubén López-Cortés et al.   TALANTA

Direct matrix assisted laser desorption ionization mass spectrometry-based analysis of wine as a powerful tool for classification purposes

(2012) J.D. Nunes-Miranda et al.   TALANTA

PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis

(2011) Richard A. Scheltema et al.   ANALYTICAL CHEMISTRY

A biclustering algorithm for extracting bit-patterns from binary datasets

(2011) Domingo S. Rodriguez-Baena et al.   BIOINFORMATICS

compomics-utilities: an open-source Java library for computational proteomics

(2011) Harald Barsnes et al.   BMC BIOINFORMATICS

Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS

(2011) Irene Granlund et al.   Journal of Proteomics

mMass3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data

(2010) Martin Strohalm et al.   ANALYTICAL CHEMISTRY

AIBench: A rapid application development framework for translational research in biomedicine

(2010) D. Glez-Peña et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Peakbin Selection in Mass Spectrometry Data Using a Consensus Approach with Estimation of Distribution Algorithms

(2010) R Armañanzas et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

mzML—a Community Standard for Mass Spectrometry Data

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

Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data

(2010) Hyungwon Choi et al.   Molecular Systems Biology

jmzML, an open-source Java API for mzML, the PSI standard for MS data

(2010) Richard G. Côté et al.   PROTEOMICS

Decision peptide-driven: A free software tool for accurate protein quantification using gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry

(2010) Hugo M. Santos et al.   TALANTA

Comparison of feature selection and classification for MALDI-MS data

(2009) Qingzhong Liu et al.   BMC GENOMICS

Software Platform for Rapidly Creating Computational Tools for Mass Spectrometry-Based Proteomics

(2009) Damon May et al.   JOURNAL OF PROTEOME RESEARCH

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

Mining whole-sample mass spectrometry proteomics data for biomarkers – An overview

(2008) Ross A. McDonald et al.   EXPERT SYSTEMS WITH APPLICATIONS

Classification and Identification of Bacteria by Mass Spectrometry and Computational Analysis

(2008) Sascha Sauer et al.   PLoS One