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Items: 1 to 20 of 103

1.

Proteomic identification of monoclonal antibodies from serum.

Boutz DR, Horton AP, Wine Y, Lavinder JJ, Georgiou G, Marcotte EM.

Anal Chem. 2014 May 20;86(10):4758-66. doi: 10.1021/ac4037679. Epub 2014 May 1.

2.

Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response.

Wine Y, Boutz DR, Lavinder JJ, Miklos AE, Hughes RA, Hoi KH, Jung ST, Horton AP, Murrin EM, Ellington AD, Marcotte EM, Georgiou G.

Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2993-8. doi: 10.1073/pnas.1213737110. Epub 2013 Feb 4.

3.

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.

4.

A proteomics approach for the identification and cloning of monoclonal antibodies from serum.

Cheung WC, Beausoleil SA, Zhang X, Sato S, Schieferl SM, Wieler JS, Beaudet JG, Ramenani RK, Popova L, Comb MJ, Rush J, Polakiewicz RD.

Nat Biotechnol. 2012 Mar 25;30(5):447-52. doi: 10.1038/nbt.2167.

PMID:
22446692
5.

Rapid identification of an antibody DNA construct rearrangement sequence variant by mass spectrometry.

Scott RA, Rogers R, Balland A, Brady LJ.

MAbs. 2014;6(6):1453-63. doi: 10.4161/mabs.36222.

6.

Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments.

Tolmachev AV, Monroe ME, Purvine SO, Moore RJ, Jaitly N, Adkins JN, Anderson GA, Smith RD.

Anal Chem. 2008 Nov 15;80(22):8514-25. doi: 10.1021/ac801376g. Epub 2008 Oct 15.

7.

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.

8.

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.

9.

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.

Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI.

Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. doi: 10.1074/mcp.M111.007690. Epub 2011 Aug 29.

10.
11.

MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.

Victor KG, Murgai M, Lyons CE, Templeton TA, Moshnikov SA, Templeton DJ.

J Am Soc Mass Spectrom. 2010 Jan;21(1):80-7. doi: 10.1016/j.jasms.2009.09.007. Epub 2009 Sep 17.

13.

PepExplorer: a similarity-driven tool for analyzing de novo sequencing results.

Leprevost FV, Valente RH, Lima DB, Perales J, Melani R, Yates JR 3rd, Barbosa VC, Junqueira M, Carvalho PC.

Mol Cell Proteomics. 2014 Sep;13(9):2480-9. doi: 10.1074/mcp.M113.037002. Epub 2014 May 30.

14.

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.

16.

Using SEQUEST with theoretically complete sequence databases.

Sadygov RG.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1858-64. doi: 10.1007/s13361-015-1228-5. Epub 2015 Aug 4.

17.

Combination of Multiple Spectral Libraries Improves the Current Search Methods Used to Identify Missing Proteins in the Chromosome-Centric Human Proteome Project.

Cho JY, Lee HJ, Jeong SK, Kim KY, Kwon KH, Yoo JS, Omenn GS, Baker MS, Hancock WS, Paik YK.

J Proteome Res. 2015 Dec 4;14(12):4959-66. doi: 10.1021/acs.jproteome.5b00578. Epub 2015 Sep 14.

PMID:
26330117
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.

19.

Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments.

Krug K, Carpy A, Behrends G, Matic K, Soares NC, Macek B.

Mol Cell Proteomics. 2013 Nov;12(11):3420-30. doi: 10.1074/mcp.M113.029165. Epub 2013 Aug 1.

20.

Precursor ion independent algorithm for top-down shotgun proteomics.

Tsai YS, Scherl A, Shaw JL, MacKay CL, Shaffer SA, Langridge-Smith PR, Goodlett DR.

J Am Soc Mass Spectrom. 2009 Nov;20(11):2154-66. doi: 10.1016/j.jasms.2009.07.024. Epub 2009 Aug 13.

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