Critical assessment of proteome-wide label-free absolute abundance estimation strategies

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

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

Large-Scale Quantitative Assessment of Different In-Solution Protein Digestion Protocols Reveals Superior Cleavage Efficiency of Tandem Lys-C/Trypsin Proteolysis over Trypsin Digestion

(2012) Timo Glatter 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

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma

(2012) Jacek R Wiśniewski et al.   Molecular Systems Biology

A Software Toolkit and Interface for Performing Stable Isotope Labeling and Top3 Quantification Using Progenesis LC-MS

(2012) Da Qi et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Including shared peptides for estimating protein abundances: A significant improvement for quantitative proteomics

(2012) Mélisande Blein-Nicolas et al.   PROTEOMICS

A Protein Epitope Signature Tag (PrEST) Library Allows SILAC-based Absolute Quantification and Multiplexed Determination of Protein Copy Numbers in Cell Lines

(2011) Marlis Zeiler et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantification of mRNA and protein and integration with protein turnover in a bacterium

(2011) T. Maier et al.   Molecular Systems Biology

Absolute quantification of microbial proteomes at different states by directed mass spectrometry

(2011) A. Schmidt et al.   Molecular Systems Biology

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome

(2011) T. Glatter et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Less label, more free: Approaches in label-free quantitative mass spectrometry

(2011) Karlie A. Neilson et al.   PROTEOMICS

Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline

(2011) David C. Trudgian et al.   PROTEOMICS

Peek a peak: a glance at statistics for quantitative label-free proteomics

(2010) Katharina Podwojski et al.   Expert Review of Proteomics

Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods

(2010) Jonas Grossmann et al.   Journal of Proteomics

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

emPAI Calc—for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry

(2009) Kosaku Shinoda et al.   BIOINFORMATICS

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

(2009) Johan Malmström et al.   NATURE

The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results

(2008) John C Braisted et al.   BMC BIOINFORMATICS

Protein abundance profiling of the Escherichia coli cytosol

(2008) Yasushi Ishihama et al.   BMC GENOMICS

Mass Spectrometry-Based Approaches Toward Absolute Quantitative Proteomics

(2008) Keiji Kito et al.   CURRENT GENOMICS

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

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