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Results: 1 to 20 of 117

1.

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

Alves G, Ogurtsov AY, Yu YK.

BMC Genomics. 2008 Oct 27;9:505. doi: 10.1186/1471-2164-9-505.

PMID:
18954448
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics.

Alves G, Ogurtsov AY, Yu YK.

PLoS One. 2010 Nov 16;5(11):e15438. doi: 10.1371/journal.pone.0015438.

PMID:
21103371
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

NCBI Peptidome: a new repository for mass spectrometry proteomics data.

Ji L, Barrett T, Ayanbule O, Troup DB, Rudnev D, Muertter RN, Tomashevsky M, Soboleva A, Slotta DJ.

Nucleic Acids Res. 2010 Jan;38(Database issue):D731-5. doi: 10.1093/nar/gkp1047. Epub 2009 Nov 26.

PMID:
19942688
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins.

Matthiesen R, Trelle MB, Højrup P, Bunkenborg J, Jensen ON.

J Proteome Res. 2005 Nov-Dec;4(6):2338-47.

PMID:
16335983
[PubMed - indexed for MEDLINE]
5.

The NCBI BioSystems database.

Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S, Liu C, Shi W, Bryant SH.

Nucleic Acids Res. 2010 Jan;38(Database issue):D492-6. doi: 10.1093/nar/gkp858. Epub 2009 Oct 23.

PMID:
19854944
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

RAId_DbS: peptide identification using database searches with realistic statistics.

Alves G, Ogurtsov AY, Yu YK.

Biol Direct. 2007 Oct 25;2:25.

PMID:
17961253
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics.

Alves G, Yu YK.

Bioinformatics. 2005 Oct 1;21(19):3726-32. Epub 2005 Aug 16.

PMID:
16105903
[PubMed - indexed for MEDLINE]
Free Article
8.

The wildcat toolbox: a set of perl script utilities for use in peptide mass spectral database searching and proteomics experiments.

Haynes PA, Miller S, Radabaugh T, Galligan M, Breci L, Rohrbough J, Hickman F, Merchant N.

J Biomol Tech. 2006 Apr;17(2):97-102.

PMID:
16741236
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Andromeda: a peptide search engine integrated into the MaxQuant environment.

Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M.

J Proteome Res. 2011 Apr 1;10(4):1794-805. doi: 10.1021/pr101065j. Epub 2011 Feb 22.

PMID:
21254760
[PubMed - indexed for MEDLINE]
10.

Integration of gel-based proteome data with pProRep.

Laukens K, Matthiesen R, Lemière F, Esmans E, Onckelen HV, Jensen ON, Witters E.

Bioinformatics. 2006 Nov 15;22(22):2838-40. Epub 2006 Oct 10.

PMID:
17032679
[PubMed - indexed for MEDLINE]
Free Article
11.

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.

Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD.

BMC Bioinformatics. 2008 Dec 16;9:542. doi: 10.1186/1471-2105-9-542.

PMID:
19087345
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Database resources of the National Center for Biotechnology Information.

Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, John Wilbur W, Yaschenko E, Ye J.

Nucleic Acids Res. 2010 Jan;38(Database issue):D5-16. doi: 10.1093/nar/gkp967. Epub 2009 Nov 12.

PMID:
19910364
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

GenBank.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.

Nucleic Acids Res. 2010 Jan;38(Database issue):D46-51. doi: 10.1093/nar/gkp1024. Epub 2009 Nov 12.

PMID:
19910366
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The Proteomics Identifications database: 2010 update.

Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L.

Nucleic Acids Res. 2010 Jan;38(Database issue):D736-42. doi: 10.1093/nar/gkp964. Epub 2009 Nov 11.

PMID:
19906717
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments.

Albaum SP, Neuweger H, Fränzel B, Lange S, Mertens D, Trötschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A.

Bioinformatics. 2009 Dec 1;25(23):3128-34. doi: 10.1093/bioinformatics/btp568. Epub 2009 Oct 6.

PMID:
19808875
[PubMed - indexed for MEDLINE]
Free Article
16.

The Multi-Q web server for multiplexed protein quantitation.

Yu CY, Tsui YH, Yian YH, Sung TY, Hsu WL.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W707-12. Epub 2007 Jun 6.

PMID:
17553828
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.

MacLean B, Eng JK, Beavis RC, McIntosh M.

Bioinformatics. 2006 Nov 15;22(22):2830-2. Epub 2006 Jul 28.

PMID:
16877754
[PubMed - indexed for MEDLINE]
Free Article
18.

Database resources of the National Center for Biotechnology Information.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E.

Nucleic Acids Res. 2007 Jan;35(Database issue):D5-12. Epub 2006 Dec 14.

PMID:
17170002
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Using annotated peptide mass spectrum libraries for protein identification.

Craig R, Cortens JC, Fenyo D, Beavis RC.

J Proteome Res. 2006 Aug;5(8):1843-9.

PMID:
16889405
[PubMed - indexed for MEDLINE]
20.

Calibrating E-values for MS2 database search methods.

Alves G, Ogurtsov AY, Wu WW, Wang G, Shen RF, Yu YK.

Biol Direct. 2007 Nov 5;2:26.

PMID:
17983478
[PubMed - indexed for MEDLINE]
Free PMC Article
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