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Items: 1 to 20 of 97

1.

PILOT_PROTEIN: identification of unmodified and modified proteins via high-resolution mass spectrometry and mixed-integer linear optimization.

Baliban RC, Dimaggio PA, Plazas-Mayorca MD, Garcia BA, Floudas CA.

J Proteome Res. 2012 Sep 7;11(9):4615-29. doi: 10.1021/pr300418j.

2.

A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry.

Baliban RC, DiMaggio PA, Plazas-Mayorca MD, Young NL, Garcia BA, Floudas CA.

Mol Cell Proteomics. 2010 May;9(5):764-79. doi: 10.1074/mcp.M900487-MCP200.

3.

Computational refinement of post-translational modifications predicted from tandem mass spectrometry.

Chung C, Liu J, Emili A, Frey BJ.

Bioinformatics. 2011 Mar 15;27(6):797-806. doi: 10.1093/bioinformatics/btr017.

4.

Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra.

Chen Y, Zhang J, Xing G, Zhao Y.

J Proteome Res. 2009 Jun;8(6):3141-7. doi: 10.1021/pr900172v.

5.

ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity.

Xu T, Park SK, Venable JD, Wohlschlegel JA, Diedrich JK, Cociorva D, Lu B, Liao L, Hewel J, Han X, Wong CC, Fonslow B, Delahunty C, Gao Y, Shah H, Yates JR 3rd.

J Proteomics. 2015 Nov 3;129:16-24. doi: 10.1016/j.jprot.2015.07.001.

6.

Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry.

Chung C, Emili A, Frey BJ.

Bioinformatics. 2013 Apr 1;29(7):821-9. doi: 10.1093/bioinformatics/btt056.

PMID:
23419374
8.

De novo sequencing with limited number of post-translational modifications per peptide.

He L, Han X, Ma B.

J Bioinform Comput Biol. 2013 Aug;11(4):1350007. doi: 10.1142/S0219720013500078.

PMID:
23859271
9.

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
10.

A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry.

DiMaggio PA Jr, Floudas CA, Lu B, Yates JR 3rd.

J Proteome Res. 2008 Apr;7(4):1584-93. doi: 10.1021/pr700577z.

PMID:
18324765
11.

An efficient algorithm for the blocked pattern matching problem.

Deng F, Wang L, Liu X.

Bioinformatics. 2015 Feb 15;31(4):532-8. doi: 10.1093/bioinformatics/btu678.

PMID:
25322837
12.

PeaksPTM: Mass spectrometry-based identification of peptides with unspecified modifications.

Han X, He L, Xin L, Shan B, Ma B.

J Proteome Res. 2011 Jul 1;10(7):2930-6. doi: 10.1021/pr200153k.

PMID:
21609001
14.

Faster SEQUEST searching for peptide identification from tandem mass spectra.

Diament BJ, Noble WS.

J Proteome Res. 2011 Sep 2;10(9):3871-9. doi: 10.1021/pr101196n.

15.

Software eyes for protein post-translational modifications.

Na S, Paek E.

Mass Spectrom Rev. 2015 Mar-Apr;34(2):133-47. doi: 10.1002/mas.21425. Review.

PMID:
24889695
16.

ISPTM: an iterative search algorithm for systematic identification of post-translational modifications from complex proteome mixtures.

Huang X, Huang L, Peng H, Guru A, Xue W, Hong SY, Liu M, Sharma S, Fu K, Caprez AP, Swanson DR, Zhang Z, Ding SJ.

J Proteome Res. 2013 Sep 6;12(9):3831-42. doi: 10.1021/pr4003883.

17.

Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs.

Li Y, Chi H, Xia L, Chu X.

BMC Bioinformatics. 2014 Apr 28;15:121. doi: 10.1186/1471-2105-15-121.

18.

The H-index of 'an approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database'.

Washburn MP.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1799-803. doi: 10.1007/s13361-015-1181-3.

PMID:
26091891
19.

Database search algorithm for identification of intact cross-links in proteins and peptides using tandem mass spectrometry.

Xu H, Hsu PH, Zhang L, Tsai MD, Freitas MA.

J Proteome Res. 2010 Jul 2;9(7):3384-93. doi: 10.1021/pr100369y.

20.

pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry.

Li D, Fu Y, Sun R, Ling CX, Wei Y, Zhou H, Zeng R, Yang Q, He S, Gao W.

Bioinformatics. 2005 Jul 1;21(13):3049-50.

PMID:
15817687

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