Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 30

1.

PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline.

Shteynberg DD, Deutsch EW, Campbell DS, Hoopmann MR, Kusebauch U, Lee D, Mendoza L, Midha MK, Sun Z, Whetton AD, Moritz RL.

J Proteome Res. 2019 Jul 22. doi: 10.1021/acs.jproteome.9b00205. [Epub ahead of print]

PMID:
31290668
2.

A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry.

Swearingen KE, Eng JK, Shteynberg D, Vigdorovich V, Springer TA, Mendoza L, Sather DN, Deutsch EW, Kappe SHI, Moritz RL.

J Proteome Res. 2019 Feb 1;18(2):652-663. doi: 10.1021/acs.jproteome.8b00638. Epub 2018 Dec 21.

PMID:
30523691
3.

Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper.

Mendoza L, Deutsch EW, Sun Z, Campbell DS, Shteynberg DD, Moritz RL.

J Proteome Res. 2018 Dec 7;17(12):4337-4344. doi: 10.1021/acs.jproteome.8b00544. Epub 2018 Sep 28.

4.

Improved Patency of ePTFE Grafts as a Hemodialysis Access Site by Seeding Autologous Endothelial Cells Expressing Fibulin-5 and VEGF.

Tzchori I, Falah M, Shteynberg D, Levin Ashkenazi D, Loberman Z, Perry L, Flugelman MY.

Mol Ther. 2018 Jul 5;26(7):1660-1668. doi: 10.1016/j.ymthe.2018.04.003. Epub 2018 Apr 5.

5.

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL.

J Proteome Res. 2016 Nov 4;15(11):4091-4100. Epub 2016 Sep 12.

6.

An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results.

Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, Moritz RL.

J Am Soc Mass Spectrom. 2016 Nov;27(11):1728-1734. Epub 2016 Jul 28.

7.

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.

Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL.

Cell. 2016 Jul 28;166(3):766-778. doi: 10.1016/j.cell.2016.06.041. Epub 2016 Jul 21.

8.

Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides.

Keller A, Bader SL, Kusebauch U, Shteynberg D, Hood L, Moritz RL.

Mol Cell Proteomics. 2016 Mar;15(3):1151-63. doi: 10.1074/mcp.M115.054478. Epub 2015 Dec 24.

9.

reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1837-47. doi: 10.1007/s13361-015-1252-5. Epub 2015 Sep 29.

10.

State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.

Deutsch EW, Sun Z, Campbell D, Kusebauch U, Chu CS, Mendoza L, Shteynberg D, Omenn GS, Moritz RL.

J Proteome Res. 2015 Sep 4;14(9):3461-73. doi: 10.1021/acs.jproteome.5b00500. Epub 2015 Jul 24.

11.

Fibulin-5 regulates keloid-derived fibroblast-like cells through integrin beta-1.

Furie N, Shteynberg D, Elkhatib R, Perry L, Ullmann Y, Feferman Y, Preis M, Flugelman MY, Tzchori I.

Int J Cosmet Sci. 2016 Feb;38(1):35-40. doi: 10.1111/ics.12245. Epub 2015 Jul 14.

PMID:
26095157
12.

Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet.

Keller A, Bader SL, Shteynberg D, Hood L, Moritz RL.

Mol Cell Proteomics. 2015 May;14(5):1411-8. doi: 10.1074/mcp.O114.044917. Epub 2015 Feb 24.

13.

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.

Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL.

Proteomics Clin Appl. 2015 Aug;9(7-8):745-54. doi: 10.1002/prca.201400164. Epub 2015 Apr 2. Review.

14.

Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

Slagel J, Mendoza L, Shteynberg D, Deutsch EW, Moritz RL.

Mol Cell Proteomics. 2015 Feb;14(2):399-404. doi: 10.1074/mcp.O114.043380. Epub 2014 Nov 23.

15.

Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells.

Surmann K, Michalik S, Hildebrandt P, Gierok P, Depke M, Brinkmann L, Bernhardt J, Salazar MG, Sun Z, Shteynberg D, Kusebauch U, Moritz RL, Wollscheid B, Lalk M, Völker U, Schmidt F.

Front Microbiol. 2014 Aug 1;5:392. doi: 10.3389/fmicb.2014.00392. eCollection 2014.

16.

State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project.

Farrah T, Deutsch EW, Omenn GS, Sun Z, Watts JD, Yamamoto T, Shteynberg D, Harris MM, Moritz RL.

J Proteome Res. 2014 Jan 3;13(1):60-75. doi: 10.1021/pr4010037. Epub 2013 Dec 6.

17.

The microvesicle component of HIV-1 inocula modulates dendritic cell infection and maturation and enhances adhesion to and activation of T lymphocytes.

Mercier SK, Donaghy H, Botting RA, Turville SG, Harman AN, Nasr N, Ji H, Kusebauch U, Mendoza L, Shteynberg D, Sandgren K, Simpson RJ, Moritz RL, Cunningham AL.

PLoS Pathog. 2013 Oct;9(10):e1003700. doi: 10.1371/journal.ppat.1003700. Epub 2013 Oct 17. Erratum in: PLoS Pathog. 2013 Oct;9(10). doi: 10.1371/annotation/059beb14-db84-4836-9fef-ec351946025a.

18.

Combining results of multiple search engines in proteomics.

Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW.

Mol Cell Proteomics. 2013 Sep;12(9):2383-93. doi: 10.1074/mcp.R113.027797. Epub 2013 May 29. Review.

19.

Oncogenic H-ras reprograms Madin-Darby canine kidney (MDCK) cell-derived exosomal proteins following epithelial-mesenchymal transition.

Tauro BJ, Mathias RA, Greening DW, Gopal SK, Ji H, Kapp EA, Coleman BM, Hill AF, Kusebauch U, Hallows JL, Shteynberg D, Moritz RL, Zhu HJ, Simpson RJ.

Mol Cell Proteomics. 2013 Aug;12(8):2148-59. doi: 10.1074/mcp.M112.027086. Epub 2013 May 3.

20.

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.

Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI.

Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. doi: 10.1074/mcp.M111.007690. Epub 2011 Aug 29.

21.

Software pipeline and data analysis for MS/MS proteomics: the trans-proteomic pipeline.

Keller A, Shteynberg D.

Methods Mol Biol. 2011;694:169-89. doi: 10.1007/978-1-60761-977-2_12.

PMID:
21082435
22.

Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction.

Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon PT, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA, Aitchison JD.

Mol Cell Proteomics. 2010 Sep;9(9):2076-88. doi: 10.1074/mcp.M000116-MCP201. Epub 2010 Apr 15.

23.

A guided tour of the Trans-Proteomic Pipeline.

Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R.

Proteomics. 2010 Mar;10(6):1150-9. doi: 10.1002/pmic.200900375. Review.

24.

Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets.

Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T, Aebersold R.

Proteomics. 2010 Mar;10(6):1190-5. doi: 10.1002/pmic.200900567.

25.

MaRiMba: a software application for spectral library-based MRM transition list assembly.

Sherwood CA, Eastham A, Lee LW, Peterson A, Eng JK, Shteynberg D, Mendoza L, Deutsch EW, Risler J, Tasman N, Aebersold R, Lam H, Martin DB.

J Proteome Res. 2009 Oct;8(10):4396-405. doi: 10.1021/pr900010h.

26.

Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N.

Hohmann L, Sherwood C, Eastham A, Peterson A, Eng JK, Eddes JS, Shteynberg D, Martin DB.

J Proteome Res. 2009 Mar;8(3):1415-22. doi: 10.1021/pr800774h.

27.

Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis.

Malmström J, Lee H, Nesvizhskii AI, Shteynberg D, Mohanty S, Brunner E, Ye M, Weber G, Eckerskorn C, Aebersold R.

J Proteome Res. 2006 Sep;5(9):2241-9.

PMID:
16944936
28.

Gene finding in the chicken genome.

Eyras E, Reymond A, Castelo R, Bye JM, Camara F, Flicek P, Huckle EJ, Parra G, Shteynberg DD, Wyss C, Rogers J, Antonarakis SE, Birney E, Guigo R, Brent MR.

BMC Bioinformatics. 2005 May 30;6:131.

29.

Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing.

Wu JQ, Shteynberg D, Arumugam M, Gibbs RA, Brent MR.

Genome Res. 2004 Apr;14(4):665-71.

30.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F; Rat Genome Sequencing Project Consortium.

Nature. 2004 Apr 1;428(6982):493-521.

PMID:
15057822

Supplemental Content

Loading ...
Support Center