A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments

A hybrid approach to protein differential expression in mass spectrometry-based proteomics

(2012) Xuan Wang et al.   BIOINFORMATICS

Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides

(2012) Banu Dost et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Comparative Analysis of Different Label-Free Mass Spectrometry Based Protein Abundance Estimates and Their Correlation with RNA-Seq Gene Expression Data

(2012) Kang Ning et al.   JOURNAL OF PROTEOME RESEARCH

Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli

(2012) L. Arike et al.   Journal of Proteomics

Computational and Statistical Analysis of Protein Mass Spectrometry Data

(2012) William Stafford Noble et al.   PLoS Computational Biology

Improved quality control processing of peptide-centric LC-MS proteomics data

(2011) Melissa M. Matzke et al.   BIOINFORMATICS

A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors

(2011) Bobbie-Jo M. Webb-Robertson et al.   PROTEOMICS

Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-Based Proteomics Data

(2010) Bobbie-Jo M. Webb-Robertson et al.   JOURNAL OF PROTEOME RESEARCH

Proteomics: a pragmatic perspective

(2010) Parag Mallick et al.   NATURE BIOTECHNOLOGY

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

A statistical framework for protein quantitation in bottom-up MS-based proteomics

(2009) Yuliya Karpievitch et al.   BIOINFORMATICS

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics

(2009) Yong Fuga Li et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Protein Quantification in Label-Free LC-MS Experiments

(2009) Timothy Clough et al.   JOURNAL OF PROTEOME RESEARCH

DAnTE: a statistical tool for quantitative analysis of -omics data

(2008) A. D. Polpitiya et al.   BIOINFORMATICS

A Computational Strategy to Analyze Label-Free Temporal Bottom-Up Proteomics Data§

(2008) Xiuxia Du et al.   JOURNAL OF PROTEOME RESEARCH

Mixed-Effects Statistical Model for Comparative LC−MS Proteomics Studies†

(2008) D. S. Daly et al.   JOURNAL OF PROTEOME RESEARCH

Absolute Protein Quantification by LC/MSEfor Global Analysis of Salicylic Acid-Induced Plant Protein Secretion Responses

(2008) Fang-yi Cheng et al.   JOURNAL OF PROTEOME RESEARCH

DESIGN AND ANALYSIS OF QUANTITATIVE DIFFERENTIAL PROTEOMICS INVESTIGATIONS USING LC-MS TECHNOLOGY

(2008) YURY V. BUKHMAN et al.   Journal of Bioinformatics and Computational Biology