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Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq.

Sheynkman GM, Shortreed MR, Frey BL, Smith LM.

Mol Cell Proteomics. 2013 Aug;12(8):2341-53. doi: 10.1074/mcp.O113.028142. Epub 2013 Apr 29.


Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events.

Menschaert G, Van Criekinge W, Notelaers T, Koch A, Crappé J, Gevaert K, Van Damme P.

Mol Cell Proteomics. 2013 Jul;12(7):1780-90. doi: 10.1074/mcp.M113.027540. Epub 2013 Feb 21.


Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.

Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, Onsongo G, Frey BL, Griffin TJ, Smith LM.

BMC Genomics. 2014 Aug 22;15:703. doi: 10.1186/1471-2164-15-703.


PEPPI: a peptidomic database of human protein isoforms for proteomics experiments.

Zhou A, Zhang F, Chen JY.

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S7. doi: 10.1186/1471-2105-11-S6-S7.


Discovery of novel genes and gene isoforms by integrating transcriptomic and proteomic profiling from mouse liver.

Wu P, Zhang H, Lin W, Hao Y, Ren L, Zhang C, Li N, Wei H, Jiang Y, He F.

J Proteome Res. 2014 May 2;13(5):2409-19. doi: 10.1021/pr4012206. Epub 2014 Apr 18.


Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics.

Helmy M, Sugiyama N, Tomita M, Ishihama Y.

Genes Cells. 2012 Aug;17(8):633-44. doi: 10.1111/j.1365-2443.2012.01615.x. Epub 2012 Jun 12.


Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data.

Bunger MK, Cargile BJ, Sevinsky JR, Deyanova E, Yates NA, Hendrickson RC, Stephenson JL Jr.

J Proteome Res. 2007 Jun;6(6):2331-40. Epub 2007 May 9.


Genome annotation of Anopheles gambiae using mass spectrometry-derived data.

Kalume DE, Peri S, Reddy R, Zhong J, Okulate M, Kumar N, Pandey A.

BMC Genomics. 2005 Sep 19;6:128.


Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides.

Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R.

Mol Cell Proteomics. 2006 Apr;5(4):652-70. Epub 2005 Dec 12.


Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data.

Ning K, Fermin D, Nesvizhskii AI.

J Proteome Res. 2012 Apr 6;11(4):2261-71. doi: 10.1021/pr201052x. Epub 2012 Feb 29.


Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets.

Ning K, Fermin D, Nesvizhskii AI.

Proteomics. 2010 Jul;10(14):2712-8. doi: 10.1002/pmic.200900473.


Improving gene annotation using peptide mass spectrometry.

Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V.

Genome Res. 2007 Feb;17(2):231-9. Epub 2006 Dec 22.


Protein identification using customized protein sequence databases derived from RNA-Seq data.

Wang X, Slebos RJ, Wang D, Halvey PJ, Tabb DL, Liebler DC, Zhang B.

J Proteome Res. 2012 Feb 3;11(2):1009-17. doi: 10.1021/pr200766z. Epub 2011 Dec 14. Erratum in: J Proteome Res. 2012 Sep 7;11(9):4764.


Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring.

Dworzanski JP, Snyder AP, Chen R, Zhang H, Wishart D, Li L.

Anal Chem. 2004 Apr 15;76(8):2355-66.


A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

Mo F, Hong X, Gao F, Du L, Wang J, Omenn GS, Lin B.

BMC Bioinformatics. 2008 Dec 16;9:537. doi: 10.1186/1471-2105-9-537.


High-throughput proteomics detection of novel splice isoforms in human platelets.

Power KA, McRedmond JP, de Stefani A, Gallagher WM, Gaora PO.

PLoS One. 2009;4(3):e5001. doi: 10.1371/journal.pone.0005001. Epub 2009 Mar 24.


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.


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.

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