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Results: 1 to 20 of 109

1.

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
2.

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
3.

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
4.

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
5.

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
6.

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]
7.

Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring.

Dworzanski JP, Snyder AP, Chen R, Zhang H, Wishart D, Li L.

Anal Chem. 2004 Apr 15;76(8):2355-66.

PMID:
15080748
[PubMed - indexed for MEDLINE]
8.

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
9.

A Perl procedure for protein identification by Peptide Mass Fingerprinting.

Tiengo A, Barbarini N, Troiani S, Rusconi L, Magni P.

BMC Bioinformatics. 2009 Oct 15;10 Suppl 12:S11. doi: 10.1186/1471-2105-10-S12-S11.

PMID:
19828071
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Improving peptide identification with single-stage mass spectrum peaks.

He Z, Yu W.

Bioinformatics. 2009 Nov 15;25(22):2969-74. doi: 10.1093/bioinformatics/btp501. Epub 2009 Aug 18.

PMID:
19689954
[PubMed - indexed for MEDLINE]
Free Article
11.

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]
12.

A ranking-based scoring function for peptide-spectrum matches.

Frank AM.

J Proteome Res. 2009 May;8(5):2241-52. doi: 10.1021/pr800678b.

PMID:
19231891
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Complexity and scoring function of MS/MS peptide de novo sequencing.

Xu C, Ma B.

Comput Syst Bioinformatics Conf. 2006:361-9.

PMID:
17369655
[PubMed - indexed for MEDLINE]
Free Article
14.

Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

Ding Y, Choi H, Nesvizhskii AI.

J Proteome Res. 2008 Nov;7(11):4878-89. doi: 10.1021/pr800484x. Epub 2008 Sep 13.

PMID:
18788775
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis.

Kapp EA, Schütz F, Connolly LM, Chakel JA, Meza JE, Miller CA, Fenyo D, Eng JK, Adkins JN, Omenn GS, Simpson RJ.

Proteomics. 2005 Aug;5(13):3475-90.

PMID:
16047398
[PubMed - indexed for MEDLINE]
16.

[A novel approach for peptide identification by tandem mass spectrometry].

Sheng QH, Tang HX, Xie T, Wang LS, Ding DF.

Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai). 2003 Aug;35(8):734-40. Chinese.

PMID:
12897969
[PubMed - indexed for MEDLINE]
Free Article
17.

An SVM scorer for more sensitive and reliable peptide identification via tandem mass spectrometry.

Wang H, Fu Y, Sun R, He S, Zeng R, Gao W.

Pac Symp Biocomput. 2006:303-14.

PMID:
17094248
[PubMed - indexed for MEDLINE]
Free Article
18.

Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0.

Matthiesen R, Bunkenborg J, Stensballe A, Jensen ON, Welinder KG, Bauw G.

Proteomics. 2004 Sep;4(9):2583-93.

PMID:
15352233
[PubMed - indexed for MEDLINE]
19.

Bioinformatics methods for protein identification using Peptide mass fingerprinting.

Song Z, Chen L, Xu D.

Methods Mol Biol. 2010;604:7-22. doi: 10.1007/978-1-60761-444-9_2.

PMID:
20013361
[PubMed - indexed for MEDLINE]
20.

A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data.

Zhang Z, Sun S, Zhu X, Chang S, Liu X, Yu C, Bu D, Chen R.

BMC Bioinformatics. 2006 Apr 26;7:222.

PMID:
16638152
[PubMed - indexed for MEDLINE]
Free PMC Article

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