Recent Publications

Proteomics

Huntingtin turnover: modulation of huntingtin degradation by cAMP-dependent protein kinase A (PKA) phosphorylation of C-HEAT domain Ser2550.

Lee Y, Kim H, Barker D, et al. Huntingtin turnover: modulation of huntingtin degradation by cAMP-dependent protein kinase A (PKA) phosphorylation of C-HEAT domain Ser2550. Hum Mol Genet. 2022. doi:10.1093/hmg/ddac165.

Transcription factor Acj6 controls dendrite targeting via a combinatorial cell-surface code.

Xie Q, Li J, Li H, et al. Transcription factor Acj6 controls dendrite targeting via a combinatorial cell-surface code. Neuron. 2022;110(14):2299-2314.e8. doi:10.1016/j.neuron.2022.04.026.

Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma.

Lee PC, Klaeger S, Le PM, et al. Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma. J Clin Invest. 2022;132(13). doi:10.1172/JCI151666.

Proteomics and Population Biology in the Cardiovascular Health Study (CHS): design of a study with mentored access and active data sharing.

Austin TR, McHugh CP, Brody JA, et al. Proteomics and Population Biology in the Cardiovascular Health Study (CHS): design of a study with mentored access and active data sharing. Eur J Epidemiol. 2022;37(7):755-765. doi:10.1007/s10654-022-00888-z.

Degradation of GSPT1 causes TP53-independent cell death in leukemia whilst sparing normal hematopoietic stem cells.

Sellar RS, Sperling AS, Słabicki M, et al. Degradation of GSPT1 causes TP53-independent cell death in leukemia whilst sparing normal hematopoietic stem cells. J Clin Invest. 2022. doi:10.1172/JCI153514.

The Parkinson's disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability.

Hallacli E, Kayatekin C, Nazeen S, et al. The Parkinson's disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability. Cell. 2022;185(12):2035-2056.e33. doi:10.1016/j.cell.2022.05.008.

RNF43 G659fs is an oncogenic colorectal cancer mutation and sensitizes tumor cells to PI3K/mTOR inhibition.

Fang L, Ford-Roshon D, Russo M, et al. RNF43 G659fs is an oncogenic colorectal cancer mutation and sensitizes tumor cells to PI3K/mTOR inhibition. Nat Commun. 2022;13(1):3181. doi:10.1038/s41467-022-30794-7.

Brain-specific deletion of GIT1 impairs cognition and alters phosphorylation of synaptic protein networks implicated in schizophrenia susceptibility.

Fass DM, Lewis MC, Ahmad R, et al. Brain-specific deletion of GIT1 impairs cognition and alters phosphorylation of synaptic protein networks implicated in schizophrenia susceptibility. Mol Psychiatry. 2022. doi:10.1038/s41380-022-01557-z.

Landscape of helper and regulatory antitumour CD4 T cells in melanoma.

Oliveira G, Stromhaug K, Cieri N, et al. Landscape of helper and regulatory antitumour CD4 T cells in melanoma. Nature. 2022;605(7910):532-538. doi:10.1038/s41586-022-04682-5.

A bidirectional switch in the Shank3 phosphorylation state biases synapses toward up- or downscaling.

Wu C-H, Tatavarty V, Beltran PMJean, et al. A bidirectional switch in the Shank3 phosphorylation state biases synapses toward up- or downscaling. Elife. 2022;11. doi:10.7554/eLife.74277.

Cancer proteogenomics: current impact and future prospects.

Mani DR, Krug K, Zhang B, et al. Cancer proteogenomics: current impact and future prospects. Nat Rev Cancer. 2022. doi:10.1038/s41568-022-00446-5.

BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes.

Schaefer EJ, Wang HC, Karp HQ, et al. BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes. Blood Cancer Discov. 2022;3(2):116-135. doi:10.1158/2643-3230.BCD-21-0115.

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer.

Ouspenskaia T, Law T, Clauser KR, et al. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nat Biotechnol. 2022;40(2):209-217. doi:10.1038/s41587-021-01021-3.

PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation.

Khadka P, Reitman ZJ, Lu S, et al. PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation. Nat Commun. 2022;13(1):604. doi:10.1038/s41467-022-28198-8.

A Congenital Anemia Reveals Distinct Targeting Mechanisms for Master Transcription Factor GATA1.

Ludwig L, Lareau CA, Bao EL, et al. A Congenital Anemia Reveals Distinct Targeting Mechanisms for Master Transcription Factor GATA1. Blood. 2022. doi:10.1182/blood.2021013753.

Identification of RIOK2 as a master regulator of human blood cell development.

Ghosh S, Raundhal M, Myers SA, et al. Identification of RIOK2 as a master regulator of human blood cell development. Nat Immunol. 2022;23(1):109-121. doi:10.1038/s41590-021-01079-w.

Proximity-Labeling Reveals Novel Host and Parasite Proteins at the Parasitophorous Vacuole Membrane.

Cygan AM, Beltran PMJean, Mendoza AG, et al. Proximity-Labeling Reveals Novel Host and Parasite Proteins at the Parasitophorous Vacuole Membrane. mBio. 2021;12(6):e0026021. doi:10.1128/mBio.00260-21.

Multiomic characterization of oncogenic signaling mediated by wild-type and mutant RIT1.

Lo A, Holmes K, Kamlapurkar S, et al. Multiomic characterization of oncogenic signaling mediated by wild-type and mutant RIT1. Sci Signal. 2021;14(711):eabc4520. doi:10.1126/scisignal.abc4520.

Genomic Profiling of Lung Adenocarcinoma in Never-Smokers.

Devarakonda S, Li Y, Rodrigues FMartins, et al. Genomic Profiling of Lung Adenocarcinoma in Never-Smokers. J Clin Oncol. 2021;39(33):3747-3758. doi:10.1200/JCO.21.01691.

Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment.

Rivera KD, Olive ME, Bergstrom EJ, et al. Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment. Mol Cell Proteomics. 2021:100154. doi:10.1016/j.mcpro.2021.100154.

Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Cao L, Huang C, Zhou DCui, et al. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell. 2021;184(19):5031-5052.e26. doi:10.1016/j.cell.2021.08.023.

is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing.

Beauchamp EM, Leventhal M, Bernard E, et al. is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing. Blood Cancer Discov. 2021;2(5):500-517. doi:10.1158/2643-3230.BCD-20-0224.

A highly multiplexed quantitative phosphosite assay for biology and preclinical studies.

Keshishian H, E McDonald R, Mundt F, et al. A highly multiplexed quantitative phosphosite assay for biology and preclinical studies. Mol Syst Biol. 2021;17(9):e10156. doi:10.15252/msb.202010156.

Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds.

Dele-Oni DO, Christianson KE, Egri SB, et al. Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds. Sci Data. 2021;8(1):226. doi:10.1038/s41597-021-01008-4.

An engineered transcriptional reporter of protein localization identifies regulators of mitochondrial and ER membrane protein trafficking in high-throughput CRISPRi screens.

Coukos R, Yao D, Sanchez MI, et al. An engineered transcriptional reporter of protein localization identifies regulators of mitochondrial and ER membrane protein trafficking in high-throughput CRISPRi screens. Elife. 2021;10. doi:10.7554/eLife.69142.

Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery.

Qin W, Myers SA, Carey DK, Carr SA, Ting AY. Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery. Nat Commun. 2021;12(1):4980. doi:10.1038/s41467-021-25259-2.

Optimized liquid and gas phase fractionation increases HLA-peptidome coverage for primary cell and tissue samples.

Klaeger S, Apffel A, Clauser KR, et al. Optimized liquid and gas phase fractionation increases HLA-peptidome coverage for primary cell and tissue samples. Mol Cell Proteomics. 2021:100133. doi:10.1016/j.mcpro.2021.100133.

Phenotype, specificity and avidity of antitumour CD8 T cells in melanoma.

Oliveira G, Stromhaug K, Klaeger S, et al. Phenotype, specificity and avidity of antitumour CD8 T cells in melanoma. Nature. 2021;596(7870):119-125. doi:10.1038/s41586-021-03704-y.

Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling.

Whiteaker JR, Sharma K, Hoffman MA, et al. Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Cell Rep Methods. 2021;1(3). doi:10.1016/j.crmeth.2021.100015.

Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs.

Weingarten-Gabbay S, Klaeger S, Sarkizova S, et al. Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs. Cell. 2021;184(15):3962-3980.e17. doi:10.1016/j.cell.2021.05.046.

Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase.

Garvie CW, Wu X, Papanastasiou M, et al. Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase. Nat Commun. 2021;12(1):4375. doi:10.1038/s41467-021-24495-w.

STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma.

Adane B, Alexe G, Seong BKyung A, et al. STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma. Cancer Cell. 2021;39(6):827-844.e10. doi:10.1016/j.ccell.2021.05.007.

Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics.

Wilhelm M, Zolg DP, Graber M, et al. Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics. Nat Commun. 2021;12(1):3346. doi:10.1038/s41467-021-23713-9.

Identification of a Novel Regulator of Clostridioides difficile Cortex Formation.

Touchette MH, de la Puebla HBenito, Feliciano CAlves, et al. Identification of a Novel Regulator of Clostridioides difficile Cortex Formation. mSphere. 2021:e0021121. doi:10.1128/mSphere.00211-21.

Human plasma proteomic profiles indicative of cardiorespiratory fitness.

Robbins JM, Peterson B, Schranner D, et al. Human plasma proteomic profiles indicative of cardiorespiratory fitness. Nat Metab. 2021. doi:10.1038/s42255-021-00400-z.

PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis.

Mani DR, Maynard M, Kothadia R, et al. PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis. Nat Methods. 2021. doi:10.1038/s41592-021-01176-6.

Cell-specific transcriptional control of mitochondrial metabolism by TIF1γ drives erythropoiesis.

Rossmann MP, Hoi K, Chan V, et al. Cell-specific transcriptional control of mitochondrial metabolism by TIF1γ drives erythropoiesis. Science. 2021;372(6543):716-721. doi:10.1126/science.aaz2740.

Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity.

Griffin GK, Wu J, Iracheta-Vellve A, et al. Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity. Nature. 2021. doi:10.1038/s41586-021-03520-4.

Avadomide induces degradation of ZMYM2 fusion oncoproteins in hematologic malignancies.

Renneville A, Gasser JA, Grinshpun DE, et al. Avadomide induces degradation of ZMYM2 fusion oncoproteins in hematologic malignancies. Blood Cancer Discov. 2021;2(3):250-265. doi:10.1158/2643-3230.bcd-20-0105.

Proteomics of protein trafficking by in vivo tissue-specific labeling.

Droujinine IA, Meyer AS, Wang D, et al. Proteomics of protein trafficking by in vivo tissue-specific labeling. Nat Commun. 2021;12(1):2382. doi:10.1038/s41467-021-22599-x.

Suppression of pancreatic ductal adenocarcinoma growth and metastasis by fibrillar collagens produced selectively by tumor cells.

Tian C, Huang Y, Clauser KR, et al. Suppression of pancreatic ductal adenocarcinoma growth and metastasis by fibrillar collagens produced selectively by tumor cells. Nat Commun. 2021;12(1):2328. doi:10.1038/s41467-021-22490-9.

Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias.

Raundhal M, Ghosh S, Myers SA, et al. Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias. Nat Immunol. 2021;22(4):520-529. doi:10.1038/s41590-021-00895-4.

Proteomic profiling reveals biomarkers and pathways in type 2 diabetes risk.

Ngo D, Benson MD, Long JZ, et al. Proteomic profiling reveals biomarkers and pathways in type 2 diabetes risk. JCI Insight. 2021;6(5). doi:10.1172/jci.insight.144392.

Biomarkers to distinguish bacterial from viral pediatric clinical pneumonia in a malaria endemic setting.

Gillette MA, Mani DR, Uschnig C, et al. Biomarkers to distinguish bacterial from viral pediatric clinical pneumonia in a malaria endemic setting. Clin Infect Dis. 2021. doi:10.1093/cid/ciaa1843.

Dual functions of SPOP and ERG dictate androgen therapy responses in prostate cancer.

Bernasocchi T, Tekle GEl, Bolis M, et al. Dual functions of SPOP and ERG dictate androgen therapy responses in prostate cancer. Nat Commun. 2021;12(1):734. doi:10.1038/s41467-020-20820-x.

Noncanonical open reading frames encode functional proteins essential for cancer cell survival.

Prensner JR, Enache OM, Luria V, et al. Noncanonical open reading frames encode functional proteins essential for cancer cell survival. Nat Biotechnol. 2021. doi:10.1038/s41587-020-00806-2.

Regulation of purine metabolism connects KCTD13 to a metabolic disorder with autistic features.

Madison JM, Duong K, Vieux EF, et al. Regulation of purine metabolism connects KCTD13 to a metabolic disorder with autistic features. iScience. 2021;24(1):101935. doi:10.1016/j.isci.2020.101935.

CBL mutations drive PI3K/AKT signaling via increased interaction with LYN and PIK3R1.

Belizaire R, Koochaki SHassan Joh, Udeshi ND, et al. CBL mutations drive PI3K/AKT signaling via increased interaction with LYN and PIK3R1. Blood. 2021. doi:10.1182/blood.2020006528.

Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma.

Huang C, Chen L, Savage SR, et al. Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma. Cancer Cell. 2021. doi:10.1016/j.ccell.2020.12.007.

The conserved translation factor LepA is required for optimal synthesis of a porin family in .

Fishbein SRS, Tomasi FG, Wolf ID, et al. The conserved translation factor LepA is required for optimal synthesis of a porin family in . J Bacteriol. 2020. doi:10.1128/JB.00604-20.

Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML.

Tothova Z, Valton A-L, Gorelov R, et al. Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML. JCI Insight. 2020. doi:10.1172/jci.insight.142149.

The SARS-CoV-2 RNA-protein interactome in infected human cells.

Schmidt N, Lareau CA, Keshishian H, et al. The SARS-CoV-2 RNA-protein interactome in infected human cells. Nat Microbiol. 2020. doi:10.1038/s41564-020-00846-z.

Avant-garde: an automated data-driven DIA data curation tool.

Jacome ASebastian, Peckner R, Shulman N, et al. Avant-garde: an automated data-driven DIA data curation tool. Nat Methods. 2020;17(12):1237-1244. doi:10.1038/s41592-020-00986-4.

Proximity labeling in mammalian cells with TurboID and split-TurboID.

Cho KF, Branon TC, Udeshi ND, Myers SA, Carr SA, Ting AY. Proximity labeling in mammalian cells with TurboID and split-TurboID. Nat Protoc. 2020;15(12):3971-3999. doi:10.1038/s41596-020-0399-0.

Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.

Krug K, Jaehnig EJ, Satpathy S, et al. Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy. Cell. 2020;183(5):1436-1456.e31. doi:10.1016/j.cell.2020.10.036.

SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs.

Weingarten-Gabbay S, Klaeger S, Sarkizova S, et al. SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs. bioRxiv. 2020. doi:10.1101/2020.10.02.324145.

BRG1 Loss Predisposes Lung Cancers to Replicative Stress and ATR Dependency.

Gupta M, Concepcion CP, Fahey CG, et al. BRG1 Loss Predisposes Lung Cancers to Replicative Stress and ATR Dependency. Cancer Res. 2020;80(18):3841-3854. doi:10.1158/0008-5472.CAN-20-1744.

RNA-protein interaction mapping via MS2- or Cas13-based APEX targeting.

Han S, Zhao BSimen, Myers SA, Carr SA, He C, Ting AY. RNA-protein interaction mapping via MS2- or Cas13-based APEX targeting. Proc Natl Acad Sci U S A. 2020;117(36):22068-22079. doi:10.1073/pnas.2006617117.

CITED4 Protects Against Adverse Remodeling in Response to Physiological and Pathological Stress.

Lerchenmüller C, Rabolli CP, Yeri A, et al. CITED4 Protects Against Adverse Remodeling in Response to Physiological and Pathological Stress. Circ Res. 2020;127(5):631-646. doi:10.1161/CIRCRESAHA.119.315881.

Neurogranin, Encoded by the Schizophrenia Risk Gene NRGN, Bidirectionally Modulates Synaptic Plasticity via Calmodulin-Dependent Regulation of the Neuronal Phosphoproteome.

Hwang H, Szucs MJ, Ding LJ, et al. Neurogranin, Encoded by the Schizophrenia Risk Gene NRGN, Bidirectionally Modulates Synaptic Plasticity via Calmodulin-Dependent Regulation of the Neuronal Phosphoproteome. Biol Psychiatry. 2020. doi:10.1016/j.biopsych.2020.07.014.

Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona.

Blume JE, Manning WC, Troiano G, et al. Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona. Nat Commun. 2020;11(1):3662. doi:10.1038/s41467-020-17033-7.

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.

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.

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.

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.

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;18(5):995-1009. doi:10.1074/mcp.RA118.001259.

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.

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. 2019;18(1):542-547. doi:10.1021/acs.jproteome.8b00611.

In Situ Peroxidase Labeling and Mass Spectrometry of Alpha-Synuclein in Rat Cortical Neurons.

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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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry.

Whiteaker JR, Zhao L, Abbatiello SE, et al. Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry. Mol Cell Proteomics. 2011;10(4):M110.005645. doi:10.1074/mcp.M110.005645.

Rictor phosphorylation on the Thr-1135 site does not require mammalian target of rapamycin complex 2.

Boulbes D, Chen C-H, Shaikenov T, et al. Rictor phosphorylation on the Thr-1135 site does not require mammalian target of rapamycin complex 2. Mol Cancer Res. 2010;8(6):896-906. doi:10.1158/1541-7786.MCR-09-0409.

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.

Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry.

Tabb DL, Vega-Montoto L, Rudnick PA, et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res. 2010;9(2):761-76. doi:10.1021/pr9006365.

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.

Rodriguez H, Tezak Z, Mesri M, et al. Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA interagency oncology task force on molecular diagnostics. Clin Chem. 2010;56(2):237-43. doi:10.1373/clinchem.2009.136416.

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.

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.

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.

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.

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.

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.

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.

Determination of the gamma-2 phase in a South African dispersed phase amalgam alloy.

Sarkar NK, Wiltshire WA. Determination of the gamma-2 phase in a South African dispersed phase amalgam alloy. J Dent Assoc S Afr. 1988;43(5):193-5.

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