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Items: 1 to 50 of 59

1.

MatrisomeDB: the ECM-protein knowledge database.

Shao X, Taha IN, Clauser KR, Gao YT, Naba A.

Nucleic Acids Res. 2019 Oct 5. pii: gkz849. doi: 10.1093/nar/gkz849. [Epub ahead of print]

PMID:
31586405
2.

Proteomic analyses of ECM during pancreatic ductal adenocarcinoma progression reveal different contributions by tumor and stromal cells.

Tian C, Clauser KR, Öhlund D, Rickelt S, Huang Y, Gupta M, Mani DR, Carr SA, Tuveson DA, Hynes RO.

Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19609-19618. doi: 10.1073/pnas.1908626116. Epub 2019 Sep 4.

PMID:
31484774
3.

TMT Labeling for the Masses: A Robust and Cost-efficient, In-solution Labeling Approach.

Zecha J, Satpathy S, Kanashova T, Avanessian SC, Kane MH, Clauser KR, Mertins P, Carr SA, Kuster B.

Mol Cell Proteomics. 2019 Jul;18(7):1468-1478. doi: 10.1074/mcp.TIR119.001385. Epub 2019 Apr 9.

PMID:
30967486
4.

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, Peckner R, Haber AL, Schweitzer LD, Krug K, Mani DR, Clauser KR, Rozenblatt-Rosen O, Hacohen N, Regev A, Carr SA.

Mol Cell Proteomics. 2019 May;18(5):995-1009. doi: 10.1074/mcp.RA118.001259. Epub 2019 Feb 21.

PMID:
30792265
5.

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry.

Mertins P, Tang LC, Krug K, Clark DJ, Gritsenko MA, Chen L, Clauser KR, Clauss TR, Shah P, Gillette MA, Petyuk VA, Thomas SN, Mani DR, Mundt F, Moore RJ, Hu Y, Zhao R, Schnaubelt M, Keshishian H, Monroe ME, Zhang Z, Udeshi ND, Mani D, Davies SR, Townsend RR, Chan DW, Smith RD, Zhang H, Liu T, Carr SA.

Nat Protoc. 2018 Jul;13(7):1632-1661. doi: 10.1038/s41596-018-0006-9.

6.

Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers.

Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J, Erdmann-Gilmore P, Primeau T, Huang S, Edwards DP, Wang X, Wang X, Kawaler E, Mani DR, Clauser KR, Gao F, Luo J, Davies SR, Johnson GL, Huang KL, Yoon CJ, Ding L, Fenyö D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX.

Cancer Res. 2018 May 15;78(10):2732-2746. doi: 10.1158/0008-5472.CAN-17-1990. Epub 2018 Feb 22.

7.

Site-specific identification and quantitation of endogenous SUMO modifications under native conditions.

Lumpkin RJ, Gu H, Zhu Y, Leonard M, Ahmad AS, Clauser KR, Meyer JG, Bennett EJ, Komives EA.

Nat Commun. 2017 Oct 27;8(1):1171. doi: 10.1038/s41467-017-01271-3.

8.

Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry.

Keshishian H, Burgess MW, Specht H, Wallace L, Clauser KR, Gillette MA, Carr SA.

Nat Protoc. 2017 Aug;12(8):1683-1701. doi: 10.1038/nprot.2017.054. Epub 2017 Jul 27.

9.

Methods, Tools and Current Perspectives in Proteogenomics.

Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR.

Mol Cell Proteomics. 2017 Jun;16(6):959-981. doi: 10.1074/mcp.MR117.000024. Epub 2017 Apr 29. Review.

10.

Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts.

Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Townsend RR, Chen X, Carr SA, Ellis MJ, Ding L.

Nat Commun. 2017 Apr 25;8:15479. doi: 10.1038/ncomms15479. No abstract available.

11.

Proteogenomic integration reveals therapeutic targets in breast cancer xenografts.

Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Reid Townsend R, Chen X, Carr SA, Ellis MJ, Ding L.

Nat Commun. 2017 Mar 28;8:14864. doi: 10.1038/ncomms14864.

12.

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction.

Abelin JG, Keskin DB, Sarkizova S, Hartigan CR, Zhang W, Sidney J, Stevens J, Lane W, Zhang GL, Eisenhaure TM, Clauser KR, Hacohen N, Rooney MS, Carr SA, Wu CJ.

Immunity. 2017 Feb 21;46(2):315-326. doi: 10.1016/j.immuni.2017.02.007.

13.

Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast.

Calvo SE, Julien O, Clauser KR, Shen H, Kamer KJ, Wells JA, Mootha VK.

Mol Cell Proteomics. 2017 Apr;16(4):512-523. doi: 10.1074/mcp.M116.063818. Epub 2017 Jan 25.

14.

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.

Sci Rep. 2017 Jan 10;7:40495. doi: 10.1038/srep40495.

15.

Glyco-centric lectin magnetic bead array (LeMBA) - proteomics dataset of human serum samples from healthy, Barrett׳s esophagus and esophageal adenocarcinoma individuals.

Shah AK, Lê Cao KA, Choi E, Chen D, Gautier B, Nancarrow D, Whiteman DC, Baker PR, Clauser KR, Chalkley RJ, Saunders NA, Barbour AP, Joshi V, Hill MM.

Data Brief. 2016 Apr 1;7:1058-62. doi: 10.1016/j.dib.2016.03.081. eCollection 2016 Jun.

16.

Proteogenomics connects somatic mutations to signalling in breast cancer.

Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA; NCI CPTAC.

Nature. 2016 Jun 2;534(7605):55-62. doi: 10.1038/nature18003. Epub 2016 May 25.

17.

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts.

Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJ, Li S, Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Liu T, Kim S, McDermott JE, Payne SH, Petyuk VA, Rodland KD, Smith RD, Yang F, Chan DW, Zhang B, Zhang H, Zhang Z, Zhou JY, Liebler DC.

J Proteome Res. 2016 Mar 4;15(3):691-706. doi: 10.1021/acs.jproteome.5b00859. Epub 2015 Dec 22.

18.

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.

Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyő D.

Mol Cell Proteomics. 2016 Mar;15(3):1060-71. doi: 10.1074/mcp.M115.056226. Epub 2015 Dec 2.

19.

Addendum: A breast cancer stem cell niche supported by juxtacrine signalling from monocytes and macrophages.

Lu H, Clauser KR, Tam WL, Fröse J, Ye X, Eaton EN, Reinhardt F, Donnenberg VS, Bhargava R, Carr SA, Weinberg RA.

Nat Cell Biol. 2015 Dec;17(12):1607. doi: 10.1038/ncb3281. No abstract available.

PMID:
26612575
20.

MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins.

Calvo SE, Clauser KR, Mootha VK.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1251-7. doi: 10.1093/nar/gkv1003. Epub 2015 Oct 7.

21.

Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis.

Naba A, Clauser KR, Hynes RO.

J Vis Exp. 2015 Jul 23;(101):e53057. doi: 10.3791/53057.

22.

The extracellular matrix: Tools and insights for the "omics" era.

Naba A, Clauser KR, Ding H, Whittaker CA, Carr SA, Hynes RO.

Matrix Biol. 2016 Jan;49:10-24. doi: 10.1016/j.matbio.2015.06.003. Epub 2015 Jul 8. Review.

23.

Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury.

Keshishian H, Burgess MW, Gillette MA, Mertins P, Clauser KR, Mani DR, Kuhn EW, Farrell LA, Gerszten RE, Carr SA.

Mol Cell Proteomics. 2015 Sep;14(9):2375-93. doi: 10.1074/mcp.M114.046813. Epub 2015 Feb 27.

24.

A breast cancer stem cell niche supported by juxtacrine signalling from monocytes and macrophages.

Lu H, Clauser KR, Tam WL, Fröse J, Ye X, Eaton EN, Reinhardt F, Donnenberg VS, Bhargava R, Carr SA, Weinberg RA.

Nat Cell Biol. 2014 Nov;16(11):1105-17. doi: 10.1038/ncb3041. Epub 2014 Sep 28. Erratum in: Nat Cell Biol. 2015 Dec;17(12):1607.

25.

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.

BMC Cancer. 2014 Jul 18;14:518. doi: 10.1186/1471-2407-14-518.

26.

Clawing through evolution: toxin diversification and convergence in the ancient lineage Chilopoda (centipedes).

Undheim EA, Jones A, Clauser KR, Holland JW, Pineda SS, King GF, Fry BG.

Mol Biol Evol. 2014 Aug;31(8):2124-48. doi: 10.1093/molbev/msu162. Epub 2014 May 20.

27.

Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels.

Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, Clauser KR, Qiao JW, Gritsenko MA, Moore RJ, Levine DA, Townsend R, Erdmann-Gilmore P, Snider JE, Davies SR, Ruggles KV, Fenyo D, Kitchens RT, Li S, Olvera N, Dao F, Rodriguez H, Chan DW, Liebler D, White F, Rodland KD, Mills GB, Smith RD, Paulovich AG, Ellis M, Carr SA.

Mol Cell Proteomics. 2014 Jul;13(7):1690-704. doi: 10.1074/mcp.M113.036392. Epub 2014 Apr 9.

28.

Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters.

Naba A, Clauser KR, Lamar JM, Carr SA, Hynes RO.

Elife. 2014 Mar 11;3:e01308. doi: 10.7554/eLife.01308.

29.

Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.

Chalkley RJ, Bandeira N, Chambers MC, Clauser KR, Cottrell JS, Deutsch EW, Kapp EA, Lam HH, McDonald WH, Neubert TA, Sun RX.

Mol Cell Proteomics. 2014 Jan;13(1):360-71. doi: 10.1074/mcp.M113.032813. Epub 2013 Oct 31.

30.

Integrated proteomic analysis of post-translational modifications by serial enrichment.

Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.

Nat Methods. 2013 Jul;10(7):634-7. doi: 10.1038/nmeth.2518. Epub 2013 Jun 9.

31.

Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides.

Guthals A, Clauser KR, Frank AM, Bandeira N.

J Proteome Res. 2013 Jun 7;12(6):2846-57. doi: 10.1021/pr400173d. Epub 2013 May 30.

32.

Shotgun protein sequencing with meta-contig assembly.

Guthals A, Clauser KR, Bandeira N.

Mol Cell Proteomics. 2012 Oct;11(10):1084-96. Epub 2012 Jul 13.

33.

Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.

Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.

Mol Cell Proteomics. 2012 May;11(5):148-59. doi: 10.1074/mcp.M111.016857. Epub 2012 Apr 14.

34.

Modification site localization scoring: strategies and performance.

Chalkley RJ, Clauser KR.

Mol Cell Proteomics. 2012 May;11(5):3-14. doi: 10.1074/mcp.R111.015305. Epub 2012 Feb 11. Review.

35.

iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.

Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong SE, Jaffe JD, Carr SA.

Mol Cell Proteomics. 2012 Jun;11(6):M111.014423. doi: 10.1074/mcp.M111.014423. Epub 2011 Dec 30.

36.

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.

Mol Cell Proteomics. 2012 Apr;11(4):M111.014647. doi: 10.1074/mcp.M111.014647. Epub 2011 Dec 9.

37.

Systematic discovery of TLR signaling components delineates viral-sensing circuits.

Chevrier N, Mertins P, Artyomov MN, Shalek AK, Iannacone M, Ciaccio MF, Gat-Viks I, Tonti E, DeGrace MM, Clauser KR, Garber M, Eisenhaure TM, Yosef N, Robinson J, Sutton A, Andersen MS, Root DE, von Andrian U, Jones RB, Park H, Carr SA, Regev A, Amit I, Hacohen N.

Cell. 2011 Nov 11;147(4):853-67. doi: 10.1016/j.cell.2011.10.022.

38.

Cdk5 is required for memory function and hippocampal plasticity via the cAMP signaling pathway.

Guan JS, Su SC, Gao J, Joseph N, Xie Z, Zhou Y, Durak O, Zhang L, Zhu JJ, Clauser KR, Carr SA, Tsai LH.

PLoS One. 2011;6(9):e25735. doi: 10.1371/journal.pone.0025735. Epub 2011 Sep 30.

39.

A face in the crowd: recognizing peptides through database search.

Eng JK, Searle BC, Clauser KR, Tabb DL.

Mol Cell Proteomics. 2011 Nov;10(11):R111.009522. doi: 10.1074/mcp.R111.009522. Epub 2011 Aug 29. Review.

40.

A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease.

Addona TA, Shi X, Keshishian H, Mani DR, Burgess M, Gillette MA, Clauser KR, Shen D, Lewis GD, Farrell LA, Fifer MA, Sabatine MS, Gerszten RE, Carr SA.

Nat Biotechnol. 2011 Jun 19;29(7):635-43. doi: 10.1038/nbt.1899.

41.

Optimizing performance of glycopeptide capture for plasma proteomics.

Berven FS, Ahmad R, Clauser KR, Carr SA.

J Proteome Res. 2010 Apr 5;9(4):1706-15. doi: 10.1021/pr900845m.

42.

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

Tabb DL, Vega-Montoto L, Rudnick PA, Variyath AM, Ham AJ, Bunk DM, Kilpatrick LE, Billheimer DD, Blackman RK, Cardasis HL, Carr SA, Clauser KR, Jaffe JD, Kowalski KA, Neubert TA, Regnier FE, Schilling B, Tegeler TJ, Wang M, Wang P, Whiteaker JR, Zimmerman LJ, Fisher SJ, Gibson BW, Kinsinger CR, Mesri M, Rodriguez H, Stein SE, Tempst P, Paulovich AG, Liebler DC, Spiegelman C.

J Proteome Res. 2010 Feb 5;9(2):761-76. doi: 10.1021/pr9006365.

43.

Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.

Paulovich AG, Billheimer D, Ham AJ, Vega-Montoto L, Rudnick PA, Tabb DL, Wang P, Blackman RK, Bunk DM, Cardasis HL, Clauser KR, Kinsinger CR, Schilling B, Tegeler TJ, Variyath AM, Wang M, Whiteaker JR, Zimmerman LJ, Fenyo D, Carr SA, Fisher SJ, Gibson BW, Mesri M, Neubert TA, Regnier FE, Rodriguez H, Spiegelman C, Stein SE, Tempst P, Liebler DC.

Mol Cell Proteomics. 2010 Feb;9(2):242-54. doi: 10.1074/mcp.M900222-MCP200. Epub 2009 Oct 26.

44.

Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.

Rudnick PA, Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P, Blonder N, Billheimer DD, Blackman RK, Bunk DM, Cardasis HL, Ham AJ, Jaffe JD, Kinsinger CR, Mesri M, Neubert TA, Schilling B, Tabb DL, Tegeler TJ, Vega-Montoto L, Variyath AM, Wang M, Wang P, Whiteaker JR, Zimmerman LJ, Carr SA, Fisher SJ, Gibson BW, Paulovich AG, Regnier FE, Rodriguez H, Spiegelman C, Tempst P, Liebler DC, Stein SE.

Mol Cell Proteomics. 2010 Feb;9(2):225-41. doi: 10.1074/mcp.M900223-MCP200. Epub 2009 Oct 16.

45.

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, Repka M, Lowery DM, Clauser KR, Zhang C, Shokat KM, Carr SA, Yaffe MB, Jallepalli PV.

PLoS Biol. 2009 May 5;7(5):e1000111. doi: 10.1371/journal.pbio.1000111. Epub 2009 May 26.

46.

Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy.

Du J, Bernasconi P, Clauser KR, Mani DR, Finn SP, Beroukhim R, Burns M, Julian B, Peng XP, Hieronymus H, Maglathlin RL, Lewis TA, Liau LM, Nghiemphu P, Mellinghoff IK, Louis DN, Loda M, Carr SA, Kung AL, Golub TR.

Nat Biotechnol. 2009 Jan;27(1):77-83. doi: 10.1038/nbt.1513. Epub 2008 Dec 21.

47.

Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate.

Lowery DM, Clauser KR, Hjerrild M, Lim D, Alexander J, Kishi K, Ong SE, Gammeltoft S, Carr SA, Yaffe MB.

EMBO J. 2007 May 2;26(9):2262-73. Epub 2007 Apr 19.

48.

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.

Bandeira N, Clauser KR, Pevzner PA.

Mol Cell Proteomics. 2007 Jul;6(7):1123-34. Epub 2007 Apr 19.

49.

Valosin-containing protein phosphorylation at Ser784 in response to DNA damage.

Livingstone M, Ruan H, Weiner J, Clauser KR, Strack P, Jin S, Williams A, Greulich H, Gardner J, Venere M, Mochan TA, DiTullio RA Jr, Moravcevic K, Gorgoulis VG, Burkhardt A, Halazonetis TD.

Cancer Res. 2005 Sep 1;65(17):7533-40.

50.

Use of mass spectrometry to identify protein biomarkers of disease severity in the synovial fluid and serum of patients with rheumatoid arthritis.

Liao H, Wu J, Kuhn E, Chin W, Chang B, Jones MD, O'Neil S, Clauser KR, Karl J, Hasler F, Roubenoff R, Zolg W, Guild BC.

Arthritis Rheum. 2004 Dec;50(12):3792-803.

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