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Items: 1 to 20 of 384

1.

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.

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GlycoMaster DB: software to assist the automated identification of N-linked glycopeptides by tandem mass spectrometry.

He L, Xin L, Shan B, Lajoie GA, Ma B.

J Proteome Res. 2014 Sep 5;13(9):3881-95. doi: 10.1021/pr401115y. Epub 2014 Aug 25.

PMID:
25113421
4.

Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID).

Kelstrup CD, Frese C, Heck AJ, Olsen JV, Nielsen ML.

Mol Cell Proteomics. 2014 Aug;13(8):1914-24. doi: 10.1074/mcp.O113.035915. Epub 2014 Jun 3.

5.

Protein identification by spectral networks analysis.

Bandeira N, Tsur D, Frank A, Pevzner PA.

Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6140-5. Epub 2007 Apr 2.

6.

A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry.

Pan C, Park BH, McDonald WH, Carey PA, Banfield JF, VerBerkmoes NC, Hettich RL, Samatova NF.

BMC Bioinformatics. 2010 Mar 5;11:118. doi: 10.1186/1471-2105-11-118.

7.

Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra.

Kim S, Gupta N, Bandeira N, Pevzner PA.

Mol Cell Proteomics. 2009 Jan;8(1):53-69. doi: 10.1074/mcp.M800103-MCP200. Epub 2008 Aug 14.

8.

Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks.

Na S, Payne SH, Bandeira N.

Mol Cell Proteomics. 2016 Nov;15(11):3501-3512. Epub 2016 Sep 8.

9.

A spectral clustering approach to MS/MS identification of post-translational modifications.

Falkner JA, Falkner JW, Yocum AK, Andrews PC.

J Proteome Res. 2008 Nov;7(11):4614-22. doi: 10.1021/pr800226w. Epub 2008 Sep 19.

PMID:
18800783
10.

The generating function approach for Peptide identification in spectral networks.

Guthals A, Boucher C, Bandeira N.

J Comput Biol. 2015 May;22(5):353-66. doi: 10.1089/cmb.2014.0165. Epub 2014 Nov 25.

11.

Algorithms for the de novo sequencing of peptides from tandem mass spectra.

Allmer J.

Expert Rev Proteomics. 2011 Oct;8(5):645-57. doi: 10.1586/epr.11.54. Review.

PMID:
21999834
12.

Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing.

Waridel P, Frank A, Thomas H, Surendranath V, Sunyaev S, Pevzner P, Shevchenko A.

Proteomics. 2007 Jul;7(14):2318-29.

PMID:
17623296
13.

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.

14.

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. Epub 2011 May 24.

PMID:
21609001
15.

Prediction of novel modifications by unrestrictive search of tandem mass spectra.

Na S, Paek E.

J Proteome Res. 2009 Oct;8(10):4418-27. doi: 10.1021/pr9001146.

PMID:
19658439
16.

Unrestrictive identification of multiple post-translational modifications from tandem mass spectrometry using an error-tolerant algorithm based on an extended sequence tag approach.

Na S, Jeong J, Park H, Lee KJ, Paek E.

Mol Cell Proteomics. 2008 Dec;7(12):2452-63. doi: 10.1074/mcp.M800101-MCP200. Epub 2008 Aug 12.

18.

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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Extending the coverage of spectral libraries: a neighbor-based approach to predicting intensities of peptide fragmentation spectra.

Ji C, Arnold RJ, Sokoloski KJ, Hardy RW, Tang H, Radivojac P.

Proteomics. 2013 Mar;13(5):756-65. doi: 10.1002/pmic.201100670. Epub 2013 Feb 4.

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