Current trends in quantitative proteomics - an update.
暂无分享,去创建一个
C. E. Parker | C. Borchers | Huiyan Li | Jun Han | J. Han | Jingxi Pan | H. Li | J. Han | J. Pan | T. Liu | H Li | J Han | J Pan | T Liu | C E Parker | C H Borchers | C. Parker | T. Liu | Teng Liu | T. Liu
[1] C. Borchers,et al. Affinity-mass spectrometric technologies for quantitative proteomics in biological fluids , 2017, bioRxiv.
[2] Jennifer A Mead,et al. MRMaid, the Web-based Tool for Designing Multiple Reaction Monitoring (MRM) Transitions* , 2009, Molecular & Cellular Proteomics.
[3] Pei Wang,et al. A targeted proteomics–based pipeline for verification of biomarkers in plasma , 2011, Nature Biotechnology.
[4] H. Rodriguez,et al. Mass spectrometry‐based targeted quantitative proteomics: Achieving sensitive and reproducible detection of proteins , 2012, Proteomics.
[5] R. Aebersold,et al. Perspectives of targeted mass spectrometry for protein biomarker verification. , 2009, Current opinion in chemical biology.
[6] T. Tomonaga,et al. Absolute quantitation of low abundance plasma APL1β peptides at sub-fmol/mL Level by SRM/MRM without immunoaffinity enrichment. , 2014, Journal of proteome research.
[7] Gennifer E. Merrihew,et al. Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry. , 2010, Analytical chemistry.
[8] Hasmik Keshishian,et al. Automated Microchromatography Enables Multiplexing of Immunoaffinity Enrichment of Peptides to Greater than 150 for Targeted MS-Based Assays. , 2016, Analytical chemistry.
[9] C. Perou,et al. Development of an immuno tandem mass spectrometry (iMALDI) assay for EGFR diagnosis , 2007, Proteomics. Clinical applications.
[10] S. Carr,et al. Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera. , 2016, Journal of proteome research.
[11] Scott A. Shaffer,et al. A novel ion funnel for focusing ions at elevated pressure using electrospray ionization mass spectrometry , 1997 .
[12] S. Hillier,et al. Newborn blood spot screening for sickle cell disease by using tandem mass spectrometry: implementation of a protocol to identify only the disease states of sickle cell disease. , 2014, Clinical chemistry.
[13] G. G. Stokes. "J." , 1890, The New Yale Book of Quotations.
[14] Bruno Domon,et al. Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring (IS-PRM)* , 2015, Molecular & Cellular Proteomics.
[15] A. Vlahou,et al. SRM/MRM targeted proteomics as a tool for biomarker validation and absolute quantification in human urine , 2015, Expert review of molecular diagnostics.
[16] C. Greenberg,et al. LC-MS/MS progress in newborn screening. , 2011, Clinical biochemistry.
[17] Brendan MacLean,et al. Building high-quality assay libraries for targeted analysis of SWATH MS data , 2015, Nature Protocols.
[18] Ping Wu,et al. Quantification of histone modifications by parallel-reaction monitoring: a method validation. , 2015, Analytical chemistry.
[19] S. Fisher,et al. Breaking the bottleneck in the protein biomarker pipeline. , 2012, Clinical chemistry.
[20] A. Makarov,et al. Evolution of Orbitrap Mass Spectrometry Instrumentation. , 2015, Annual review of analytical chemistry.
[21] M. Mann,et al. Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation , 2010, Molecular & Cellular Proteomics.
[22] Christoph H Borchers,et al. Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation. , 2014, Journal of proteome research.
[23] Eric W. Deutsch,et al. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis , 2013, Nature.
[24] Heidi Zhang,et al. Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. , 2007, Journal of proteome research.
[25] S. Lehmann,et al. Absolute quantification of 35 plasma biomarkers in human saliva using targeted MS. , 2016, Bioanalysis.
[26] D R Mani,et al. Simplified and Efficient Quantification of Low-abundance Proteins at Very High Multiplex via Targeted Mass Spectrometry* , 2014, Molecular & Cellular Proteomics.
[27] 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.
[28] Luis Mendoza,et al. PASSEL: The PeptideAtlas SRMexperiment library , 2012, Proteomics.
[29] Ruedi Aebersold,et al. On the development of plasma protein biomarkers. , 2011, Journal of proteome research.
[30] E. Diamandis,et al. The bottleneck in the cancer biomarker pipeline and protein quantification through mass spectrometry-based approaches: current strategies for candidate verification. , 2010, Clinical chemistry.
[31] Brendan MacLean,et al. Bioinformatics Applications Note Gene Expression Skyline: an Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments , 2022 .
[32] C. E. Parker,et al. Mass-spectrometry-based clinical proteomics--a review and prospective. , 2010, The Analyst.
[33] Darryl B. Hardie,et al. Precise quantitation of 136 urinary proteins by LC/MRM-MS using stable isotope labeled peptides as internal standards for biomarker discovery and/or verification studies. , 2015, Methods.
[34] Pei Wang,et al. The interface between biomarker discovery and clinical validation: The tar pit of the protein biomarker pipeline , 2008, Proteomics. Clinical applications.
[35] Yang Xu,et al. Merck's perspective on the implementation of dried blood spot technology in clinical drug development - why, when and how. , 2013, Bioanalysis.
[36] Yasset Perez-Riverol,et al. A multi-center study benchmarks software tools for label-free proteome quantification , 2016, Nature Biotechnology.
[37] Christoph H Borchers,et al. Standardized protocols for quality control of MRM-based plasma proteomic workflows. , 2013, Journal of proteome research.
[38] Christoph H Borchers,et al. MRM for the verification of cancer biomarker proteins: recent applications to human plasma and serum , 2014, Expert review of proteomics.
[39] Michael J MacCoss,et al. Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma* , 2015, Molecular & Cellular Proteomics.
[40] Juergen Kast,et al. Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring. , 2009, Journal of proteomics.
[41] Y. Yu,et al. Ultra-performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) and UPLC/MS(E) analysis of RNA oligonucleotides. , 2010, Rapid communications in mass spectrometry : RCM.
[42] Andrew J. Percy,et al. Clinical translation of MS-based, quantitative plasma proteomics: status, challenges, requirements, and potential , 2016, Expert review of proteomics.
[43] C. Borchers,et al. Developing an iMALDI method. , 2013, Methods in molecular biology.
[44] D. Formanowicz,et al. Deeper insight into chronic kidney disease-related atherosclerosis: comparative proteomic studies of blood plasma using 2DE and mass spectrometry , 2015, Journal of Translational Medicine.
[45] Luis Mendoza,et al. MaRiMba: a software application for spectral library-based MRM transition list assembly. , 2009, Journal of proteome research.
[46] Derek J. Bailey,et al. Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics* , 2012, Molecular & Cellular Proteomics.
[47] Jarrett D. Egertson,et al. Multiplexed MS/MS for Improved Data Independent Acquisition , 2013, Nature Methods.
[48] N. Rauniyar,et al. Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry , 2015, International journal of molecular sciences.
[49] M. Goshe,et al. Improving protein and proteome coverage through data-independent multiplexed peptide fragmentation. , 2010, Journal of proteome research.
[50] Christoph H Borchers,et al. Towards the development of an immuno MALDI (iMALDI) mass spectrometry assay for the diagnosis of hypertension , 2010, Journal of the American Society for Mass Spectrometry.
[51] Ruedi Aebersold,et al. System-wide Quantitative Proteomics of the Metabolic Syndrome Blockinin Blockinmice: Blockingenotypic Blockinand Blockindietary Blockineffects , 2022 .
[52] Josephine Ec Burnett,et al. Dried blood spot sampling: practical considerations and recommendation for use with preclinical studies. , 2011, Bioanalysis.
[53] D. Eichner,et al. Quantification of insulin-like growth factor-1 in dried blood spots for detection of growth hormone abuse in sport , 2013, Analytical and Bioanalytical Chemistry.
[54] Alexander G. Camenzind,et al. Quantitation of spatially-localized proteins in tissue samples using MALDI-MRM imaging. , 2012, Analytical chemistry.
[55] D. Goodlett,et al. Faster, quantitative, and accurate precursor acquisition independent from ion count. , 2011, Analytical chemistry.
[56] Bindu Nanduri,et al. Prediction of peptides observable by mass spectrometry applied at the experimental set level , 2007, BMC Bioinformatics.
[57] Darryl B. Hardie,et al. SISCAPA Peptide Enrichment on Magnetic Beads Using an In-line Bead Trap Device*S , 2009, Molecular & Cellular Proteomics.
[58] Kathryn S Lilley,et al. Taming the isobaric tagging elephant in the room in quantitative proteomics , 2011, Nature Methods.
[59] K. Parker,et al. Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.
[60] Jörg Grigull,et al. Endometrial Carcinoma Biomarker Discovery and Verification Using Differentially Tagged Clinical Samples with Multidimensional Liquid Chromatography and Tandem Mass Spectrometry*S , 2007, Molecular & Cellular Proteomics.
[61] Darryl B. Hardie,et al. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). , 2004, Journal of proteome research.
[62] C. Tian,et al. Software for quantitative proteomic analysis using stable isotope labeling and data independent acquisition. , 2011, Analytical chemistry.
[63] B. Domon,et al. Quantification of proteins in urine samples using targeted mass spectrometry methods. , 2015, Methods in molecular biology.
[64] Charlotte Sværke Jørgensen,et al. Non-specific binding in solid phase immunoassays for autoantibodies correlates with inflammation markers. , 2014, Journal of immunological methods.
[65] Alexander G. Camenzind,et al. An automated assay for the clinical measurement of plasma renin activity by immuno-MALDI (iMALDI). , 2015, Biochimica et biophysica acta.
[66] Tao Xu,et al. Bioinformatics Applications Note Sequence Analysis Xdia: Improving on the Label-free Data-independent Analysis , 2022 .
[67] C. Bessant,et al. Free computational resources for designing selected reaction monitoring transitions , 2010, Proteomics.
[68] S. Carr,et al. Multiplexed Immunoaffinity Enrichment of Peptides with Anti-peptide Antibodies and Quantification by Stable Isotope Dilution Multiple Reaction Monitoring Mass Spectrometry. , 2016, Methods in molecular biology.
[69] Oliver M. Bernhardt,et al. Reproducible and Consistent Quantification of the Saccharomyces cerevisiae Proteome by SWATH-mass spectrometry* , 2015, Molecular & Cellular Proteomics.
[70] Christoph H Borchers,et al. Development of MRM-based assays for the absolute quantitation of plasma proteins. , 2013, Methods in molecular biology.
[71] Monica H. Elliott,et al. Current trends in quantitative proteomics. , 2009, Journal of mass spectrometry : JMS.
[72] Alexander Lazarev,et al. Sample Preparation in Biological Mass Spectrometry , 2011 .
[73] D R Mani,et al. Interlaboratory Evaluation of Automated, Multiplexed Peptide Immunoaffinity Enrichment Coupled to Multiple Reaction Monitoring Mass Spectrometry for Quantifying Proteins in Plasma* , 2011, Molecular & Cellular Proteomics.
[74] Christoph H Borchers,et al. Multiple Reaction Monitoring-based, Multiplexed, Absolute Quantitation of 45 Proteins in Human Plasma* , 2009, Molecular & Cellular Proteomics.
[75] R. Caprioli,et al. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. , 1997, Analytical chemistry.
[76] Ben C. Collins,et al. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data , 2014, Nature Biotechnology.
[77] N. Anderson,et al. Quantification of a proteotypic peptide from protein C inhibitor by liquid chromatography-free SISCAPA-MALDI mass spectrometry: application to identification of recurrence of prostate cancer. , 2013, Clinical chemistry.
[78] Yassene Mohammed,et al. Qualis-SIS: automated standard curve generation and quality assessment for multiplexed targeted quantitative proteomic experiments with labeled standards. , 2015, Journal of proteome research.
[79] Mehdi Mirzaei,et al. Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment , 2015 .
[80] Hasmik Keshishian,et al. Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury* , 2015, Molecular & Cellular Proteomics.
[81] M. Mann,et al. Mass spectrometry–based proteomics turns quantitative , 2005, Nature chemical biology.
[82] 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.
[83] Andrew J. Percy,et al. Multiple Reaction Monitoring Enables Precise Quantification of 97 Proteins in Dried Blood Spots* , 2015, Molecular & Cellular Proteomics.
[84] S. Carr,et al. A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease , 2011, Nature Biotechnology.
[85] R. Aebersold,et al. mProphet: automated data processing and statistical validation for large-scale SRM experiments , 2011, Nature Methods.
[86] G. Jarvik,et al. Parallel reaction monitoring (PRM) and selected reaction monitoring (SRM) exhibit comparable linearity, dynamic range and precision for targeted quantitative HDL proteomics. , 2015, Journal of proteomics.
[87] B. Simons,et al. Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). , 2011, Analytical chemistry.
[88] Birgit Schilling,et al. Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance* , 2009, Molecular & Cellular Proteomics.
[89] Christoph H Borchers,et al. Multiplexed Quantitation of Endogenous Proteins in Dried Blood Spots by Multiple Reaction Monitoring - Mass Spectrometry , 2012, Molecular & Cellular Proteomics.
[90] Juan P Albar,et al. Multicenter experiment for quality control of peptide-centric LC-MS/MS analysis - A longitudinal performance assessment with nLC coupled to orbitrap MS analyzers. , 2015, Journal of proteomics.
[91] Randall W. Nelson,et al. Parallel Workflow for High-Throughput (>1,000 Samples/Day) Quantitative Analysis of Human Insulin-Like Growth Factor 1 Using Mass Spectrometric Immunoassay , 2014, PloS one.
[92] Richard D. Smith,et al. Ionization and transmission efficiency in an electrospray ionization—mass spectrometry interface , 2007, Journal of the American Society for Mass Spectrometry.
[93] Martin von Bergen,et al. Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM) , 2013, Analytical and Bioanalytical Chemistry.
[94] C. Borchers,et al. Comparison of standard- and nano-flow liquid chromatography platforms for MRM-based quantitation of putative plasma biomarker proteins , 2012, Analytical and Bioanalytical Chemistry.
[95] Rainer Paape,et al. Precision of heavy-light peptide ratios measured by maldi-tof mass spectrometry. , 2012, Journal of proteome research.
[96] Daniel B. Martin,et al. Computational prediction of proteotypic peptides for quantitative proteomics , 2007, Nature Biotechnology.
[97] H. Rodriguez,et al. Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: An NCI‐CPTC initiative perspective , 2010, Proteomics. Clinical applications.
[98] Juncong Yang,et al. MRM‐based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma , 2012, Proteomics.
[99] Susan E. Abbatiello,et al. Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach* , 2014, Molecular & Cellular Proteomics.
[100] Christoph H Borchers,et al. Method and platform standardization in MRM-based quantitative plasma proteomics. , 2013, Journal of proteomics.
[101] Anatoly I Grigoriev,et al. Targeted Quantitative Screening of Chromosome 18 Encoded Proteome in Plasma Samples of Astronaut Candidates. , 2016, Journal of proteome research.
[102] Nichole L. King,et al. Targeted Quantitative Analysis of Streptococcus pyogenes Virulence Factors by Multiple Reaction Monitoring*S , 2008, Molecular & Cellular Proteomics.
[103] I. Wilson,et al. UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation. , 2006, Rapid communications in mass spectrometry : RCM.
[104] Samuel I. Miller,et al. Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. , 2009, Analytical chemistry.
[105] Dana Pascovici,et al. SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries* , 2016, Molecular & Cellular Proteomics.
[106] T. Colgan,et al. Absolute quantification of potential cancer markers in clinical tissue homogenates using multiple reaction monitoring on a hybrid triple quadrupole/linear ion trap tandem mass spectrometer. , 2009, Analytical chemistry.
[107] S. Carr,et al. Antibody-based capture of target peptides in multiple reaction monitoring experiments. , 2015, Methods in molecular biology.
[108] C. Borchers,et al. Increased Depth and Breadth of Plasma Protein Quantitation via Two-Dimensional Liquid Chromatography/Multiple Reaction Monitoring-Mass Spectrometry with Labeled Peptide Standards. , 2016, Methods in molecular biology.
[109] C. Borchers,et al. Improving the biomarker pipeline. , 2010, Clinical chemistry.
[110] D. Eichner,et al. Sensitive quantification of IGF-1 and its synthetic analogs in dried blood spots. , 2014, Bioanalysis.
[111] Ruedi Aebersold,et al. Mass spectrometric protein maps for biomarker discovery and clinical research , 2013, Expert review of molecular diagnostics.
[112] John D. Venable,et al. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra , 2004, Nature Methods.
[113] Christoph H Borchers,et al. Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (LC-MRM-MS)* , 2013, Molecular & Cellular Proteomics.
[114] D. Goodlett,et al. Shotgun collision‐induced dissociation of peptides using a time of flight mass analyzer , 2003, Proteomics.
[115] Ulf Landegren,et al. Opportunities for sensitive plasma proteome analysis. , 2012, Analytical chemistry.
[116] Yassene Mohammed,et al. PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments. , 2014, Journal of proteomics.
[117] M. Sadílek,et al. Tryptic peptide analysis of ceruloplasmin in dried blood spots using liquid chromatography-tandem mass spectrometry: application to newborn screening. , 2008, Clinical chemistry.
[118] C. Borchers,et al. An immunoaffinity tandem mass spectrometry (iMALDI) assay for detection of Francisella tularensis. , 2007, Analytica chimica acta.
[119] N. Anderson,et al. The Human Plasma Proteome , 2002, Molecular & Cellular Proteomics.
[120] M. Chen,et al. Bead-Extractor Assisted Ready-to-Use Reagent System (BEARS) for Immunoprecipitation Coupled to MALDI-MS. , 2017, Analytical chemistry.
[121] R. Aebersold,et al. Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions , 2012, Nature Methods.
[122] Lisa M. Chung,et al. Review of software tools for design and analysis of large scale MRM proteomic datasets. , 2013, Methods.
[123] Richard D. Smith,et al. Advances in targeted proteomics and applications to biomedical research , 2016, Proteomics.
[124] Alexander G. Camenzind,et al. Duplexed iMALDI for the detection of angiotensin I and angiotensin II. , 2012, Methods.
[125] B. Keevil. The analysis of dried blood spot samples using liquid chromatography tandem mass spectrometry. , 2011, Clinical biochemistry.
[126] S. Gygi,et al. MS3 eliminates ratio distortion in isobaric labeling-based multiplexed quantitative proteomics , 2011, Nature Methods.
[127] Thomas J. Wang. Significance of circulating troponins in heart failure: if these walls could talk. , 2007, Circulation.
[128] Amanda G. Paulovich,et al. An Automated and Multiplexed Method for High Throughput Peptide Immunoaffinity Enrichment and Multiple Reaction Monitoring Mass Spectrometry-based Quantification of Protein Biomarkers* , 2009, Molecular & Cellular Proteomics.
[129] D. Galasko,et al. Cerebrospinal Fluid Peptides as Potential Parkinson Disease Biomarkers: A Staged Pipeline for Discovery and Validation* , 2015, Molecular & Cellular Proteomics.
[130] Henry H. N. Lam,et al. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows , 2008, EMBO reports.
[131] C. Borchers,et al. The use of multiplexed MRM for the discovery of biomarkers to differentiate iron-deficiency anemia from anemia of inflammation. , 2012, Journal of proteomics.
[132] J. Adamski,et al. Targeted Metabolomics of Dried Blood Spot Extracts , 2013, Chromatographia.
[133] James G. Bollinger,et al. A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva , 2016, Proteomics.
[134] N Leigh Anderson,et al. High-throughput SISCAPA quantitation of peptides from human plasma digests by ultrafast, liquid chromatography-free mass spectrometry. , 2012, Journal of proteome research.
[135] J. Yates,et al. Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics , 2014, Journal of proteome research.
[136] D. Chace,et al. Use of tandem mass spectrometry for multianalyte screening of dried blood specimens from newborns. , 2003, Clinical chemistry.
[137] Matthew J. Rardin,et al. Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows. , 2015, Analytical chemistry.
[138] Michael J. Sweredoski,et al. High resolution parallel reaction monitoring with electron transfer dissociation for middle-down proteomics. , 2015, Analytical chemistry.
[139] J. Mesirov,et al. Prediction of high-responding peptides for targeted protein assays by mass spectrometry , 2009, Nature Biotechnology.