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Items: 1 to 50 of 103

1.

Reproducibility and Transparency by Design.

Petyuk VA, Gatto L, Payne SH.

Mol Cell Proteomics. 2019 Aug 9;18(8 suppl 1):S202-S204. doi: 10.1074/mcp.IP119.001567. Epub 2019 Jul 4. No abstract available.

2.

Extracting Pathway-level Signatures from Proteogenomic Data in Breast Cancer Using Independent Component Analysis.

Liu W, Payne SH, Ma S, Fenyö D.

Mol Cell Proteomics. 2019 Aug 9;18(8 suppl 1):S169-S182. doi: 10.1074/mcp.TIR119.001442. Epub 2019 Jun 18.

3.

Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability.

Huang KL, Wu Y, Primeau T, Wang YT, Gao Y, McMichael JF, Scott AD, Cao S, Wendl MC, Johnson KJ, Ruggles K, Held J, Payne SH, Davies S, Dar A, Kinsinger CR, Mesri M, Rodriguez H, Ellis MJ, Townsend RR, Chen F, Fenyö D, Li S, Liu T, Carr SA, Ding L.

Mol Cell Proteomics. 2019 Aug;18(8):1630-1650. doi: 10.1074/mcp.RA118.001243. Epub 2019 Jun 13.

PMID:
31196969
4.

Identification and Quantification of Proteoforms by Mass Spectrometry.

Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, Ge Y, Kelleher NL, LeDuc RD, Liu X, Payne SH, Sun L, Thomas PM, Tucholski T, Wang Z, Wu S, Wu Z, Yu D, Shortreed MR, Smith LM.

Proteomics. 2019 May;19(10):e1800361. doi: 10.1002/pmic.201800361. Review.

PMID:
31050378
5.

Correction for Christensen et al., "Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli".

Christensen DG, Meyer JG, Baumgartner JT, D'Souza AK, Nelson WC, Payne SH, Kuhn ML, Schilling B, Wolfe AJ.

MBio. 2019 Apr 9;10(2). pii: e00592-19. doi: 10.1128/mBio.00592-19. No abstract available.

6.

Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards.

Gibbons BC, Fillmore TL, Gao Y, Moore RJ, Liu T, Nakayasu ES, Metz TO, Payne SH.

J Proteome Res. 2019 Feb 1;18(2):694-699. doi: 10.1021/acs.jproteome.8b00688. Epub 2018 Dec 19.

7.

Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli.

Christensen DG, Meyer JG, Baumgartner JT, D'Souza AK, Nelson WC, Payne SH, Kuhn ML, Schilling B, Wolfe AJ.

MBio. 2018 Oct 23;9(5). pii: e01905-18. doi: 10.1128/mBio.01905-18. Erratum in: MBio. 2019 Apr 9;10(2):.

8.

Individual Variability of Protein Expression in Human Tissues.

Kushner IK, Clair G, Purvine SO, Lee JY, Adkins JN, Payne SH.

J Proteome Res. 2018 Nov 2;17(11):3914-3922. doi: 10.1021/acs.jproteome.8b00580. Epub 2018 Oct 18.

PMID:
30300549
9.

Proteomics Goes to Court: A Statistical Foundation for Forensic Toxin/Organism Identification Using Bottom-Up Proteomics.

Jarman KH, Heller NC, Jenson SC, Hutchison JR, Kaiser BLD, Payne SH, Wunschel DS, Merkley ED.

J Proteome Res. 2018 Sep 7;17(9):3075-3085. doi: 10.1021/acs.jproteome.8b00212. Epub 2018 Aug 28.

PMID:
30109807
10.

Integrative omics analyses broaden treatment targets in human cancer.

Sengupta S, Sun SQ, Huang KL, Oh C, Bailey MH, Varghese R, Wyczalkowski MA, Ning J, Tripathi P, McMichael JF, Johnson KJ, Kandoth C, Welch J, Ma C, Wendl MC, Payne SH, Fenyö D, Townsend RR, Dipersio JF, Chen F, Ding L.

Genome Med. 2018 Jul 27;10(1):60. doi: 10.1186/s13073-018-0564-z.

11.

ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data.

Lee JY, Choi H, Colangelo CM, Davis D, Hoopmann MR, Käll L, Lam H, Payne SH, Perez-Riverol Y, The M, Wilson R, Weintraub ST, Palmblad M.

J Biomol Tech. 2018 Jul;29(2):39-45. doi: 10.7171/jbt.18-2902-003. Epub 2018 Jun 21.

12.

Author Correction: Informed-Proteomics: open-source software package for top-down proteomics.

Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, Smith RD, Payne SH, Kim S.

Nat Methods. 2018 Jul;15(7):554. doi: 10.1038/s41592-018-0040-0.

PMID:
29899368
13.

Blazing Signature Filter: a library for fast pairwise similarity comparisons.

Lee JY, Fujimoto GM, Wilson R, Wiley HS, Payne SH.

BMC Bioinformatics. 2018 Jun 11;19(1):221. doi: 10.1186/s12859-018-2210-6.

14.

Inhibition of interleukin-1 receptor-associated kinase-1 is a therapeutic strategy for acute myeloid leukemia subtypes.

Hosseini MM, Kurtz SE, Abdelhamed S, Mahmood S, Davare MA, Kaempf A, Elferich J, McDermott JE, Liu T, Payne SH, Shinde U, Rodland KD, Mori M, Druker BJ, Singer JW, Agarwal A.

Leukemia. 2018 Nov;32(11):2374-2387. doi: 10.1038/s41375-018-0112-2. Epub 2018 Mar 29.

15.

An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies.

Bilbao A, Gibbons BC, Slysz GW, Crowell KL, Monroe ME, Ibrahim YM, Smith RD, Payne SH, Baker ES.

Int J Mass Spectrom. 2018 Apr;427:91-99. doi: 10.1016/j.ijms.2017.11.003. Epub 2017 Nov 6.

16.

A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms.

The M, Edfors F, Perez-Riverol Y, Payne SH, Hoopmann MR, Palmblad M, Forsström B, Käll L.

J Proteome Res. 2018 May 4;17(5):1879-1886. doi: 10.1021/acs.jproteome.7b00899. Epub 2018 Apr 16.

17.

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ; Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L.

Cell Rep. 2018 Apr 3;23(1):270-281.e3. doi: 10.1016/j.celrep.2018.03.052.

18.

A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry.

Zheng X, Aly NA, Zhou Y, Dupuis KT, Bilbao A, Paurus VL, Orton DJ, Wilson R, Payne SH, Smith RD, Baker ES.

Chem Sci. 2017 Nov 1;8(11):7724-7736. doi: 10.1039/c7sc03464d. Epub 2017 Sep 28.

19.

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism.

Nakayasu ES, Burnet MC, Walukiewicz HE, Wilkins CS, Shukla AK, Brooks S, Plutz MJ, Lee BD, Schilling B, Wolfe AJ, Müller S, Kirby JR, Rao CV, Cort JR, Payne SH.

MBio. 2017 Nov 28;8(6). pii: e01894-17. doi: 10.1128/mBio.01894-17.

20.

Normal Palmar Anatomy and Variations That Impact Median Nerve Decompression.

Seiler JG 3rd, Daruwalla JH, Payne SH, Faucher GK.

J Am Acad Orthop Surg. 2017 Sep;25(9):e194-e203. doi: 10.5435/JAAOS-D-16-00038. Review.

PMID:
28837460
21.

Informed-Proteomics: open-source software package for top-down proteomics.

Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, Smith RD, Payne SH, Kim S.

Nat Methods. 2017 Sep;14(9):909-914. doi: 10.1038/nmeth.4388. Epub 2017 Aug 7. Erratum in: Nat Methods. 2018 Jul;15(7):554.

22.

PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data.

Ting YS, Egertson JD, Bollinger JG, Searle BC, Payne SH, Noble WS, MacCoss MJ.

Nat Methods. 2017 Sep;14(9):903-908. doi: 10.1038/nmeth.4390. Epub 2017 Aug 7.

23.

Genes essential for phototrophic growth by a purple alphaproteobacterium.

Yang J, Yin L, Lessner FH, Nakayasu ES, Payne SH, Fixen KR, Gallagher L, Harwood CS.

Environ Microbiol. 2017 Sep;19(9):3567-3578. doi: 10.1111/1462-2920.13852. Epub 2017 Jul 24.

PMID:
28677146
24.

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association.

Ma J, Casey CP, Zheng X, Ibrahim YM, Wilkins CS, Renslow RS, Thomas DG, Payne SH, Monroe ME, Smith RD, Teeguarden JG, Baker ES, Metz TO.

Bioinformatics. 2017 Sep 1;33(17):2715-2722. doi: 10.1093/bioinformatics/btx305.

25.

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.

26.

LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data.

Kyle JE, Crowell KL, Casey CP, Fujimoto GM, Kim S, Dautel SE, Smith RD, Payne SH, Metz TO.

Bioinformatics. 2017 Jun 1;33(11):1744-1746. doi: 10.1093/bioinformatics/btx046.

27.

Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks.

Na S, Payne SH, Bandeira N.

Mol Cell Proteomics. 2016 Nov;15(11):3501-3512. Epub 2016 Sep 8.

28.

Corrigendum: The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.

Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, Lipton MS, Smith RD, De Leenheer P, Payne SH, Johnston AW, Davie-Martin CL, Halsey KH, Giovannoni SJ.

Nat Microbiol. 2016 Oct 3;1(11):16210. doi: 10.1038/nmicrobiol.2016.210. No abstract available.

PMID:
27694837
29.

The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.

Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, Lipton MS, Smith RD, De Leenheer P, Payne SH, Johnston AW, Davie-Martin CL, Halsey KH, Giovannoni SJ.

Nat Microbiol. 2016 May 16;1(8):16065. doi: 10.1038/nmicrobiol.2016.65. Erratum in: Nat Microbiol. 2016 Oct 03;1(11):16210.

PMID:
27573103
30.

A Skyline Plugin for Pathway-Centric Data Browsing.

Degan MG, Ryadinskiy L, Fujimoto GM, Wilkins CS, Lichti CF, Payne SH.

J Am Soc Mass Spectrom. 2016 Nov;27(11):1752-1757. Epub 2016 Aug 16.

PMID:
27530777
31.

Severe Brachial Plexus Injuries in American Football.

Daly CA, Payne SH, Seiler JG.

Orthopedics. 2016 Nov 1;39(6):e1188-e1192. doi: 10.3928/01477447-20160721-03. Epub 2016 Aug 3.

PMID:
27482729
32.

A Multicenter, Prospective, Randomized, Pilot Study of Outcomes for Digital Nerve Repair in the Hand Using Hollow Conduit Compared With Processed Allograft Nerve.

Means KR Jr, Rinker BD, Higgins JP, Payne SH Jr, Merrell GA, Wilgis EF.

Hand (N Y). 2016 Jun;11(2):144-51. doi: 10.1177/1558944715627233. Epub 2016 Feb 17.

33.

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD; CPTAC Investigators.

Cell. 2016 Jul 28;166(3):755-765. doi: 10.1016/j.cell.2016.05.069. Epub 2016 Jun 29.

34.

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.

35.

Toward a standard in structural genome annotation for prokaryotes.

Tripp HJ, Sutton G, White O, Wortman J, Pati A, Mikhailova N, Ovchinnikova G, Payne SH, Kyrpides NC, Ivanova N.

Stand Genomic Sci. 2015 Jul 25;10:45. doi: 10.1186/s40793-015-0034-9. eCollection 2015.

36.

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity.

Payne SH, Monroe ME, Overall CC, Kiebel GR, Degan M, Gibbons BC, Fujimoto GM, Purvine SO, Adkins JN, Lipton MS, Smith RD.

Sci Data. 2015 Aug 18;2:150041. doi: 10.1038/sdata.2015.41. eCollection 2015.

37.

Correcting systematic bias and instrument measurement drift with mzRefinery.

Gibbons BC, Chambers MC, Monroe ME, Tabb DL, Payne SH.

Bioinformatics. 2015 Dec 1;31(23):3838-40. doi: 10.1093/bioinformatics/btv437. Epub 2015 Aug 4.

38.

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data.

Ting YS, Egertson JD, Payne SH, Kim S, MacLean B, Käll L, Aebersold R, Smith RD, Noble WS, MacCoss MJ.

Mol Cell Proteomics. 2015 Sep;14(9):2301-7. doi: 10.1074/mcp.O114.047035. Epub 2015 Jul 27.

39.

An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics.

Wu C, Monroe ME, Xu Z, Slysz GW, Payne SH, Rodland KD, Liu T, Smith RD.

J Am Soc Mass Spectrom. 2015 Dec;26(12):2002-8. doi: 10.1007/s13361-015-1169-z. Epub 2015 May 27.

40.

The utility of protein and mRNA correlation.

Payne SH.

Trends Biochem Sci. 2015 Jan;40(1):1-3. doi: 10.1016/j.tibs.2014.10.010. Epub 2014 Nov 23.

41.

Bayesian proteoform modeling improves protein quantification of global proteomic measurements.

Webb-Robertson BJ, Matzke MM, Datta S, Payne SH, Kang J, Bramer LM, Nicora CD, Shukla AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM.

Mol Cell Proteomics. 2014 Dec;13(12):3639-46. doi: 10.1074/mcp.M113.030932.

42.

Comprehensive quantitative analysis of ovarian and breast cancer tumor peptidomes.

Xu Z, Wu C, Xie F, Slysz GW, Tolic N, Monroe ME, Petyuk VA, Payne SH, Fujimoto GM, Moore RJ, Fillmore TL, Schepmoes AA, Levine DA, Townsend RR, Davies SR, Li S, Ellis M, Boja E, Rivers R, Rodriguez H, Rodland KD, Liu T, Smith RD.

J Proteome Res. 2015 Jan 2;14(1):422-33. doi: 10.1021/pr500840w. Epub 2014 Nov 10.

43.

Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements.

Webb-Robertson BJ, Matzke MM, Datta S, Payne SH, Kang J, Bramer LM, Nicora CD, Shukla AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM.

Mol Cell Proteomics. 2014 Aug 16. pii: mcp.O113.030932. [Epub ahead of print]

44.

Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry.

Crowell KL, Baker ES, Payne SH, Ibrahim YM, Monroe ME, Slysz GW, LaMarche BL, Petyuk VA, Piehowski PD, Danielson WF 3rd, Anderson GA, Smith RD.

Int J Mass Spectrom. 2013 Nov 15;354-355:312-317.

45.

GlyQ-IQ: glycomics quintavariate-informed quantification with high-performance computing and GlycoGrid 4D visualization.

Kronewitter SR, Slysz GW, Marginean I, Hagler CD, LaMarche BL, Zhao R, Harris MY, Monroe ME, Polyukh CA, Crowell KL, Fillmore TL, Carlson TS, Camp DG 2nd, Moore RJ, Payne SH, Anderson GA, Smith RD.

Anal Chem. 2014 Jul 1;86(13):6268-76. doi: 10.1021/ac501492f. Epub 2014 Jun 13.

46.

Detecting and removing data artifacts in Hadamard transform ion mobility-mass spectrometry measurements.

Prost SA, Crowell KL, Baker ES, Ibrahim YM, Clowers BH, Monroe ME, Anderson GA, Smith RD, Payne SH.

J Am Soc Mass Spectrom. 2014 Dec;25(12):2020-2027. doi: 10.1007/s13361-014-0895-y. Epub 2014 May 6.

47.

Signatures for mass spectrometry data quality.

Amidan BG, Orton DJ, Lamarche BL, Monroe ME, Moore RJ, Venzin AM, Smith RD, Sego LH, Tardiff MF, Payne SH.

J Proteome Res. 2014 Apr 4;13(4):2215-22. doi: 10.1021/pr401143e. Epub 2014 Mar 24.

48.

Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013.

MS-SIG 2013 Organizers, Ryu SY, Payne SH, Schaab C, Xiao W.

Bioinformatics. 2014 Jul 15;30(14):2089-90. doi: 10.1093/bioinformatics/btu116. Epub 2014 Mar 3. No abstract available.

49.

PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations.

Tovchigrechko A, Venepally P, Payne SH.

Bioinformatics. 2014 May 15;30(10):1469-70. doi: 10.1093/bioinformatics/btu051. Epub 2014 Jan 27.

50.

Automated data extraction from in situ protein-stable isotope probing studies.

Slysz GW, Steinke L, Ward DM, Klatt CG, Clauss TR, Purvine SO, Payne SH, Anderson GA, Smith RD, Lipton MS.

J Proteome Res. 2014 Mar 7;13(3):1200-10. doi: 10.1021/pr400633j. Epub 2014 Feb 21.

PMID:
24467184

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