Generic workflow for quality assessment of quantitative label-free LC-MS analysis

Retention time alignment algorithms for LC/MS data must consider non-linear shifts

(2009) Katharina Podwojski et al.   BIOINFORMATICS

Bioinformatics analysis of mass spectrometry-based proteomics data sets

(2009) Chanchal Kumar et al.   FEBS LETTERS

The Proteios Software Environment: An Extensible Multiuser Platform for Management and Analysis of Proteomics Data

(2009) Jari Häkkinen et al.   JOURNAL OF PROTEOME RESEARCH

Development and Evaluation of Normalization Methods for Label-free Relative Quantification of Endogenous Peptides

(2009) Kim Kultima et al.   MOLECULAR & CELLULAR PROTEOMICS

Comparative analysis to guide quality improvements in proteomics

(2009) Matthias Mann   NATURE METHODS

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

Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

(2008) Eva Lange et al.   BMC BIOINFORMATICS

Computational Quantification of Peptides from LC-MS Data

(2008) Ole Schulz-Trieglaff et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

An Assessment of Software Solutions for the Analysis of Mass Spectrometry Based Quantitative Proteomics Data

(2008) Lukas N. Mueller et al.   JOURNAL OF PROTEOME RESEARCH

Alignment of LC-MS images, with applications to biomarker discovery and protein identification

(2008) Mathias Vandenbogaert et al.   PROTEOMICS