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Proteomics

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.
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.
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.
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.
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.
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.
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.
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.
Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts.
Tabb DL, Wang X, Carr SA, et al. Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts. J Proteome Res. 2016;15(3):691-706. doi:10.1021/acs.jproteome.5b00859.
Rps14 haploinsufficiency causes a block in erythroid differentiation mediated by S100A8 and S100A9.
Schneider RK, Schenone M, Ferreira MVentura, et al. Rps14 haploinsufficiency causes a block in erythroid differentiation mediated by S100A8 and S100A9. Nat Med. 2016;22(3):288-97. doi:10.1038/nm.4047.
Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2.
Hung V, Udeshi ND, Lam SS, et al. Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. Nat Protoc. 2016;11(3):456-75. doi:10.1038/nprot.2016.018.
An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.
Ruggles KV, Tang Z, Wang X, et al. An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer. Mol Cell Proteomics. 2016;15(3):1060-71. doi:10.1074/mcp.M115.056226.
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.
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.
A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells.
Jolly AL, Luan C-H, Dusel BE, et al. A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells. Cell Rep. 2016;14(3):611-20. doi:10.1016/j.celrep.2015.12.051.
The extracellular matrix: Tools and insights for the "omics" era.
Naba A, Clauser KR, Ding H, Whittaker CA, Carr SA, Hynes RO. The extracellular matrix: Tools and insights for the "omics" era. Matrix Biol. 2016;49:10-24. doi:10.1016/j.matbio.2015.06.003.
Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays.
Hoofnagle AN, Whiteaker JR, Carr SA, et al. Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays. Clin Chem. 2016;62(1):48-69. doi:10.1373/clinchem.2015.250563.
Responses to Bacteria, Virus, and Malaria Distinguish the Etiology of Pediatric Clinical Pneumonia.
Valim C, Ahmad R, Lanaspa M, et al. Responses to Bacteria, Virus, and Malaria Distinguish the Etiology of Pediatric Clinical Pneumonia. Am J Respir Crit Care Med. 2016;193(4):448-59. doi:10.1164/rccm.201506-1100OC.
H2A.Z.1 Monoubiquitylation Antagonizes BRD2 to Maintain Poised Chromatin in ESCs.
Surface LE, Fields PA, Subramanian V, et al. H2A.Z.1 Monoubiquitylation Antagonizes BRD2 to Maintain Poised Chromatin in ESCs. Cell Rep. 2016;14(5):1142-55. doi:10.1016/j.celrep.2015.12.100.
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.
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.
Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera.
De Marchi T, Kuhn E, Dekker LJ, et al. Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera. J Proteome Res. 2016;15(4):1230-42. doi:10.1021/acs.jproteome.5b01119.
Multiplexed Immunoaffinity Enrichment of Peptides with Anti-peptide Antibodies and Quantification by Stable Isotope Dilution Multiple Reaction Monitoring Mass Spectrometry.
Kuhn E, Carr SA. Multiplexed Immunoaffinity Enrichment of Peptides with Anti-peptide Antibodies and Quantification by Stable Isotope Dilution Multiple Reaction Monitoring Mass Spectrometry. Methods Mol Biol. 2016;1410:135-67. doi:10.1007/978-1-4939-3524-6_9.
Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.
Whiteaker JR, Halusa GN, Hoofnagle AN, et al. Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays. Methods Mol Biol. 2016;1410:223-36. doi:10.1007/978-1-4939-3524-6_13.
Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase.
Chen C-L, Hu Y, Udeshi ND, et al. Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase. Proc Natl Acad Sci U S A. 2015;112(39):12093-8. doi:10.1073/pnas.1515623112.
Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury.
Keshishian H, Burgess MW, Gillette MA, et al. Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury. Mol Cell Proteomics. 2015;14(9):2375-93. doi:10.1074/mcp.M114.046813.
Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.
Abbatiello SE, Schilling B, Mani DR, et al. Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Mol Cell Proteomics. 2015;14(9):2357-74. doi:10.1074/mcp.M114.047050.
Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow.
Svinkina T, Gu H, Silva JC, et al. Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow. Mol Cell Proteomics. 2015;14(9):2429-40. doi:10.1074/mcp.O114.047555.
Corrigendum: Selective killing of cancer cells by a small molecule targeting the stress response to ROS.
Raj L, Ide T, Gurkar AU, et al. Corrigendum: Selective killing of cancer cells by a small molecule targeting the stress response to ROS. Nature. 2015;526(7574):596. doi:10.1038/nature15370.
Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis.
Kroksveen AC, Jaffe JD, Aasebø E, et al. Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis. Proteomics. 2015;15(19):3361-9. doi:10.1002/pmic.201400142.
Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.
Jovanovic M, Rooney MS, Mertins P, et al. Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens. Science. 2015;347(6226):1259038. doi:10.1126/science.1259038.
Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy.
Begun J, Lassen KG, Jijon HB, et al. Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy. Cell Rep. 2015;11(12):1905-18. doi:10.1016/j.celrep.2015.05.045.
Kinase-Independent Small-Molecule Inhibition of JAK-STAT Signaling.
Chou DHung-Chieh, Vetere A, Choudhary A, et al. Kinase-Independent Small-Molecule Inhibition of JAK-STAT Signaling. J Am Chem Soc. 2015;137(24):7929-34. doi:10.1021/jacs.5b04284.
Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator.
Maier VK, Feeney CM, Taylor JE, et al. Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator. Mol Cell Proteomics. 2015;14(6):1435-46. doi:10.1074/mcp.M114.044586.
A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.
Parnas O, Jovanovic M, Eisenhaure TM, et al. A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks. Cell. 2015;162(3):675-86. doi:10.1016/j.cell.2015.06.059.
Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS.
Krönke J, Fink EC, Hollenbach PW, et al. Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS. Nature. 2015;523(7559):183-8. doi:10.1038/nature14610.
On Credibility, Clarity, and Compliance.
Burlingame AL, Carr SA, Bradshaw RA, Chalkley RJ. On Credibility, Clarity, and Compliance. Mol Cell Proteomics. 2015;14(7):1731-3. doi:10.1074/mcp.E115.052506.
Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry.
Creech AL, Taylor JE, Maier VK, et al. Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry. Methods. 2015;72:57-64. doi:10.1016/j.ymeth.2014.10.033.
Antibody-based capture of target peptides in multiple reaction monitoring experiments.
De Marchi T, Kuhn E, Carr SA, Umar A. Antibody-based capture of target peptides in multiple reaction monitoring experiments. Methods Mol Biol. 2015;1293:123-35. doi:10.1007/978-1-4939-2519-3_7.
Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters.
Naba A, Clauser KR, Lamar JM, Carr SA, Hynes RO. Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters. eLife. 2014;3:e01308.
Proteogenomic characterization of human colon and rectal cancer.
Zhang B, Wang J, Wang X, et al. Proteogenomic characterization of human colon and rectal cancer. Nature. 2014;513(7518):382-7. doi:10.1038/nature13438.
A framework for installable external tools in Skyline.
Broudy D, Killeen T, Choi M, et al. A framework for installable external tools in Skyline. Bioinformatics. 2014;30(17):2521-3. doi:10.1093/bioinformatics/btu148.
Prostate cancer. Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer.
Theurillat J-PP, Udeshi ND, Errington WJ, et al. Prostate cancer. Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer. Science. 2014;346(6205):85-9. doi:10.1126/science.1250255.
Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense.
Lassen KG, Kuballa P, Conway KL, et al. Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense. Proc Natl Acad Sci U S A. 2014;111(21):7741-6. doi:10.1073/pnas.1407001111.
Mycobacterial Esx-3 requires multiple components for iron acquisition.
M Siegrist S, Steigedal M, Ahmad R, et al. Mycobacterial Esx-3 requires multiple components for iron acquisition. MBio. 2014;5(3):e01073-14. doi:10.1128/mBio.01073-14.
Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.
Carr SA, Abbatiello SE, Ackermann BL, et al. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics. 2014;13(3):907-17. doi:10.1074/mcp.M113.036095.
Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver.
Naba A, Clauser KR, Whittaker CA, Carr SA, Tanabe KK, Hynes RO. Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver. BMC Cancer. 2014;14:518. doi:10.1186/1471-2407-14-518.
Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging.
Hung V, Zou P, Rhee H-W, et al. Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging. Mol Cell. 2014;55(2):332-41. doi:10.1016/j.molcel.2014.06.003.
CPTAC Assay Portal: a repository of targeted proteomic assays.
Whiteaker JR, Halusa GN, Hoofnagle AN, et al. CPTAC Assay Portal: a repository of targeted proteomic assays. Nat Methods. 2014;11(7):703-4. doi:10.1038/nmeth.3002.
Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells.
Krönke J, Udeshi ND, Narla A, et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science. 2014;343(6168):301-5. doi:10.1126/science.1244851.
Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins.
Kennedy JJ, Abbatiello SE, Kim K, et al. Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Nat Methods. 2014;11(2):149-55. doi:10.1038/nmeth.2763.
High reliability in respiratory rate assessment in children with respiratory symptomatology in a rural area in Mozambique.
Lanaspa M, Valim C, Acácio S, et al. High reliability in respiratory rate assessment in children with respiratory symptomatology in a rural area in Mozambique. J Trop Pediatr. 2014;60(2):93-8. doi:10.1093/tropej/fmt081.
Simplified and efficient quantification of low-abundance proteins at very high multiplex via targeted mass spectrometry.
Burgess MW, Keshishian H, Mani DR, Gillette MA, Carr SA. Simplified and efficient quantification of low-abundance proteins at very high multiplex via targeted mass spectrometry. Mol Cell Proteomics. 2014;13(4):1137-49. doi:10.1074/mcp.M113.034660.
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).
Abbatiello SE, Mani DR, Schilling B, 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). Mol Cell Proteomics. 2013;12(9):2623-39. doi:10.1074/mcp.M112.027078.
Large-scale identification of ubiquitination sites by mass spectrometry.
Udeshi ND, Mertins P, Svinkina T, Carr SA. Large-scale identification of ubiquitination sites by mass spectrometry. Nat Protoc. 2013;8(10):1950-60. doi:10.1038/nprot.2013.120.
Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium.
Ellis MJ, Gillette M, Carr SA, et al. Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium. Cancer Discov. 2013;3(10):1108-12. doi:10.1158/2159-8290.CD-13-0219.
Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia.
Jaffe JD, Wang Y, Chan HMan, et al. Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia. Nat Genet. 2013;45(11):1386-91. doi:10.1038/ng.2777.
Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging.
Rhee H-W, Zou P, Udeshi ND, et al. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science. 2013;339(6125):1328-31. doi:10.1126/science.1230593.
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.
Udeshi ND, Svinkina T, Mertins P, et al. 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. Mol Cell Proteomics. 2013;12(3):825-31. doi:10.1074/mcp.O112.027094.
Integrated proteomic analysis of post-translational modifications by serial enrichment.
Mertins P, Qiao JW, Patel J, et al. Integrated proteomic analysis of post-translational modifications by serial enrichment. Nat Methods. 2013;10(7):634-7. doi:10.1038/nmeth.2518.
Complementary RNA and protein profiling identifies iron as a key regulator of mitochondrial biogenesis.
Rensvold JW, Ong S-E, Jeevananthan A, Carr SA, Mootha VK, Pagliarini DJ. Complementary RNA and protein profiling identifies iron as a key regulator of mitochondrial biogenesis. Cell Rep. 2013;3(1):237-45. doi:10.1016/j.celrep.2012.11.029.
Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry.
Gillette MA, Carr SA. Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat Methods. 2013;10(1):28-34. doi:10.1038/nmeth.2309.
Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach.
Lee MN, Roy M, Ong S-E, et al. Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach. Nat Immunol. 2013;14(2):179-85. doi:10.1038/ni.2509.
EMRE is an essential component of the mitochondrial calcium uniporter complex.
Sancak Y, Markhard AL, Kitami T, et al. EMRE is an essential component of the mitochondrial calcium uniporter complex. Science. 2013;342(6164):1379-82. doi:10.1126/science.1242993.
Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies.
Skates SJ, Gillette MA, LaBaer J, et al. Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies. J Proteome Res. 2013;12(12):5383-94. doi:10.1021/pr400132j.
High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.
Schwartz S, Agarwala SD, Mumbach MR, et al. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell. 2013;155(6):1409-21. doi:10.1016/j.cell.2013.10.047.
Identification of Trypanosome proteins in plasma from African sleeping sickness patients infected with T. b. rhodesiense.
Eyford BA, Ahmad R, Enyaru JC, Carr SA, Pearson TW. Identification of Trypanosome proteins in plasma from African sleeping sickness patients infected with T. b. rhodesiense. PLoS One. 2013;8(8):e71463. doi:10.1371/journal.pone.0071463.
Magnetic barcode assay for genetic detection of pathogens.
Liong M, Hoang AN, Chung J, et al. Magnetic barcode assay for genetic detection of pathogens. Nat Commun. 2013;4:1752. doi:10.1038/ncomms2745.
Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2.
Greulich H, Kaplan B, Mertins P, et al. Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2. Proc Natl Acad Sci U S A. 2012;109(36):14476-81. doi:10.1073/pnas.1203201109.
H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions.
Ku M, Jaffe JD, Koche RP, et al. H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions. Genome Biol. 2012;13(10):R85. doi:10.1186/gb-2012-13-10-r85.
Shotgun protein sequencing with meta-contig assembly.
Guthals A, Clauser KR, Bandeira N. Shotgun protein sequencing with meta-contig assembly. Mol Cell Proteomics. 2012;11(10):1084-96. doi:10.1074/mcp.M111.015768.
Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules.
Peach SE, Rudomin EL, Udeshi ND, Carr SA, Jaffe JD. Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. Mol Cell Proteomics. 2012;11(5):128-37. doi:10.1074/mcp.M111.015941.
Modification site localization scoring: strategies and performance.
Chalkley RJ, Clauser KR. Modification site localization scoring: strategies and performance. Mol Cell Proteomics. 2012;11(5):3-14. doi:10.1074/mcp.R111.015305.
Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
Udeshi ND, Mani DR, Eisenhaure T, et al. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol Cell Proteomics. 2012;11(5):148-59. doi:10.1074/mcp.M111.016857.
Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma.
Kuhn E, Whiteaker JR, Mani DR, et al. Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol Cell Proteomics. 2012;11(6):M111.013854. doi:10.1074/mcp.M111.013854.
iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.
Mertins P, Udeshi ND, Clauser KR, et al. iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics. Mol Cell Proteomics. 2012;11(6):M111.014423. doi:10.1074/mcp.M111.014423.
ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression.
Abdel-Wahab O, Adli M, LaFave LM, et al. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell. 2012;22(2):180-93. doi:10.1016/j.ccr.2012.06.032.
Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL.
Wen Q, Goldenson B, Silver SJ, et al. Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL. Cell. 2012;150(3):575-89. doi:10.1016/j.cell.2012.06.032.
The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices.
Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, Hynes RO. The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices. Mol Cell Proteomics. 2012;11(4):M111.014647. doi:10.1074/mcp.M111.014647.
Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics.
Mani DR, Abbatiello SE, Carr SA. Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics. BMC Bioinformatics. 2012;13 Suppl 16:S9. doi:10.1186/1471-2105-13-S16-S9.
Quantitative assessment of ChIP-grade antbodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules
Peach SE, Rudomin EL, Udeshi ND, Carr SA, Jaffe JD. Quantitative assessment of ChIP-grade antbodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. Molecular & Cellular Proteomics. 2012.
Mutations in MTFMT underlie a human disorder of formylation causing impaired mitochondrial translation.
Tucker EJ, Hershman SG, Köhrer C, et al. Mutations in MTFMT underlie a human disorder of formylation causing impaired mitochondrial translation. Cell Metab. 2011;14(3):428-34. doi:10.1016/j.cmet.2011.07.010.
STK33 kinase activity is nonessential in KRAS-dependent cancer cells.
Babij C, Zhang Y, Kurzeja RJ, et al. STK33 kinase activity is nonessential in KRAS-dependent cancer cells. Cancer Res. 2011;71(17):5818-26. doi:10.1158/0008-5472.CAN-11-0778.
Comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers.
Burgener A, Rahman S, Ahmad R, et al. Comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers. J Proteome Res. 2011;10(11):5139-49. doi:10.1021/pr200596r.
A face in the crowd: recognizing peptides through database search.
Eng JK, Searle BC, Clauser KR, Tabb DL. A face in the crowd: recognizing peptides through database search. Mol Cell Proteomics. 2011;10(11):R111.009522. doi:10.1074/mcp.R111.009522.
Quantification of proteins using peptide immunoaffinity enrichment coupled with mass spectrometry.
Zhao L, Whiteaker JR, Pope ME, et al. Quantification of proteins using peptide immunoaffinity enrichment coupled with mass spectrometry. J Vis Exp. 2011;(53). doi:10.3791/2812.
Exoplasmic cysteine Cys384 of the HDL receptor SR-BI is critical for its sensitivity to a small-molecule inhibitor and normal lipid transport activity.
Yu M, Romer KA, Nieland TJF, et al. Exoplasmic cysteine Cys384 of the HDL receptor SR-BI is critical for its sensitivity to a small-molecule inhibitor and normal lipid transport activity. Proc Natl Acad Sci U S A. 2011;108(30):12243-8. doi:10.1073/pnas.1109078108.
Clustering with position-specific constraints on variance: applying redescending M-estimators to label-free LC-MS data analysis.
Frühwirth R, Mani DR, Pyne S. Clustering with position-specific constraints on variance: applying redescending M-estimators to label-free LC-MS data analysis. BMC Bioinformatics. 2011;12:358. doi:10.1186/1471-2105-12-358.
Status and prospects for discovery and verification of new biomarkers of cardiovascular disease by proteomics.
Gerszten RE, Asnani A, Carr SA. Status and prospects for discovery and verification of new biomarkers of cardiovascular disease by proteomics. Circ Res. 2011;109(4):463-74. doi:10.1161/CIRCRESAHA.110.225003.
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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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.
Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry.
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Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.
Paulovich AG, Billheimer D, Ham A-JL, et al. Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Mol Cell Proteomics. 2010;9(2):242-54. doi:10.1074/mcp.M900222-MCP200.
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.
Integration of proteomic-based tools for improved biomarkers of myocardial injury.
Gerszten RE, Carr SA, Sabatine M. Integration of proteomic-based tools for improved biomarkers of myocardial injury. Clin Chem. 2010;56(2):194-201. doi:10.1373/clinchem.2009.127878.
Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry.
Abbatiello SE, Mani DR, Keshishian H, Carr SA. Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry. Clin Chem. 2010;56(2):291-305. doi:10.1373/clinchem.2009.138420.
Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.
Rudnick PA, Clauser KR, Kilpatrick LE, et al. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol Cell Proteomics. 2010;9(2):225-41. doi:10.1074/mcp.M900223-MCP200.
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.
Regnier FE, Skates SJ, Mesri M, et al. Protein-based multiplex assays: mock presubmissions to the US Food and Drug Administration. Clin Chem. 2010;56(2):165-71. doi:10.1373/clinchem.2009.140087.
Optimizing performance of glycopeptide capture for plasma proteomics.
Berven FS, Ahmad R, Clauser KR, Carr SA. Optimizing performance of glycopeptide capture for plasma proteomics. J Proteome Res. 2010;9(4):1706-15. doi:10.1021/pr900845m.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.