Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions
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Title
Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions
Authors
Keywords
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Journal
NATURE METHODS
Volume 9, Issue 6, Pages 555-566
Publisher
Springer Nature
Online
2012-06-05
DOI
10.1038/nmeth.2015
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Note: Only part of the references are listed.- ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry
- (2011) Mi-Youn K Brusniak et al. BMC BIOINFORMATICS
- In-Depth Proteomics of Ovarian Cancer Ascites: Combining Shotgun Proteomics and Selected Reaction Monitoring Mass Spectrometry
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- (2011) R. Costenoble et al. Molecular Systems Biology
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- (2011) Nicolas Bisson et al. NATURE BIOTECHNOLOGY
- mProphet: automated data processing and statistical validation for large-scale SRM experiments
- (2011) Lukas Reiter et al. NATURE METHODS
- Mutant proteins as cancer-specific biomarkers
- (2011) Q. Wang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer
- (2011) I. Cima et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy
- (2011) Philip Brownridge et al. PROTEOMICS
- Targeted label-free quantitative analysis of secretory proteins from adipocytes in response to oxidative stress
- (2010) Sunkyu Choi et al. ANALYTICAL BIOCHEMISTRY
- Effect of Collision Energy Optimization on the Measurement of Peptides by Selected Reaction Monitoring (SRM) Mass Spectrometry
- (2010) Brendan MacLean et al. ANALYTICAL CHEMISTRY
- Determination of Protein Stoichiometry within Protein Complexes Using Absolute Quantification and Multiple Reaction Monitoring
- (2010) Carla Schmidt et al. ANALYTICAL CHEMISTRY
- Assay Development for the Determination of Phosphorylation Stoichiometry Using Multiple Reaction Monitoring Methods with and without Phosphatase Treatment: Application to Breast Cancer Signaling Pathways
- (2010) Dominik Domanski et al. ANALYTICAL CHEMISTRY
- A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
- (2010) B.-J. M. Webb-Robertson et al. BIOINFORMATICS
- Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
- (2010) Brendan MacLean et al. BIOINFORMATICS
- The evolving role of mass spectrometry in cancer biomarker discovery
- (2010) Pei Wang et al. CANCER BIOLOGY & THERAPY
- Libraries of Specific Assays Covering Whole Proteomes: From Yeast to Man
- (2010) N. L. Anderson CLINICAL CHEMISTRY
- A Modified “Cross-talk” between Histone H2B Lys-120 Ubiquitination and H3 Lys-79 Methylation
- (2010) Agus Darwanto et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Combination of Improved18O Incorporation and Multiple Reaction Monitoring: A Universal Strategy for Absolute Quantitative Verification of Serum Candidate Biomarkers of Liver Cancer
- (2010) Yan Zhao et al. JOURNAL OF PROTEOME RESEARCH
- A Quantitative Study of the Effects of Chaotropic Agents, Surfactants, and Solvents on the Digestion Efficiency of Human Plasma Proteins by Trypsin
- (2010) Jennifer L. Proc et al. JOURNAL OF PROTEOME RESEARCH
- Quantification of β-Catenin Signaling Components in Colon Cancer Cell Lines, Tissue Sections, and Microdissected Tumor Cells using Reaction Monitoring Mass Spectrometry
- (2010) Yi Chen et al. JOURNAL OF PROTEOME RESEARCH
- Collision Energy Optimization of b- and y-Ions for Multiple Reaction Monitoring Mass Spectrometry
- (2010) Carly A. Holstein (Sherwood) et al. JOURNAL OF PROTEOME RESEARCH
- Synthetic Peptide Arrays for Pathway-Level Protein Monitoring by Liquid Chromatography-Tandem Mass Spectrometry
- (2010) Johannes A. Hewel et al. MOLECULAR & CELLULAR PROTEOMICS
- Targeted Quantitation of Site-Specific Cysteine Oxidation in Endogenous Proteins Using a Differential Alkylation and Multiple Reaction Monitoring Mass Spectrometry Approach
- (2010) Jason M. Held et al. MOLECULAR & CELLULAR PROTEOMICS
- Enhanced Sensitivity for Selected Reaction Monitoring Mass Spectrometry-based Targeted Proteomics Using a Dual Stage Electrodynamic Ion Funnel Interface
- (2010) Mahmud Hossain et al. MOLECULAR & CELLULAR PROTEOMICS
- Characterizing the connectivity of poly-ubiquitin chains by selected reaction monitoring mass spectrometry
- (2010) Hamid Mirzaei et al. Molecular BioSystems
- Options and considerations when selecting a quantitative proteomics strategy
- (2010) Bruno Domon et al. NATURE BIOTECHNOLOGY
- A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans
- (2010) Marko Jovanovic et al. NATURE METHODS
- PHOSIDA 2011: the posttranslational modification database
- (2010) F. Gnad et al. NUCLEIC ACIDS RESEARCH
- Evaluation of blood collection tubes using selected reaction monitoring MS: Implications for proteomic biomarker studies
- (2010) Sarah A. Randall et al. PROTEOMICS
- Increased Throughput for Low-Abundance Protein Biomarker Verification by Liquid Chromatography/Tandem Mass Spectrometry
- (2009) Michael Berna et al. ANALYTICAL CHEMISTRY
- Multiple Reaction Monitoring Cubed for Protein Quantification at the Low Nanogram/Milliliter Level in Nondepleted Human Serum
- (2009) T. Fortin et al. ANALYTICAL CHEMISTRY
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- (2009) Steven R. Danielson et al. ANALYTICAL CHEMISTRY
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- (2009) Johann Holzmann et al. ANALYTICAL CHEMISTRY
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- (2009) Dmitry R. Bandura et al. ANALYTICAL CHEMISTRY
- Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics
- (2009) Paola Picotti et al. CELL
- Automated Detection of Inaccurate and Imprecise Transitions in Peptide Quantification by Multiple Reaction Monitoring Mass Spectrometry
- (2009) S. E. Abbatiello et al. CLINICAL CHEMISTRY
- Developing Multiplexed Assays for Troponin I and Interleukin-33 in Plasma by Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry
- (2009) E. Kuhn et al. CLINICAL CHEMISTRY
- Perspectives of targeted mass spectrometry for protein biomarker verification
- (2009) Ruth Hüttenhain et al. CURRENT OPINION IN CHEMICAL BIOLOGY
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- (2009) Andrew N. Hoofnagle et al. JOURNAL OF IMMUNOLOGICAL METHODS
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- (2009) Carly A. Sherwood et al. JOURNAL OF PROTEOME RESEARCH
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- (2009) Carly A. Sherwood et al. JOURNAL OF PROTEOME RESEARCH
- Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry
- (2009) David L. Tabb et al. JOURNAL OF PROTEOME RESEARCH
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- (2009) Terri A Addona et al. NATURE BIOTECHNOLOGY
- High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
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- (2009) Katherine G. Zulak et al. PLANT JOURNAL
- A guide to the Proteomics Identifications Database proteomics data repository
- (2009) Juan Antonio Vizcaíno et al. PROTEOMICS
- Quantification of Thyroglobulin, a Low-Abundance Serum Protein, by Immunoaffinity Peptide Enrichment and Tandem Mass Spectrometry
- (2008) A. N. Hoofnagle et al. CLINICAL CHEMISTRY
- PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
- (2008) Eric W Deutsch et al. EMBO REPORTS
- Multiple Reaction Monitoring of mTRAQ-Labeled Peptides Enables Absolute Quantification of Endogenous Levels of a Potential Cancer Marker in Cancerous and Normal Endometrial Tissues
- (2008) Leroi V. DeSouza et al. JOURNAL OF PROTEOME RESEARCH
- Use of an Immunoaffinity-Mass Spectrometry-based Approach for the Quantification of Protein Biomarkers from Serum Samples of Lung Cancer Patients
- (2008) Gordon R. Nicol et al. MOLECULAR & CELLULAR PROTEOMICS
- Coupled Global and Targeted Proteomics of Human Embryonic Stem Cells during Induced Differentiation
- (2008) Anastasia K. Yocum et al. MOLECULAR & CELLULAR PROTEOMICS
- Targeted Quantitative Analysis ofStreptococcus pyogenesVirulence Factors by Multiple Reaction Monitoring
- (2008) Vinzenz Lange et al. MOLECULAR & CELLULAR PROTEOMICS
- MRMaid, the Web-based Tool for Designing Multiple Reaction Monitoring (MRM) Transitions
- (2008) Jennifer A. Mead et al. MOLECULAR & CELLULAR PROTEOMICS
- MRMer, an Interactive Open Source and Cross-platform System for Data Extraction and Visualization of Multiple Reaction Monitoring Experiments
- (2008) Daniel B. Martin et al. MOLECULAR & CELLULAR PROTEOMICS
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- (2008) Tanguy Fortin et al. MOLECULAR & CELLULAR PROTEOMICS
- Selected reaction monitoring for quantitative proteomics: a tutorial
- (2008) Vinzenz Lange et al. Molecular Systems Biology
- PhosphoPep—a database of protein phosphorylation sites in model organisms
- (2008) Bernd Bodenmiller et al. NATURE BIOTECHNOLOGY
- Building consensus spectral libraries for peptide identification in proteomics
- (2008) Henry Lam et al. NATURE METHODS
- A database of mass spectrometric assays for the yeast proteome
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- Protein Standard Absolute Quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks
- (2008) Alain Dupuis et al. PROTEOMICS
- Stable isotopic labeling in proteomics
- (2008) Kris Gevaert et al. PROTEOMICS
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