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Items: 1 to 20 of 233

1.

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.

2.

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
3.

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.

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.

Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets.

Devabhaktuni A, Elias JE.

J Proteome Res. 2016 Mar 4;15(3):732-42. doi: 10.1021/acs.jproteome.5b00861. Epub 2016 Jan 25.

PMID:
26743026
6.

Exhaustive database searching for amino acid mutations in proteomes.

Hyatt D, Pan C.

Bioinformatics. 2012 Jul 15;28(14):1895-901. doi: 10.1093/bioinformatics/bts274. Epub 2012 May 10.

PMID:
22581177
7.

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
8.

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
9.

How much peptide sequence information is contained in ion trap tandem mass spectra?

Cox J, Hubner NC, Mann M.

J Am Soc Mass Spectrom. 2008 Dec;19(12):1813-20. doi: 10.1016/j.jasms.2008.07.024. Epub 2008 Aug 7.

10.

MSNovo: a dynamic programming algorithm for de novo peptide sequencing via tandem mass spectrometry.

Mo L, Dutta D, Wan Y, Chen T.

Anal Chem. 2007 Jul 1;79(13):4870-8. Epub 2007 Jun 6.

PMID:
17550227
11.

De novo sequencing methods in proteomics.

Hughes C, Ma B, Lajoie GA.

Methods Mol Biol. 2010;604:105-21. doi: 10.1007/978-1-60761-444-9_8.

PMID:
20013367
12.

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. Epub 2008 Mar 7.

PMID:
18324765
13.

De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics.

Egertson JD, Eng JK, Bereman MS, Hsieh EJ, Merrihew GE, MacCoss MJ.

J Am Soc Mass Spectrom. 2012 Dec;23(12):2075-82. doi: 10.1007/s13361-012-0482-z. Epub 2012 Sep 25.

14.

De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra.

Vyatkina K, Wu S, Dekker LJ, VanDuijn MM, Liu X, Tolić N, Dvorkin M, Alexandrova S, Luider TM, Paša-Tolić L, Pevzner PA.

J Proteome Res. 2015 Nov 6;14(11):4450-62. doi: 10.1021/pr501244v. Epub 2015 Oct 13.

PMID:
26412692
15.

NovoExD: De novo Peptide Sequencing for ETD/ECD Spectra.

Yan Y, Kusalik AJ, Wu FX.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Mar-Apr;14(2):337-344. doi: 10.1109/TCBB.2015.2389813.

PMID:
28368811
16.

DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy.

Halligan BD, Ruotti V, Twigger SN, Greene AS.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W376-81.

17.
18.

Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification.

Kim S, Bandeira N, Pevzner PA.

Mol Cell Proteomics. 2009 Jun;8(6):1391-400. doi: 10.1074/mcp.M800535-MCP200. Epub 2009 Mar 2.

19.

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

Frank AM.

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

20.

De novo peptide sequencing using CID and HCD spectra pairs.

Yan Y, Kusalik AJ, Wu FX.

Proteomics. 2016 Oct;16(20):2615-2624. doi: 10.1002/pmic.201500251. Epub 2016 Aug 24.

PMID:
27402425

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