Proteomics meets the scientific method

By delivering precise, reproducible quantification of proteins of interest in biological samples, targeted proteomics approaches are allowing researchers to apply the scientific method using mass spectrometry.

[1]  Pei Wang,et al.  A targeted proteomics–based pipeline for verification of biomarkers in plasma , 2011, Nature Biotechnology.

[2]  Ruedi Aebersold,et al.  Reproducible isolation of distinct, overlapping segments of the phosphoproteome , 2007, Nature Methods.

[3]  M. Mann,et al.  Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast , 2008, Nature.

[4]  Michelle L. Reyzer,et al.  MALDI imaging mass spectrometry: molecular snapshots of biochemical systems , 2007, Nature Methods.

[5]  Leigh Anderson,et al.  Quantitative Mass Spectrometric Multiple Reaction Monitoring Assays for Major Plasma Proteins* , 2006, Molecular & Cellular Proteomics.

[6]  Sean C. Bendall,et al.  Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum , 2011, Science.

[7]  R. Aebersold,et al.  Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions , 2012, Nature Methods.

[8]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[9]  Karen Sachs,et al.  Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators , 2012, Nature Biotechnology.

[10]  D. Lauffenburger,et al.  Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks , 2007, Proceedings of the National Academy of Sciences.

[11]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[12]  B. Cravatt,et al.  Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. , 2008, Annual review of biochemistry.

[13]  T. Pawson,et al.  Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor , 2011, Nature Biotechnology.

[14]  B. Domon,et al.  Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer* , 2012, Molecular & Cellular Proteomics.

[15]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[16]  Gary D Bader,et al.  The human genome and drug discovery after a decade. Roads (still) not taken , 2011, 1102.0448.

[17]  J. Sumner THE ISOLATION AND CRYSTALLIZATION OF THE ENZYME UREASE PRELIMINARY PAPER , 1926 .

[18]  Lukas N. Mueller,et al.  Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics , 2009, Cell.

[19]  J. Bohlmann,et al.  Targeted proteomics using selected reaction monitoring reveals the induction of specific terpene synthases in a multi-level study of methyl jasmonate-treated Norway spruce (Picea abies). , 2009, The Plant journal : for cell and molecular biology.

[20]  Ludovic C. Gillet,et al.  Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis* , 2012, Molecular & Cellular Proteomics.

[21]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[22]  Ruedi Aebersold,et al.  High-throughput generation of selected reaction-monitoring assays for proteins and proteomes , 2010, Nature Methods.

[23]  Richard Z. Liu,et al.  Quantification of beta-catenin signaling components in colon cancer cell lines, tissue sections, and microdissected tumor cells using reaction monitoring mass spectrometry. , 2010, Journal of proteome research.

[24]  Derek J. Bailey,et al.  Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics* , 2012, Molecular & Cellular Proteomics.

[25]  Xu Shi,et al.  Quantification of Cardiovascular Biomarkers in Patient Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution* , 2009, Molecular & Cellular Proteomics.

[26]  S. Gygi,et al.  Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Christoph H Borchers,et al.  Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma , 2009, Nature Biotechnology.

[28]  Scott R. Kronewitter,et al.  Analysis of serum total and free PSA using immunoaffinity depletion coupled to SRM: correlation with clinical immunoassay tests. , 2012, Journal of proteomics.

[29]  U. Sauer,et al.  Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics , 2011, Molecular systems biology.

[30]  S. Lemeer,et al.  The phosphoproteomics data explosion. , 2009, Current opinion in chemical biology.

[31]  Ruedi Aebersold,et al.  Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate , 2012, Proteomics.