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Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma.
Gillette MA, Satpathy S, Cao S, et al. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. Cell. 2020;182(1):200-225.e35. doi:10.1016/j.cell.2020.06.013.
Steroid resistance in Diamond Blackfan anemia associates with p57Kip2 dysregulation in erythroid progenitors.
Ashley RJ, Yan H, Wang N, et al. Steroid resistance in Diamond Blackfan anemia associates with p57Kip2 dysregulation in erythroid progenitors. J Clin Invest. 2020;130(4):2097-2110. doi:10.1172/JCI132284.
Multi-Omics Analysis Identifies MGA as a Negative Regulator of the MYC Pathway in Lung Adenocarcinoma.
Llabata P, Mitsuishi Y, Choi PS, et al. Multi-Omics Analysis Identifies MGA as a Negative Regulator of the MYC Pathway in Lung Adenocarcinoma. Mol Cancer Res. 2020;18(4):574-584. doi:10.1158/1541-7786.MCR-19-0657.
Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches.
Hebert JD, Myers SA, Naba A, et al. Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches. Cancer Res. 2020;80(7):1475-1485. doi:10.1158/0008-5472.CAN-19-2961.
Virtual Issue: Technological Innovations.
Gingras A-C, Carr SA, Burlingame AL. Virtual Issue: Technological Innovations. Mol Cell Proteomics. 2020;19(4):572-573. doi:10.1074/mcp.E120.002042.
Increased mitochondrial apoptotic priming with targeted therapy predicts clinical response to re-induction chemotherapy.
Garcia JS, Bhatt S, Fell G, et al. Increased mitochondrial apoptotic priming with targeted therapy predicts clinical response to re-induction chemotherapy. Am J Hematol. 2020;95(3):245-250. doi:10.1002/ajh.25692.
Discovery of suppressors of CRMP2 phosphorylation reveals compounds that mimic the behavioral effects of lithium on amphetamine-induced hyperlocomotion.
Zhao W-N, Tobe BTD, Udeshi ND, et al. Discovery of suppressors of CRMP2 phosphorylation reveals compounds that mimic the behavioral effects of lithium on amphetamine-induced hyperlocomotion. Transl Psychiatry. 2020;10(1):76. doi:10.1038/s41398-020-0753-6.
Spontaneous Glycan Reattachment Following N-Glycanase Treatment of Influenza and HIV Vaccine Antigens.
Keating CL, Kuhn E, Bals J, et al. Spontaneous Glycan Reattachment Following N-Glycanase Treatment of Influenza and HIV Vaccine Antigens. J Proteome Res. 2020;19(2):733-743. doi:10.1021/acs.jproteome.9b00620.
A large peptidome dataset improves HLA class I epitope prediction across most of the human population.
Sarkizova S, Klaeger S, Le PM, et al. A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nat Biotechnol. 2020;38(2):199-209. doi:10.1038/s41587-019-0322-9.
Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS.
Mullahoo J, Zhang T, Clauser K, Carr SA, Jaffe JD, Papanastasiou M. Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS. Methods. 2020. doi:10.1016/j.ymeth.2020.01.016.
Microscaled proteogenomic methods for precision oncology.
Satpathy S, Jaehnig EJ, Krug K, et al. Microscaled proteogenomic methods for precision oncology. Nat Commun. 2020;11(1):532. doi:10.1038/s41467-020-14381-2.
Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators.
Li J, Han S, Li H, et al. Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators. Cell. 2020;180(2):373-386.e15. doi:10.1016/j.cell.2019.12.029.
Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation.
Basak A, Munschauer M, Lareau CA, et al. Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation. Nat Genet. 2020. doi:10.1038/s41588-019-0568-7.
Rapid and deep-scale ubiquitylation profiling for biology and translational research.
Udeshi ND, Mani DC, Satpathy S, et al. Rapid and deep-scale ubiquitylation profiling for biology and translational research. Nat Commun. 2020;11(1):359. doi:10.1038/s41467-019-14175-1.
Phosphorylation of RAB7 by TBK1/IKKε Regulates Innate Immune Signaling in Triple-Negative Breast Cancer.
Ritter JL, Zhu Z, Thai TC, et al. Phosphorylation of RAB7 by TBK1/IKKε Regulates Innate Immune Signaling in Triple-Negative Breast Cancer. Cancer Res. 2020;80(1):44-56. doi:10.1158/0008-5472.CAN-19-1310.
Domain-specific Quantification of Prion Protein in Cerebrospinal Fluid by Targeted Mass Spectrometry.
Minikel EVallabh, Kuhn E, Cocco AR, et al. Domain-specific Quantification of Prion Protein in Cerebrospinal Fluid by Targeted Mass Spectrometry. Mol Cell Proteomics. 2019;18(12):2388-2400. doi:10.1074/mcp.RA119.001702.
A rapid triage test for active pulmonary tuberculosis in adult patients with persistent cough.
Ahmad R, Xie L, Pyle M, et al. A rapid triage test for active pulmonary tuberculosis in adult patients with persistent cough. Sci Transl Med. 2019;11(515). doi:10.1126/scitranslmed.aaw8287.
Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS.
Papanastasiou M, Mullahoo J, DeRuff KC, et al. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS. Mol Cell Proteomics. 2019;18(10):2089-2098. doi:10.1074/mcp.RA119.001325.
Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies.
Guièze R, Liu VM, Rosebrock D, et al. Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies. Cancer Cell. 2019. doi:10.1016/j.ccell.2019.08.005.
Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of Hepatitis C Virus-Infected Cells and Liver to Identify Pathways Associated With Disease Development.
Lupberger J, Croonenborghs T, Suarez AAndres Roc, et al. Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of Hepatitis C Virus-Infected Cells and Liver to Identify Pathways Associated With Disease Development. Gastroenterology. 2019;157(2):537-551.e9. doi:10.1053/j.gastro.2019.04.003.
Patterns of substrate affinity, competition, and degradation kinetics underlie biological activity of thalidomide analogs.
Sperling AS, Burgess M, Keshishian H, et al. Patterns of substrate affinity, competition, and degradation kinetics underlie biological activity of thalidomide analogs. Blood. 2019;134(2):160-170. doi:10.1182/blood.2019000789.
TMT Labeling for the Masses: A Robust and Cost-efficient, In-solution Labeling Approach.
Zecha J, Satpathy S, Kanashova T, et al. TMT Labeling for the Masses: A Robust and Cost-efficient, In-solution Labeling Approach. Mol Cell Proteomics. 2019;18(7):1468-1478. doi:10.1074/mcp.TIR119.001385.
Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability.
Huang K-lin, Wu Y, Primeau T, et al. Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability. Mol Cell Proteomics. 2019. doi:10.1074/mcp.RA118.001243.
Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma.
Bandopadhayay P, Piccioni F, O'Rourke R, et al. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun. 2019;10(1):2400. doi:10.1038/s41467-019-10307-9.
Trio Haploinsufficiency Causes Neurodevelopmental Disease-Associated Deficits.
Katrancha SMarie, Shaw JE, Zhao AY, et al. Trio Haploinsufficiency Causes Neurodevelopmental Disease-Associated Deficits. Cell Rep. 2019;26(10):2805-2817.e9. doi:10.1016/j.celrep.2019.02.022.
A Curated Resource for Phosphosite-specific Signature Analysis.
Krug K, Mertins P, Zhang B, et al. A Curated Resource for Phosphosite-specific Signature Analysis. Mol Cell Proteomics. 2019;18(3):576-593. doi:10.1074/mcp.TIR118.000943.
Streamlined protocol for deep proteomic profiling of FAC-sorted cells and its application to freshly isolated murine immune cells.
Myers SA, Rhoads A, Cocco AR, et al. Streamlined protocol for deep proteomic profiling of FAC-sorted cells and its application to freshly isolated murine immune cells. Mol Cell Proteomics. 2019. doi:10.1074/mcp.RA118.001259.
In Situ Peroxidase Labeling and Mass Spectrometry of Alpha-Synuclein in Rat Cortical Neurons.
Sanz R, Ovando-Roche P, Udeshi ND, Carr SA, Chung CYeun, Khurana V. In Situ Peroxidase Labeling and Mass Spectrometry of Alpha-Synuclein in Rat Cortical Neurons. Methods Mol Biol. 2019;1948:235-246. doi:10.1007/978-1-4939-9124-2_18.
Tetracyclines Modify Translation by Targeting Key Human rRNA Substructures.
Mortison JD, Schenone M, Myers JA, et al. Tetracyclines Modify Translation by Targeting Key Human rRNA Substructures. Cell Chem Biol. 2018;25(12):1506-1518.e13. doi:10.1016/j.chembiol.2018.09.010.
Evaluation of Advanced Precursor Determination for Tandem Mass Tag (TMT)-Based Quantitative Proteomics across Instrument Platforms.
Myers SA, Klaeger S, Satpathy S, et al. Evaluation of Advanced Precursor Determination for Tandem Mass Tag (TMT)-Based Quantitative Proteomics across Instrument Platforms. J Proteome Res. 2018. doi:10.1021/acs.jproteome.8b00611.
Homo-PROTACs for the Chemical Knockdown of Cereblon.
Steinebach C, Lindner S, Udeshi ND, et al. Homo-PROTACs for the Chemical Knockdown of Cereblon. ACS Chem Biol. 2018;13(9):2771-2782. doi:10.1021/acschembio.8b00693.
Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups.
Archer TC, Ehrenberger T, Mundt F, et al. Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups. Cancer Cell. 2018;34(3):396-410.e8. doi:10.1016/j.ccell.2018.08.004.
Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast.
Wang YJ, Vaidyanathan PP, Rojas-Duran MF, et al. Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast. PLoS Biol. 2018;16(9):e2005903. doi:10.1371/journal.pbio.2005903.
The NORAD lncRNA assembles a topoisomerase complex critical for genome stability.
Munschauer M, Nguyen CT, Sirokman K, et al. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. Nature. 2018;561(7721):132-136. doi:10.1038/s41586-018-0453-z.
Efficient proximity labeling in living cells and organisms with TurboID.
Branon TC, Bosch JA, Sanchez AD, et al. Efficient proximity labeling in living cells and organisms with TurboID. Nat Biotechnol. 2018. doi:10.1038/nbt.4201.
Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis.
Sandoval GJ, Pulice JL, Pakula H, et al. Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis. Mol Cell. 2018;71(4):554-566.e7. doi:10.1016/j.molcel.2018.06.040.
Crbn is sufficient to confer sensitivity to thalidomide and its derivatives in mice.
Fink EC, McConkey M, Adams DN, et al. Crbn is sufficient to confer sensitivity to thalidomide and its derivatives in mice. Blood. 2018. doi:10.1182/blood-2018-05-852798.
A phosphoproteomic signature in endothelial cells predicts vascular toxicity of tyrosine kinase inhibitors used in CML.
Gopal S, Lu Q, Man JJ, et al. A phosphoproteomic signature in endothelial cells predicts vascular toxicity of tyrosine kinase inhibitors used in CML. Blood Adv. 2018;2(14):1680-1684. doi:10.1182/bloodadvances.2018020396.
Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes.
Graham DB, Jasso GJ, Mok A, et al. Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes. Cell Rep. 2018;24(4):838-850. doi:10.1016/j.celrep.2018.06.081.
Noncanonical translation via deadenylated 3' UTRs maintains primordial germ cells.
Jin YN, Schlueter PJ, Jurisch-Yaksi N, et al. Noncanonical translation via deadenylated 3' UTRs maintains primordial germ cells. Nat Chem Biol. 2018. doi:10.1038/s41589-018-0098-0.
The C9orf72-interacting protein Smcr8 is a negative regulator of autoimmunity and lysosomal exocytosis.
Zhang Y, Burberry A, Wang J-Y, et al. The C9orf72-interacting protein Smcr8 is a negative regulator of autoimmunity and lysosomal exocytosis. Genes Dev. 2018;32(13-14):929-943. doi:10.1101/gad.313932.118.
PPM1D truncating mutations confer resistance to chemotherapy and sensitivity to PPM1D inhibition in hematopoietic cells.
Kahn JD, Miller PG, Silver AJ, et al. PPM1D truncating mutations confer resistance to chemotherapy and sensitivity to PPM1D inhibition in hematopoietic cells. Blood. 2018. doi:10.1182/blood-2018-05-850339.
Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types.
Mead BE, Ordovas-Montanes J, Braun AP, et al. Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. BMC Biol. 2018;16(1):62. doi:10.1186/s12915-018-0527-2.
Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.
Sharma V, Eckels J, Schilling B, et al. Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline. Mol Cell Proteomics. 2018;17(6):1239-1244. doi:10.1074/mcp.RA117.000543.
Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition.
Wong GS, Zhou J, Bin Liu J, et al. Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition. Nat Med. 2018. doi:10.1038/s41591-018-0022-x.
Anti-apoptotic Protein BIRC5 Maintains Survival of HIV-1-Infected CD4 T Cells.
Kuo H-H, Ahmad R, Lee GQ, et al. Anti-apoptotic Protein BIRC5 Maintains Survival of HIV-1-Infected CD4 T Cells. Immunity. 2018. doi:10.1016/j.immuni.2018.04.004.
Discovery of proteins associated with a predefined genomic locus via dCas9-APEX-mediated proximity labeling.
Myers SA, Wright J, Peckner R, Kalish BT, Zhang F, Carr SA. Discovery of proteins associated with a predefined genomic locus via dCas9-APEX-mediated proximity labeling. Nat Methods. 2018. doi:10.1038/s41592-018-0007-1.
Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics.
Peckner R, Myers SA, Jacome ASebastian, et al. Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics. Nat Methods. 2018;15(5):371-378. doi:10.1038/nmeth.4643.
A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations.
Litichevskiy L, Peckner R, Abelin JG, et al. A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations. Cell Syst. 2018;6(4):424-443.e7. doi:10.1016/j.cels.2018.03.012.
Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis.
Khajuria RK, Munschauer M, Ulirsch JC, et al. Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis. Cell. 2018;173(1):90-103.e19. doi:10.1016/j.cell.2018.02.036.
is a colitis risk gene that regulates stability of epithelial adherens junctions.
Mohanan V, Nakata T, A Desch N, et al. is a colitis risk gene that regulates stability of epithelial adherens junctions. Science. 2018;359(6380):1161-1166. doi:10.1126/science.aan0814.
Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis.
Cheng Z, Otto GMaxwell, Powers ENicole, et al. Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis. Cell. 2018;172(5):910-923.e16. doi:10.1016/j.cell.2018.01.035.
Activity of the PI3K-δ,γ inhibitor duvelisib in a phase 1 trial and preclinical models of T-cell lymphoma.
Horwitz SM, Koch R, Porcu P, et al. Activity of the PI3K-δ,γ inhibitor duvelisib in a phase 1 trial and preclinical models of T-cell lymphoma. Blood. 2018;131(8):888-898. doi:10.1182/blood-2017-08-802470.
Mass spectrometry-based proteomics reveals potential roles of NEK9 and MAP2K4 in resistance to PI3K inhibitors in triple negative breast cancers.
Mundt F, Rajput S, Li S, et al. Mass spectrometry-based proteomics reveals potential roles of NEK9 and MAP2K4 in resistance to PI3K inhibitors in triple negative breast cancers. Cancer Res. 2018. doi:10.1158/0008-5472.CAN-17-1990.
The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.
Keenan AB, Jenkins SL, Jagodnik KM, et al. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Syst. 2018;6(1):13-24. doi:10.1016/j.cels.2017.11.001.
Quantitative Proteomic Profiling Reveals Novel Surface Antigens and Possible Vaccine Candidates.
Bark SKNilsson, Ahmad R, Dantzler K, et al. Quantitative Proteomic Profiling Reveals Novel Surface Antigens and Possible Vaccine Candidates. Mol Cell Proteomics. 2018;17(1):43-60. doi:10.1074/mcp.RA117.000076.
Receptor tyrosine kinase activation of RhoA is mediated by AKT phosphorylation of DLC1.
Tripathi BK, Grant T, Qian X, et al. Receptor tyrosine kinase activation of RhoA is mediated by AKT phosphorylation of DLC1. J Cell Biol. 2017;216(12):4255-4270. doi:10.1083/jcb.201703105.
Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues.
Zhou J-Y, Chen L, Zhang B, et al. Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues. J Proteome Res. 2017;16(12):4523-4530. doi:10.1021/acs.jproteome.7b00362.
Antibodies to biotin enable large-scale detection of biotinylation sites on proteins.
Udeshi ND, Pedram K, Svinkina T, et al. Antibodies to biotin enable large-scale detection of biotinylation sites on proteins. Nat Methods. 2017;14(12):1167-1170. doi:10.1038/nmeth.4465.
Lysine trimethylation regulates 78-kDa glucose-regulated protein proteostasis during endoplasmic reticulum stress.
Sieber J, Wieder N, Ostrosky-Frid M, et al. Lysine trimethylation regulates 78-kDa glucose-regulated protein proteostasis during endoplasmic reticulum stress. J Biol Chem. 2017;292(46):18878-18885. doi:10.1074/jbc.M117.797084.
Site-specific identification and quantitation of endogenous SUMO modifications under native conditions.
Lumpkin RJ, Gu H, Zhu Y, et al. Site-specific identification and quantitation of endogenous SUMO modifications under native conditions. Nat Commun. 2017;8(1):1171. doi:10.1038/s41467-017-01271-3.
Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors.
Janouskova H, Tekle GEl, Bellini E, et al. Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors. Nat Med. 2017;23(9):1046-1054. doi:10.1038/nm.4372.
Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry.
Keshishian H, Burgess MW, Specht H, et al. Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry. Nat Protoc. 2017;12(8):1683-1701. doi:10.1038/nprot.2017.054.
HIF activation causes synthetic lethality between the tumor suppressor and the histone methyltransferase.
Chakraborty AA, Nakamura E, Qi J, et al. HIF activation causes synthetic lethality between the tumor suppressor and the histone methyltransferase. Sci Transl Med. 2017;9(398). doi:10.1126/scitranslmed.aal5272.
An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling.
Mertins P, Przybylski D, Yosef N, et al. An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling. Cell Rep. 2017;19(13):2853-2866. doi:10.1016/j.celrep.2017.06.016.
Probing the lithium-response pathway in hiPSCs implicates the phosphoregulatory set-point for a cytoskeletal modulator in bipolar pathogenesis.
Tobe BTD, Crain AM, Winquist AM, et al. Probing the lithium-response pathway in hiPSCs implicates the phosphoregulatory set-point for a cytoskeletal modulator in bipolar pathogenesis. Proc Natl Acad Sci U S A. 2017;114(22):E4462-E4471. doi:10.1073/pnas.1700111114.
Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation.
Hung V, Lam SS, Udeshi ND, et al. Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation. Elife. 2017;6. doi:10.7554/eLife.24463.
Proteogenomic integration reveals therapeutic targets in breast cancer xenografts.
Huang K-lin, Li S, Mertins P, et al. Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nat Commun. 2017;8:14864. doi:10.1038/ncomms14864.
Proximity Biotinylation as a Method for Mapping Proteins Associated with mtDNA in Living Cells.
Han S, Udeshi ND, Deerinck TJ, et al. Proximity Biotinylation as a Method for Mapping Proteins Associated with mtDNA in Living Cells. Cell Chem Biol. 2017;24(3):404-414. doi:10.1016/j.chembiol.2017.02.002.
New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins.
Abbatiello S, Ackermann BL, Borchers C, et al. New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins. Mol Cell Proteomics. 2017;16(3):327-328. doi:10.1074/mcp.E117.067801.
In Situ Peroxidase Labeling and Mass-Spectrometry Connects Alpha-Synuclein Directly to Endocytic Trafficking and mRNA Metabolism in Neurons.
Chung CYeun, Khurana V, Yi S, et al. In Situ Peroxidase Labeling and Mass-Spectrometry Connects Alpha-Synuclein Directly to Endocytic Trafficking and mRNA Metabolism in Neurons. Cell Syst. 2017;4(2):242-250.e4. doi:10.1016/j.cels.2017.01.002.
Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment.
Gomez JE, Kaufmann-Malaga BB, Wivagg CN, et al. Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment. Elife. 2017;6. doi:10.7554/eLife.20420.
Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction.
Abelin JG, Keskin DB, Sarkizova S, et al. Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. Immunity. 2017;46(2):315-326. doi:10.1016/j.immuni.2017.02.007.
Castration Resistance in Prostate Cancer Is Mediated by the Kinase NEK6.
Choudhury AD, Schinzel AC, Cotter MB, et al. Castration Resistance in Prostate Cancer Is Mediated by the Kinase NEK6. Cancer Res. 2017;77(3):753-765. doi:10.1158/0008-5472.CAN-16-0455.
Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression.
Naba A, Clauser KR, Mani DR, Carr SA, Hynes RO. Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression. Sci Rep. 2017;7:40495. doi:10.1038/srep40495.
Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction.
Wang J, Ma Z, Carr SA, et al. Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction. Mol Cell Proteomics. 2017;16(1):121-134. doi:10.1074/mcp.M116.060301.
TMEM258 Is a Component of the Oligosaccharyltransferase Complex Controlling ER Stress and Intestinal Inflammation.
Graham DB, Lefkovith A, Deelen P, et al. TMEM258 Is a Component of the Oligosaccharyltransferase Complex Controlling ER Stress and Intestinal Inflammation. Cell Rep. 2016;17(11):2955-2965. doi:10.1016/j.celrep.2016.11.042.
Transcriptional categorization of the etiology of pneumonia syndrome in pediatric patients in malaria endemic areas.
Silterra J, Gillette MA, Lanaspa M, et al. Transcriptional categorization of the etiology of pneumonia syndrome in pediatric patients in malaria endemic areas. J Infect Dis. 2016. doi:10.1093/infdis/jiw531.
Reconstituted B cell receptor signaling reveals carbohydrate-dependent mode of activation.
Villar RF, Patel J, Weaver GC, et al. Reconstituted B cell receptor signaling reveals carbohydrate-dependent mode of activation. Sci Rep. 2016;6:36298. doi:10.1038/srep36298.
A proposal for validation of antibodies.
Uhlen M, Bandrowski A, Carr S, et al. A proposal for validation of antibodies. Nat Methods. 2016;13(10):823-7. doi:10.1038/nmeth.3995.
Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in β-Catenin-Active Cancers.
Rosenbluh J, Mercer J, Shrestha Y, et al. Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in β-Catenin-Active Cancers. Cell Syst. 2016;3(3):302-316.e4. doi:10.1016/j.cels.2016.09.001.
Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts.
Loh KH, Stawski PS, Draycott AS, et al. Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts. Cell. 2016;166(5):1295-1307.e21. doi:10.1016/j.cell.2016.07.041.
Automated Microchromatography Enables Multiplexing of Immunoaffinity Enrichment of Peptides to Greater than 150 for Targeted MS-Based Assays.
Ippoliti PJ, Kuhn E, Mani DR, et al. Automated Microchromatography Enables Multiplexing of Immunoaffinity Enrichment of Peptides to Greater than 150 for Targeted MS-Based Assays. Anal Chem. 2016;88(15):7548-55. doi:10.1021/acs.analchem.6b00946.
Aptamer-Based Proteomic Profiling Reveals Novel Candidate Biomarkers and Pathways in Cardiovascular Disease.
Ngo D, Sinha S, Shen D, et al. Aptamer-Based Proteomic Profiling Reveals Novel Candidate Biomarkers and Pathways in Cardiovascular Disease. Circulation. 2016;134(4):270-85. doi:10.1161/CIRCULATIONAHA.116.021803.
Mitochondrial dysfunction remodels one-carbon metabolism in human cells.
Bao XRobert, Ong S-E, Goldberger O, et al. Mitochondrial dysfunction remodels one-carbon metabolism in human cells. Elife. 2016;5. doi:10.7554/eLife.10575.
Proteogenomics connects somatic mutations to signalling in breast cancer.
Mertins P, Mani DR, Ruggles KV, et al. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 2016;534(7605):55-62. doi:10.1038/nature18003.
Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes.
Abelin JG, Patel J, Lu X, et al. Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes. Mol Cell Proteomics. 2016;15(5):1622-41. doi:10.1074/mcp.M116.058354.
Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera.
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Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts.
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An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.
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Rps14 haploinsufficiency causes a block in erythroid differentiation mediated by S100A8 and S100A9.
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Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2.
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Responses to Bacteria, Virus, and Malaria Distinguish the Etiology of Pediatric Clinical Pneumonia.
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H2A.Z.1 Monoubiquitylation Antagonizes BRD2 to Maintain Poised Chromatin in ESCs.
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A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells.
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The extracellular matrix: Tools and insights for the "omics" era.
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Multiplexed Immunoaffinity Enrichment of Peptides with Anti-peptide Antibodies and Quantification by Stable Isotope Dilution Multiple Reaction Monitoring Mass Spectrometry.
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Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays.
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Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.
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Corrigendum: Selective killing of cancer cells by a small molecule targeting the stress response to ROS.
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Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis.
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Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase.
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Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.
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Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow.
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Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury.
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A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.
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Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS.
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On Credibility, Clarity, and Compliance.
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Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy.
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Kinase-Independent Small-Molecule Inhibition of JAK-STAT Signaling.
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Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator.
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Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.
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Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry.
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Antibody-based capture of target peptides in multiple reaction monitoring experiments.
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Prostate cancer. Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer.
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Proteogenomic characterization of human colon and rectal cancer.
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A framework for installable external tools in Skyline.
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Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver.
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Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging.
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CPTAC Assay Portal: a repository of targeted proteomic assays.
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Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense.
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Mycobacterial Esx-3 requires multiple components for iron acquisition.
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Simplified and efficient quantification of low-abundance proteins at very high multiplex via targeted mass spectrometry.
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High reliability in respiratory rate assessment in children with respiratory symptomatology in a rural area in Mozambique.
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Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters.
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Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.
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Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins.
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Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells.
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EMRE is an essential component of the mitochondrial calcium uniporter complex.
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Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies.
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High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.
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Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia.
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Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium.
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Large-scale identification of ubiquitination sites by mass spectrometry.
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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).
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Integrated proteomic analysis of post-translational modifications by serial enrichment.
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Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging.
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Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
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Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach.
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Complementary RNA and protein profiling identifies iron as a key regulator of mitochondrial biogenesis.
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Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry.
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Identification of Trypanosome proteins in plasma from African sleeping sickness patients infected with T. b. rhodesiense.
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Magnetic barcode assay for genetic detection of pathogens.
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H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions.
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Shotgun protein sequencing with meta-contig assembly.
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Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2.
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ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression.
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Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL.
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iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.
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Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma.
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Modification site localization scoring: strategies and performance.
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Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
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Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules.
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The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices.
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Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics.
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Quantitative assessment of ChIP-grade antbodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules
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Comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers.
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A face in the crowd: recognizing peptides through database search.
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Mutations in MTFMT underlie a human disorder of formylation causing impaired mitochondrial translation.
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STK33 kinase activity is nonessential in KRAS-dependent cancer cells.
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Clustering with position-specific constraints on variance: applying redescending M-estimators to label-free LC-MS data analysis.
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Status and prospects for discovery and verification of new biomarkers of cardiovascular disease by proteomics.
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Quantification of proteins using peptide immunoaffinity enrichment coupled with mass spectrometry.
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Exoplasmic cysteine Cys384 of the HDL receptor SR-BI is critical for its sensitivity to a small-molecule inhibitor and normal lipid transport activity.
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Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry.
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Rictor phosphorylation on the Thr-1135 site does not require mammalian target of rapamycin complex 2.
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Optimizing performance of glycopeptide capture for plasma proteomics.
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Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry.
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Integration of proteomic-based tools for improved biomarkers of myocardial injury.
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Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry.
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Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.
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Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA interagency oncology task force on molecular diagnostics.
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Protein-based multiplex assays: mock presubmissions to the US Food and Drug Administration.
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Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.
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Introduction: Advances in protein analysis for the clinical laboratory.
Hortin GL, Carr SA, N Anderson L. Introduction: Advances in protein analysis for the clinical laboratory. Clin Chem. 2010;56(2):149-51. doi:10.1373/clinchem.2009.132803.
A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint.
van Vugt MATM, Gardino AK, Linding R, et al. A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint. PLoS Biol. 2010;8(1):e1000287. doi:10.1371/journal.pbio.1000287.
ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth.
Markljung E, Jiang L, Jaffe JD, et al. ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. PLoS Biol. 2009;7(12):e1000256. doi:10.1371/journal.pbio.1000256.
Empirical Bayes analysis of quantitative proteomics experiments.
Margolin AA, Ong S-E, Schenone M, et al. Empirical Bayes analysis of quantitative proteomics experiments. PLoS One. 2009;4(10):e7454. doi:10.1371/journal.pone.0007454.
Proteomic and genetic approaches identify Syk as an AML target.
Hahn CK, Berchuck JE, Ross KN, et al. Proteomic and genetic approaches identify Syk as an AML target. Cancer Cell. 2009;16(4):281-94. doi:10.1016/j.ccr.2009.08.018.
Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution.
Keshishian H, Addona T, Burgess M, et al. Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics. 2009;8(10):2339-49. doi:10.1074/mcp.M900140-MCP200.
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma.
Addona TA, Abbatiello SE, Schilling B, et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol. 2009;27(7):633-41. doi:10.1038/nbt.1546.
Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx).
Rudomin EL, Carr SA, Jaffe JD. Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx). J Proteome Res. 2009;8(6):3154-60. doi:10.1021/pr801017a.
Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry.
Kuhn E, Addona T, Keshishian H, et al. Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin Chem. 2009;55(6):1108-17. doi:10.1373/clinchem.2009.123935.
Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells.
Burkard ME, Maciejowski J, Rodriguez-Bravo V, et al. Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells. PLoS Biol. 2009;7(5):e1000111. doi:10.1371/journal.pbio.1000111.
A human proteome detection and quantitation project.
N Anderson L, Anderson NG, Pearson TW, et al. A human proteome detection and quantitation project. Mol Cell Proteomics. 2009;8(5):883-6. doi:10.1074/mcp.R800015-MCP200.
Identifying the proteins to which small-molecule probes and drugs bind in cells.
Ong S-E, Schenone M, Margolin AA, et al. Identifying the proteins to which small-molecule probes and drugs bind in cells. Proc Natl Acad Sci U S A. 2009;106(12):4617-22. doi:10.1073/pnas.0900191106.
Prediction of high-responding peptides for targeted protein assays by mass spectrometry.
Fusaro VA, Mani DR, Mesirov JP, Carr SA. Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol. 2009;27(2):190-8. doi:10.1038/nbt.1524.
Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy.
Du J, Bernasconi P, Clauser KR, et al. Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy. Nat Biotechnol. 2009;27(1):77-83. doi:10.1038/nbt.1513.
Protein quantitation through targeted mass spectrometry: the way out of biomarker purgatory?
Carr SA, Anderson L. Protein quantitation through targeted mass spectrometry: the way out of biomarker purgatory?. Clin Chem. 2008;54(11):1749-52. doi:10.1373/clinchem.2008.114686.
Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury.
Lewis GD, Wei R, Liu E, et al. Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury. J Clin Invest. 2008;118(10):3503-12. doi:10.1172/JCI35111.
Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification.
Jaffe JD, Keshishian H, Chang B, Addona TA, Gillette MA, Carr SA. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification. Mol Cell Proteomics. 2008;7(10):1952-62. doi:10.1074/mcp.M800218-MCP200.
A mitochondrial protein compendium elucidates complex I disease biology.
Pagliarini DJ, Calvo SE, Chang B, et al. A mitochondrial protein compendium elucidates complex I disease biology. Cell. 2008;134(1):112-23. doi:10.1016/j.cell.2008.06.016.
Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity.
Shaham O, Wei R, Wang TJ, et al. Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity. Mol Syst Biol. 2008;4:214. doi:10.1038/msb.2008.50.
Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution.
Keshishian H, Addona T, Burgess M, Kuhn E, Carr SA. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics. 2007;6(12):2212-29. doi:10.1074/mcp.M700354-MCP200.
Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate.
Lowery DM, Clauser KR, Hjerrild M, et al. Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate. EMBO J. 2007;26(9):2262-73. doi:10.1038/sj.emboj.7601683.
PRAS40 is an insulin-regulated inhibitor of the mTORC1 protein kinase.
Sancak Y, Thoreen CC, Peterson TR, et al. PRAS40 is an insulin-regulated inhibitor of the mTORC1 protein kinase. Mol Cell. 2007;25(6):903-15. doi:10.1016/j.molcel.2007.03.003.
PEPPeR, a platform for experimental proteomic pattern recognition.
Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA. PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics. 2006;5(10):1927-41. doi:10.1074/mcp.M600222-MCP200.
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.
Lamb J, Crawford ED, Peck D, et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006;313(5795):1929-35. doi:10.1126/science.1132939.
mSin1 is necessary for Akt/PKB phosphorylation, and its isoforms define three distinct mTORC2s.
Frias MA, Thoreen CC, Jaffe JD, et al. mSin1 is necessary for Akt/PKB phosphorylation, and its isoforms define three distinct mTORC2s. Curr Biol. 2006;16(18):1865-70. doi:10.1016/j.cub.2006.08.001.
Protein biomarker discovery and validation: the long and uncertain path to clinical utility.
Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol. 2006;24(8):971-83. doi:10.1038/nbt1235.
Systematic identification of human mitochondrial disease genes through integrative genomics.
Calvo S, Jain M, Xie X, et al. Systematic identification of human mitochondrial disease genes through integrative genomics. Nat Genet. 2006;38(5):576-82. doi:10.1038/ng1776.
Mapping posttranslational modifications of proteins by MS-based selective detection: application to phosphoproteomics.
Carr SA, Annan RS, Huddleston MJ. Mapping posttranslational modifications of proteins by MS-based selective detection: application to phosphoproteomics. Methods in enzymology. 2005;405:82-115. doi:10.1016/S0076-6879(05)05005-6.
Place of pattern in proteomic biomarker discovery.
Gillette MA, Mani DR, Carr SA. Place of pattern in proteomic biomarker discovery. J Proteome Res. 2005;4(4):1143-54. doi:10.1021/pr0500962.
Selective detection of glycopeptides on ion trap mass spectrometers.
Sullivan B, Addona TA, Carr SA. Selective detection of glycopeptides on ion trap mass spectrometers. Anal Chem. 2004;76(11):3112-8. doi:10.1021/ac035427d.