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Items: 1 to 20 of 103

1.

An Efficient Algorithm for Clustering of Large-Scale Mass Spectrometry Data.

Saeed F, Pisitkun T, Knepper MA, Hoffert JD.

Proceedings (IEEE Int Conf Bioinformatics Biomed). 2012 Oct 4:1-4.

2.

CAMS-RS: Clustering Algorithm for Large-Scale Mass Spectrometry Data Using Restricted Search Space and Intelligent Random Sampling.

Saeed F, Hoffert JD, Knepper MA.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jan-Feb;11(1):128-41. doi: 10.1109/TCBB.2013.152.

PMID:
26355513
3.

CAMS-RS: Clustering Algorithm for Large-Scale Mass Spectrometry Data using Restricted Search Space and Intelligent Random Sampling.

Saeed F, Hoffert JD, Knepper MA.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov 22. [Epub ahead of print]

PMID:
24277952
4.

Exploiting Thread-Level and Instruction-Level Parallelism to Cluster Mass Spectrometry Data using Multicore Architectures.

Saeed F, Hoffert JD, Pisitkun T, Knepper MA.

Netw Model Anal Health Inform Bioinform. 2014 Apr;3:54.

5.

An Efficient Dynamic Programming Algorithm for Phosphorylation Site Assignment of Large-Scale Mass Spectrometry Data.

Saeed F, Pisitkun T, Hoffert JD, Wang G, Gucek M, Knepper MA.

Proceedings (IEEE Int Conf Bioinformatics Biomed). 2012 Oct 4:618-625.

6.

GPQuest: A Spectral Library Matching Algorithm for Site-Specific Assignment of Tandem Mass Spectra to Intact N-glycopeptides.

Toghi Eshghi S, Shah P, Yang W, Li X, Zhang H.

Anal Chem. 2015;87(10):5181-8. doi: 10.1021/acs.analchem.5b00024. Epub 2015 May 6.

7.

Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra.

Rieder V, Schork KU, Kerschke L, Blank-Landeshammer B, Sickmann A, Rahnenführer J.

J Proteome Res. 2017 Nov 3;16(11):4035-4044. doi: 10.1021/acs.jproteome.7b00427.

PMID:
28959885
8.

Clustering millions of tandem mass spectra.

Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA.

J Proteome Res. 2008 Jan;7(1):113-22. Epub 2007 Dec 8.

9.

PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data.

Saeed F, Pisitkun T, Hoffert JD, Rashidian S, Wang G, Gucek M, Knepper MA.

Proteome Sci. 2013 Nov 7;11(Suppl 1):S14. doi: 10.1186/1477-5956-11-S1-S14. Epub 2013 Nov 7.

10.

DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data.

Fu Y, Xiu LY, Jia W, Ye D, Sun RX, Qian XH, He SM.

Mol Cell Proteomics. 2011 May;10(5):M110.000455. doi: 10.1074/mcp.M110.000455. Epub 2011 Feb 14.

11.

High-throughput database search and large-scale negative polarity liquid chromatography-tandem mass spectrometry with ultraviolet photodissociation for complex proteomic samples.

Madsen JA, Xu H, Robinson MR, Horton AP, Shaw JB, Giles DK, Kaoud TS, Dalby KN, Trent MS, Brodbelt JS.

Mol Cell Proteomics. 2013 Sep;12(9):2604-14. doi: 10.1074/mcp.O113.028258. Epub 2013 May 21.

12.

pNovo: de novo peptide sequencing and identification using HCD spectra.

Chi H, Sun RX, Yang B, Song CQ, Wang LH, Liu C, Fu Y, Yuan ZF, Wang HP, He SM, Dong MQ.

J Proteome Res. 2010 May 7;9(5):2713-24. doi: 10.1021/pr100182k.

PMID:
20329752
13.

Implementation and application of a versatile clustering tool for tandem mass spectrometry data.

Flikka K, Meukens J, Helsens K, Vandekerckhove J, Eidhammer I, Gevaert K, Martens L.

Proteomics. 2007 Sep;7(18):3245-58.

PMID:
17708593
14.

LC-MSsim--a simulation software for liquid chromatography mass spectrometry data.

Schulz-Trieglaff O, Pfeifer N, Gröpl C, Kohlbacher O, Reinert K.

BMC Bioinformatics. 2008 Oct 8;9:423. doi: 10.1186/1471-2105-9-423.

15.

pNovo+: de novo peptide sequencing using complementary HCD and ETD tandem mass spectra.

Chi H, Chen H, He K, Wu L, Yang B, Sun RX, Liu J, Zeng WF, Song CQ, He SM, Dong MQ.

J Proteome Res. 2013 Feb 1;12(2):615-25. doi: 10.1021/pr3006843. Epub 2012 Dec 28.

PMID:
23272783
16.

MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra.

Dorfer V, Pichler P, Stranzl T, Stadlmann J, Taus T, Winkler S, Mechtler K.

J Proteome Res. 2014 Aug 1;13(8):3679-84. doi: 10.1021/pr500202e. Epub 2014 Jun 26.

17.

The spectral networks paradigm in high throughput mass spectrometry.

Guthals A, Watrous JD, Dorrestein PC, Bandeira N.

Mol Biosyst. 2012 Oct;8(10):2535-44. doi: 10.1039/c2mb25085c. Review.

18.

Enhanced peptide quantification using spectral count clustering and cluster abundance.

Lee S, Kwon MS, Lee HJ, Paik YK, Tang H, Lee JK, Park T.

BMC Bioinformatics. 2011 Oct 28;12:423. doi: 10.1186/1471-2105-12-423.

19.

PepSOM: an algorithm for peptide identification by tandem mass spectrometry based on SOM.

Ning K, Ng HK, Leong HW.

Genome Inform. 2006;17(2):194-205.

PMID:
17503392
20.

A dynamic noise level algorithm for spectral screening of peptide MS/MS spectra.

Xu H, Freitas MA.

BMC Bioinformatics. 2010 Aug 23;11:436. doi: 10.1186/1471-2105-11-436.

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