Toward a Consensus on Applying Quantitative Liquid Chromatography‐Tandem Mass Spectrometry Proteomics in Translational Pharmacology Research: A White Paper
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Jill Barber | Bhagwat Prasad | Amin Rostami-Hodjegan | Philip C Smith | Per Artursson | Brahim Achour | Cornelis Eca Hop | Yurong Lai | Jacek R Wisniewski | Daniel Spellman | Yasuo Uchida | Michael Zientek | Jashvant D Unadkat | Daniel S Spellman | J. Wiśniewski | P. Artursson | Y. Lai | A. Rostami-Hodjegan | J. Unadkat | B. Achour | C. Hop | J. Barber | B. Prasad | Yasuo Uchida | Michael A. Zientek | Philip C. Smith | Yurong Lai | Brahim Achour
[1] Brendan MacLean,et al. Bioinformatics Applications Note Gene Expression Skyline: an Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments , 2022 .
[2] Matthias Mann,et al. BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes , 2018, Nature Methods.
[3] M. Mann,et al. Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma , 2012, Molecular systems biology.
[4] T. Pearson,et al. High precision quantification of human plasma proteins using the automated SISCAPA Immuno-MS workflow. , 2016, New biotechnology.
[5] 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.
[6] C. Booth,et al. Magnitude of clinical benefit of cancer drugs approved based on single-arm trials (SAT) by the US Food and Drug Administration (FDA). , 2018, Annals of oncology : official journal of the European Society for Medical Oncology.
[7] Peter Willett,et al. What is a tutorial , 2013 .
[8] L. Benet,et al. The Presence of a Transporter-Induced Protein Binding Shift: A New Explanation for Protein-Facilitated Uptake and Improvement for In Vitro-In Vivo Extrapolation , 2019, Drug Metabolism and Disposition.
[9] Tetsuya Terasaki,et al. Simultaneous absolute quantification of 11 cytochrome P450 isoforms in human liver microsomes by liquid chromatography tandem mass spectrometry with in silico target peptide selection. , 2011, Journal of pharmaceutical sciences.
[10] Li Wang,et al. Transporter Expression in Liver Tissue from Subjects with Alcoholic or Hepatitis C Cirrhosis Quantified by Targeted Quantitative Proteomics , 2016, Drug Metabolism and Disposition.
[11] D. Tibboel,et al. Proteomics of human liver membrane transporters: a focus on fetuses and newborn infants , 2018, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.
[12] 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.
[13] R. Subramanian,et al. Comparison of information-dependent acquisition, SWATH, and MS(All) techniques in metabolite identification study employing ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. , 2014, Analytical chemistry.
[14] Ludovic C. Gillet,et al. Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial , 2018, Molecular systems biology.
[15] K. Knights,et al. Scaling factors for the in vitro-in vivo extrapolation (IV-IVE) of renal drug and xenobiotic glucuronidation clearance. , 2016, British journal of clinical pharmacology.
[16] Bhagwat Prasad,et al. Critical Issues and Optimized Practices in Quantification of Protein Abundance Level to Determine Interindividual Variability in DMET Proteins by LC‐MS/MS Proteomics , 2018, Clinical pharmacology and therapeutics.
[17] J. Connolly. Comparative Cost Analysis , 1967, Journal of the Royal Aeronautical Society.
[18] J. Unadkat,et al. Optimized Approaches for Quantification of Drug Transporters in Tissues and Cells by MRM Proteomics , 2014, The AAPS Journal.
[19] W. Humphreys,et al. Abundance of Phase 1 and 2 Drug-Metabolizing Enzymes in Alcoholic and Hepatitis C Cirrhotic Livers: A Quantitative Targeted Proteomics Study , 2018, Drug Metabolism and Disposition.
[20] T. Goosen,et al. Data Generated by Quantitative Liquid Chromatography-Mass Spectrometry Proteomics Are Only the Start and Not the Endpoint: Optimization of Quantitative Concatemer-Based Measurement of Hepatic Uridine-5′-Diphosphate–Glucuronosyltransferase Enzymes with Reference to Catalytic Activity , 2018, Drug Metabolism and Disposition.
[21] G. Warhurst,et al. In Vitro–In Vivo Extrapolation Scaling Factors for Intestinal P-Glycoprotein and Breast Cancer Resistance Protein: Part I: A Cross-Laboratory Comparison of Transporter-Protein Abundances and Relative Expression Factors in Human Intestine and Caco-2 Cells , 2016, Drug Metabolism and Disposition.
[22] T. Terasaki,et al. Modulation and compensation of the mRNA expression of energy related transporters in the brain of glucose transporter 1-deficient mice. , 2006, Biological & pharmaceutical bulletin.
[23] M. Mann,et al. Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides per Protein*S , 2005, Molecular & Cellular Proteomics.
[24] R. Evers,et al. Interindividual Variability in Hepatic Organic Anion-Transporting Polypeptides and P-Glycoprotein (ABCB1) Protein Expression: Quantification by Liquid Chromatography Tandem Mass Spectroscopy and Influence of Genotype, Age, and Sex , 2014, Drug Metabolism and Disposition.
[25] Issam Zineh,et al. Quantitative Systems Pharmacology: A Regulatory Perspective on Translation , 2019, CPT: pharmacometrics & systems pharmacology.
[26] J. Wiśniewski,et al. Hepatic Uptake of Atorvastatin: Influence of Variability in Transporter Expression on Uptake Clearance and Drug-Drug Interactions , 2014, Drug Metabolism and Disposition.
[27] G. Warhurst,et al. Lost in Centrifugation: Accounting for Transporter Protein Losses in Quantitative Targeted Absolute Proteomics , 2014, Drug Metabolism and Disposition.
[28] P. Ciborowski,et al. Pressure-assisted sample preparation for proteomic analysis. , 2013, Analytical biochemistry.
[29] J. Backman,et al. Implications of intercorrelation between hepatic CYP3A4‐CYP2C8 enzymes for the evaluation of drug–drug interactions: a case study with repaglinide , 2018, British journal of clinical pharmacology.
[30] J. Wiśniewski,et al. In-depth quantitative analysis and comparison of the human hepatocyte and hepatoma cell line HepG2 proteomes. , 2016, Journal of proteomics.
[31] Amin Rostami-Hodjegan,et al. In Vitro–In Vivo Extrapolation Scaling Factors for Intestinal P-glycoprotein and Breast Cancer Resistance Protein: Part II. The Impact of Cross-Laboratory Variations of Intestinal Transporter Relative Expression Factors on Predicted Drug Disposition , 2016, Drug Metabolism and Disposition.
[32] S. Heyward,et al. A Comparison of Total and Plasma Membrane Abundance of Transporters in Suspended, Plated, Sandwich-Cultured Human Hepatocytes Versus Human Liver Tissue Using Quantitative Targeted Proteomics and Cell Surface Biotinylation , 2019, Drug Metabolism and Disposition.
[33] T. Goosen,et al. Quantitative Characterization of Major Hepatic UDP-Glucuronosyltransferase Enzymes in Human Liver Microsomes: Comparison of Two Proteomic Methods and Correlation with Catalytic Activity , 2017, Drug Metabolism and Disposition.
[34] Marco Y. Hein,et al. A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards* , 2014, Molecular & Cellular Proteomics.
[35] Yingying Guo,et al. Ethnic Variability in the Expression of Hepatic Drug Transporters: Absolute Quantification by an Optimized Targeted Quantitative Proteomic Approach , 2015, Drug Metabolism and Disposition.
[36] Kuresh Youdim,et al. Reaction Phenotyping: Advances in the Experimental Strategies Used to Characterize the Contribution of Drug-Metabolizing Enzymes , 2015, Drug Metabolism and Disposition.
[37] J. Wiśniewski,et al. Comparative Proteomic Analysis of Human Liver Tissue and Isolated Hepatocytes with a Focus on Proteins Determining Drug Exposure. , 2015, Journal of proteome research.
[38] M. Mann,et al. Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. , 2010, Journal of proteome research.
[39] D. Martins‐de‐Souza,et al. A Guide to Mass Spectrometry-Based Quantitative Proteomics. , 2018, Methods in molecular biology.
[40] M. Reuss,et al. Indirect protein quantification of drug-transforming enzymes using peptide group-specific immunoaffinity enrichment and mass spectrometry , 2015, Scientific Reports.
[41] S. Heyward,et al. Targeted LC-MS/MS Proteomics-Based Strategy To Characterize in Vitro Models Used in Drug Metabolism and Transport Studies. , 2018, Analytical chemistry.
[42] A. Rostami-Hodjegan,et al. Global Proteomic Analysis of Human Liver Microsomes: Rapid Characterization and Quantification of Hepatic Drug-Metabolizing Enzymes , 2017, Drug Metabolism and Disposition.
[43] R. Aebersold,et al. mProphet: automated data processing and statistical validation for large-scale SRM experiments , 2011, Nature Methods.
[44] C. Eyers,et al. The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. , 2014, Nature chemistry.
[45] Laura L. Elo,et al. A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation , 2017, Briefings Bioinform..
[46] X. Chu,et al. Ontogeny of Hepatic Drug Transporters as Quantified by LC‐MS/MS Proteomics , 2016, Clinical pharmacology and therapeutics.
[47] J. Wiśniewski. Label-Free and Standard-Free Absolute Quantitative Proteomics Using the "Total Protein" and "Proteomic Ruler" Approaches. , 2017, Methods in enzymology.
[48] Hendrik Neubert,et al. Targeted quantitative proteomics for the analysis of 14 UGT1As and -2Bs in human liver using NanoUPLC-MS/MS with selected reaction monitoring. , 2013, Journal of proteome research.
[49] Jeffrey R. Whiteaker,et al. Optimized Protocol for Quantitative Multiple Reaction Monitoring-Based Proteomic Analysis of Formalin-Fixed, Paraffin-Embedded Tissues. , 2016, Journal of proteome research.
[50] Brendan MacLean,et al. Panorama: A Targeted Proteomics Knowledge Base , 2014, Journal of proteome research.
[51] M. Ostrowski,et al. Protein Abundance of Clinically Relevant Drug Transporters in the Human Liver and Intestine: A Comparative Analysis in Paired Tissue Specimens , 2019, Clinical pharmacology and therapeutics.
[52] Juan Antonio Vizcaíno,et al. How to submit MS proteomics data to ProteomeXchange via the PRIDE database , 2014, Proteomics.
[53] Bhagwat Prasad,et al. Age-Dependent Absolute Abundance of Hepatic Carboxylesterases (CES1 and CES2) by LC-MS/MS Proteomics: Application to PBPK Modeling of Oseltamivir In Vivo Pharmacokinetics in Infants , 2017, Drug Metabolism and Disposition.
[54] A. D. Rodrigues,et al. Comparison of Proteomic Quantification Approaches for Hepatic Drug Transporters: Multiplexed Global Quantitation Correlates with Targeted Proteomic Quantitation , 2018, Drug Metabolism and Disposition.
[55] Wooin Lee,et al. The N‐terminal region of organic anion transporting polypeptide 1B3 (OATP1B3) plays an essential role in regulating its plasma membrane trafficking , 2017, Biochemical pharmacology.
[56] Yuan Chen,et al. Strategies of Drug Transporter Quantitation by LC-MS: Importance of Peptide Selection and Digestion Efficiency , 2017, The AAPS Journal.
[57] K. Parker,et al. Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.
[58] Y. Lai,et al. Quantitative assessment of the contribution of sodium‐dependent taurocholate co‐transporting polypeptide (NTCP) to the hepatic uptake of rosuvastatin, pitavastatin and fluvastatin , 2013, Biopharmaceutics & drug disposition.
[59] Jashvant D. Unadkat,et al. Successful Prediction of In Vivo Hepatobiliary Clearances and Hepatic Concentrations of Rosuvastatin Using Sandwich-Cultured Rat Hepatocytes, Transporter-Expressing Cell Lines, and Quantitative Proteomics , 2018, Drug Metabolism and Disposition.
[60] M. Mann,et al. Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells , 2014, Nature Methods.
[61] M. Vrana,et al. The Promises of Quantitative Proteomics in Precision Medicine. , 2017, Journal of pharmaceutical sciences.
[62] J. Wiśniewski,et al. A simple approach for restoration of differentiation and function in cryopreserved human hepatocytes , 2019, Archives of Toxicology.
[63] Jill Barber,et al. Expression of Hepatic Drug-Metabolizing Cytochrome P450 Enzymes and Their Intercorrelations: A Meta-Analysis , 2014, Drug Metabolism and Disposition.
[64] M. Ostrowski,et al. Protein abundance of clinically relevant multidrug transporters along the entire length of the human intestine. , 2014, Molecular pharmaceutics.
[65] J. Wiśniewski,et al. Subcellular fractionation of human liver reveals limits in global proteomic quantification from isolated fractions. , 2016, Analytical biochemistry.
[66] A. Rostami-Hodjegan,et al. Ten years of QconCATs: Application of multiplexed quantification to small medically relevant proteomes , 2015 .
[67] A. Rostami-Hodjegan,et al. GASP and FASP are Complementary for LC–MS/MS Proteomic Analysis of Drug‐Metabolizing Enzymes and Transporters in Pig Liver , 2018, Proteomics.
[68] C. Heidecke,et al. Absolute protein quantification of clinically relevant cytochrome P450 enzymes and UDP-glucuronosyltransferases by mass spectrometry-based targeted proteomics. , 2014, Journal of pharmaceutical and biomedical analysis.
[69] J. Unadkat,et al. Optimization and Application of a Biotinylation Method for Quantification of Plasma Membrane Expression of Transporters in Cells , 2017, The AAPS Journal.
[70] Tetsuya Terasaki,et al. Quantitative Atlas of Membrane Transporter Proteins: Development and Application of a Highly Sensitive Simultaneous LC/MS/MS Method Combined with Novel In-silico Peptide Selection Criteria , 2008, Pharmaceutical Research.
[71] Ben C. Collins,et al. Quantitative proteomics: challenges and opportunities in basic and applied research , 2017, Nature Protocols.
[72] A. Rostami-Hodjegan,et al. Alternative fusion protein strategies to express recalcitrant QconCAT proteins for quantitative proteomics of human drug metabolizing enzymes and transporters. , 2013, Journal of proteome research.
[73] Christopher S. Hughes,et al. Extending the Compatibility of the SP3 Paramagnetic Bead Processing Approach for Proteomics. , 2018, Journal of proteome research.
[74] R. Harrington. Part II , 2004 .
[75] J. Wiśniewski,et al. Fast and sensitive total protein and Peptide assays for proteomic analysis. , 2015, Analytical chemistry.
[76] C. Wolf,et al. A Targeted in Vivo SILAC Approach for Quantification of Drug Metabolism Enzymes: Regulation by the Constitutive Androstane Receptor , 2013, Journal of proteome research.
[77] I. Turko,et al. Natural flanking sequences for peptides included in a quantification concatamer internal standard. , 2015, Analytical chemistry.
[78] Aleksandra Galetin,et al. Meta-Analysis of Expression of Hepatic Organic Anion–Transporting Polypeptide (OATP) Transporters in Cellular Systems Relative to Human Liver Tissue , 2015, Drug Metabolism and Disposition.
[79] S. Gygi,et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.
[80] Daniel C. Liebler,et al. Equivalence of Protein Inventories Obtained from Formalin-fixed Paraffin-embedded and Frozen Tissue in Multidimensional Liquid Chromatography-Tandem Mass Spectrometry Shotgun Proteomic Analysis* , 2009, Molecular & Cellular Proteomics.
[81] Matthias Mann,et al. Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis. , 2012, Analytical chemistry.
[82] S. Gaskell,et al. Quantification of the proteins of the bacterial ribosome using QconCAT technology. , 2014, Journal of proteome research.
[83] J. Unadkat,et al. The Importance of Incorporating OCT2 Plasma Membrane Expression and Membrane Potential in IVIVE of Metformin Renal Secretory Clearance , 2018, Drug Metabolism and Disposition.
[84] Brendan MacLean,et al. CPTAC Assay Portal: a repository of targeted proteomic assays , 2014, Nature Methods.
[85] M. Mann,et al. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC) , 2006, Nature Protocols.
[86] Susan E. Abbatiello,et al. New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins , 2017, Molecular & Cellular Proteomics.
[87] A. Rostami-Hodjegan,et al. Choice of LC-MS Methods for the Absolute Quantification of Drug-Metabolizing Enzymes and Transporters in Human Tissue: a Comparative Cost Analysis , 2015, The AAPS Journal.
[88] M. Mann,et al. Super-SILAC mix for quantitative proteomics of human tumor tissue , 2010, Nature Methods.
[89] J. Wiśniewski,et al. Multiple-Enzyme-Digestion Strategy Improves Accuracy and Sensitivity of Label- and Standard-Free Absolute Quantification to a Level That Is Achievable by Analysis with Stable Isotope-Labeled Standard Spiking. , 2018, Journal of proteome research.
[90] U. Broeckel,et al. Age‐ and Genotype‐Dependent Variability in the Protein Abundance and Activity of Six Major Uridine Diphosphate‐Glucuronosyltransferases in Human Liver , 2018, Clinical pharmacology and therapeutics.
[91] M. Mann,et al. Large-scale Proteomic Analysis of the Human Spliceosome References , 2006 .
[92] M. Mann,et al. Quantitative, high-resolution proteomics for data-driven systems biology. , 2011, Annual review of biochemistry.
[93] M. Ostrowski,et al. Protein Abundance of Clinically Relevant Drug‐Metabolizing Enzymes in the Human Liver and Intestine: A Comparative Analysis in Paired Tissue Specimens , 2018, Clinical pharmacology and therapeutics.
[94] Response to "Determining Allele-Specific Protein Expression (ASPE) Using a Novel Quantitative Concatamer Based Proteomics Method". , 2018, Journal of proteome research.
[95] Matthias Mann,et al. Loss-less Nano-fractionator for High Sensitivity, High Coverage Proteomics * , 2017, Molecular & Cellular Proteomics.
[96] Markus Müller,et al. Processing strategies and software solutions for data‐independent acquisition in mass spectrometry , 2015, Proteomics.
[97] Stefan Tenzer,et al. Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range. , 2017, Journal of proteome research.
[98] F. Schmidt. Meta-Analysis , 2008 .
[99] A. Rostami-Hodjegan,et al. Simultaneous Quantification of the Abundance of Several Cytochrome P450 and Uridine 5′-Diphospho-Glucuronosyltransferase Enzymes in Human Liver Microsomes Using Multiplexed Targeted Proteomics , 2014, Drug Metabolism and Disposition.
[100] A. Nesvizhskii,et al. Determining Allele-Specific Protein Expression (ASPE) Using a Novel Quantitative Concatamer Based Proteomics Method. , 2018, Journal of proteome research.
[101] J. Wiśniewski,et al. Variability in Mass Spectrometry-based Quantification of Clinically Relevant Drug Transporters and Drug Metabolizing Enzymes. , 2017, Molecular pharmaceutics.