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Items: 1 to 20 of 69

1.

A Combination of DNA-peptide Probes and Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS): A Quasi-Targeted Proteomics Approach for Multiplexed MicroRNA Quantification.

Xu F, Zhou W, Cao J, Xu Q, Jiang D, Chen Y.

Theranostics. 2017 Jul 8;7(11):2849-2862. doi: 10.7150/thno.19113. eCollection 2017.

2.

Food allergen detection by mass spectrometry: the role of systems biology.

Croote D, Quake SR.

NPJ Syst Biol Appl. 2016 Sep 29;2:16022. doi: 10.1038/npjsba.2016.22. eCollection 2016. Review.

3.

Machine Learning on Signal-to-Noise Ratios Improves Peptide Array Design in SAMDI Mass Spectrometry.

Xue AY, Szymczak LC, Mrksich M, Bagheri N.

Anal Chem. 2017 Sep 5;89(17):9039-9047. doi: 10.1021/acs.analchem.7b01728. Epub 2017 Aug 7.

4.

Peptide Markers for Rapid Detection of KPC Carbapenemase by LC-MS/MS.

Wang H, Drake SK, Youn JH, Rosenberg AZ, Chen Y, Gucek M, Suffredini AF, Dekker JP.

Sci Rep. 2017 May 31;7(1):2531. doi: 10.1038/s41598-017-02749-2.

5.

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.

PMID:
28228285
6.

Nano Random Forests to mine protein complexes and their relationships in quantitative proteomics data.

MontaƱo-Gutierrez LF, Ohta S, Kustatscher G, Earnshaw WC, Rappsilber J.

Mol Biol Cell. 2017 Mar 1;28(5):673-680. doi: 10.1091/mbc.E16-06-0370. Epub 2017 Jan 5.

7.

Comparative proteomics of a model MCF10A-KRasG12V cell line reveals a distinct molecular signature of the KRasG12V cell surface.

Ye X, Chan KC, Waters AM, Bess M, Harned A, Wei BR, Loncarek J, Luke BT, Orsburn BC, Hollinger BD, Stephens RM, Bagni R, Martinko A, Wells JA, Nissley DV, McCormick F, Whiteley G, Blonder J.

Oncotarget. 2016 Dec 27;7(52):86948-86971. doi: 10.18632/oncotarget.13566.

8.

A proteogenomic approach for protein-level evidence of genomic variants in cancer cells.

Yeom J, Kabir MH, Lim B, Ahn HS, Kim SY, Lee C.

Sci Rep. 2016 Oct 13;6:35305. doi: 10.1038/srep35305.

9.

Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry.

Jung S, Danziger SA, Panchaud A, von Haller P, Aitchison JD, Goodlett DR.

J Proteomics Bioinform. 2015;8(10):231-239.

10.

Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids.

Wu C, Duan J, Liu T, Smith RD, Qian WJ.

J Chromatogr B Analyt Technol Biomed Life Sci. 2016 May 15;1021:57-68. doi: 10.1016/j.jchromb.2016.01.015. Epub 2016 Jan 12. Review.

11.

Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards.

Bollinger JG, Stergachis AB, Johnson RS, Egertson JD, MacCoss MJ.

Methods Mol Biol. 2016;1410:207-21. doi: 10.1007/978-1-4939-3524-6_12.

12.

Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays.

Hoofnagle AN, Whiteaker JR, Carr SA, Kuhn E, Liu T, Massoni SA, Thomas SN, Townsend RR, Zimmerman LJ, Boja E, Chen J, Crimmins DL, Davies SR, Gao Y, Hiltke TR, Ketchum KA, Kinsinger CR, Mesri M, Meyer MR, Qian WJ, Schoenherr RM, Scott MG, Shi T, Whiteley GR, Wrobel JA, Wu C, Ackermann BL, Aebersold R, Barnidge DR, Bunk DM, Clarke N, Fishman JB, Grant RP, Kusebauch U, Kushnir MM, Lowenthal MS, Moritz RL, Neubert H, Patterson SD, Rockwood AL, Rogers J, Singh RJ, Van Eyk JE, Wong SH, Zhang S, Chan DW, Chen X, Ellis MJ, Liebler DC, Rodland KD, Rodriguez H, Smith RD, Zhang Z, Zhang H, Paulovich AG.

Clin Chem. 2016 Jan;62(1):48-69. doi: 10.1373/clinchem.2015.250563.

13.

Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry.

Rauniyar N.

Int J Mol Sci. 2015 Dec 2;16(12):28566-81. doi: 10.3390/ijms161226120. Review.

14.

Label-free Quantitative Analysis of Changes in Broiler Liver Proteins under Heat Stress using SWATH-MS Technology.

Tang X, Meng Q, Gao J, Zhang S, Zhang H, Zhang M.

Sci Rep. 2015 Oct 13;5:15119. doi: 10.1038/srep15119.

15.

Advancing Urinary Protein Biomarker Discovery by Data-Independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer.

Muntel J, Xuan Y, Berger ST, Reiter L, Bachur R, Kentsis A, Steen H.

J Proteome Res. 2015 Nov 6;14(11):4752-62. doi: 10.1021/acs.jproteome.5b00826. Epub 2015 Oct 22.

16.

Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments.

Searle BC, Egertson JD, Bollinger JG, Stergachis AB, MacCoss MJ.

Mol Cell Proteomics. 2015 Sep;14(9):2331-40. doi: 10.1074/mcp.M115.051300. Epub 2015 Jun 22.

17.

Targeted proteomics for biomarker discovery and validation of hepatocellular carcinoma in hepatitis C infected patients.

Mustafa GM, Larry D, Petersen JR, Elferink CJ.

World J Hepatol. 2015 Jun 8;7(10):1312-24. doi: 10.4254/wjh.v7.i10.1312. Review.

18.

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, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA.

Mol Cell Proteomics. 2015 Sep;14(9):2357-74. doi: 10.1074/mcp.M114.047050. Epub 2015 Feb 18.

19.

Studying macromolecular complex stoichiometries by peptide-based mass spectrometry.

Wohlgemuth I, Lenz C, Urlaub H.

Proteomics. 2015 Mar;15(5-6):862-79. doi: 10.1002/pmic.201400466. Epub 2015 Feb 6. Review.

20.

Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment (PPA).

Muntel J, Boswell SA, Tang S, Ahmed S, Wapinski I, Foley G, Steen H, Springer M.

Mol Cell Proteomics. 2015 Feb;14(2):430-40. doi: 10.1074/mcp.M114.044321. Epub 2014 Dec 3.

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