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Items: 1 to 20 of 110

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.

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.

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.

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
5.
6.

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.

7.
8.

Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution.

Alves G, Yu YK.

Bioinformatics. 2016 Sep 1;32(17):2642-9. doi: 10.1093/bioinformatics/btw225. Epub 2016 Apr 29.

PMID:
27153659
9.

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
10.

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
11.

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.

12.

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
13.

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.

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.

15.

Mass spectrometry-based protein identification with accurate statistical significance assignment.

Alves G, Yu YK.

Bioinformatics. 2015 Mar 1;31(5):699-706. doi: 10.1093/bioinformatics/btu717. Epub 2014 Oct 31.

16.

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.

17.

PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments.

Mohammed Y, Domański D, Jackson AM, Smith DS, Deelder AM, Palmblad M, Borchers CH.

J Proteomics. 2014 Jun 25;106:151-61. doi: 10.1016/j.jprot.2014.04.018. Epub 2014 Apr 22.

PMID:
24769191
18.

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
19.

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.

20.

PIQMIe: a web server for semi-quantitative proteomics data management and analysis.

Kuzniar A, Kanaar R.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W100-6. doi: 10.1093/nar/gku478. Epub 2014 May 26.

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