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Items: 1 to 20 of 197

1.

LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia.

Fröhlich T, Arnold GJ, Fritsch R, Mayr T, Laforsch C.

BMC Genomics. 2009 Apr 21;10:171. doi: 10.1186/1471-2164-10-171.

2.

DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs.

Rieder V, Blank-Landeshammer B, Stuhr M, Schell T, Biß K, Kollipara L, Meyer A, Pfenninger M, Westphal H, Sickmann A, Rahnenführer J.

BMC Bioinformatics. 2017 Mar 3;18(1):148. doi: 10.1186/s12859-017-1514-2.

3.

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.

4.

Shotgun ecotoxicoproteomics of Daphnia pulex: biochemical effects of the anticancer drug tamoxifen.

Borgatta M, Hernandez C, Decosterd LA, Chèvre N, Waridel P.

J Proteome Res. 2015 Jan 2;14(1):279-91. doi: 10.1021/pr500916m. Epub 2014 Nov 13.

PMID:
25350372
5.

Differential peptide labeling (iTRAQ) in LC-MS/MS based proteomics in Daphnia reveal mechanisms of an antipredator response.

Effertz C, Müller S, Elert Ev.

J Proteome Res. 2015 Feb 6;14(2):888-96. doi: 10.1021/pr500948a. Epub 2014 Dec 23.

PMID:
25494525
6.

Controlling proteome degradation in Daphnia pulex.

Kemp CJ, Kültz D.

J Exp Zool A Ecol Genet Physiol. 2012 Dec;317(10):645-51. doi: 10.1002/jez.1766. Epub 2012 Oct 1.

7.

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.

8.

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, Fausto N, Hafen E, Hood L, Katze MG, Kennedy KA, Kregenow F, Lee H, Lin B, Martin D, Ranish JA, Rawlings DJ, Samelson LE, Shiio Y, Watts JD, Wollscheid B, Wright ME, Yan W, Yang L, Yi EC, Zhang H, Aebersold R.

Genome Biol. 2005;6(1):R9. Epub 2004 Dec 10.

9.

Fit-for-purpose curated database application in mass spectrometry-based targeted protein identification and validation.

Cheng K, Sloan A, McCorrister S, Babiuk S, Bowden TR, Wang G, Knox JD.

BMC Res Notes. 2014 Jul 10;7:444. doi: 10.1186/1756-0500-7-444.

10.

Global proteomic analysis of protein acetylation affecting metabolic regulation in Daphnia pulex.

Kwon OK, Sim J, Kim SJ, Oh HR, Nam DH, Lee S.

Biochimie. 2016 Feb;121:219-27. doi: 10.1016/j.biochi.2015.12.007. Epub 2015 Dec 15.

PMID:
26700148
11.

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.

12.

Proteomic profiling and protein identification by MALDI-TOF mass spectrometry in unsequenced parasitic nematodes.

Millares P, Lacourse EJ, Perally S, Ward DA, Prescott MC, Hodgkinson JE, Brophy PM, Rees HH.

PLoS One. 2012;7(3):e33590. doi: 10.1371/journal.pone.0033590. Epub 2012 Mar 29.

13.

YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

Colangelo CM, Shifman M, Cheung KH, Stone KL, Carriero NJ, Gulcicek EE, Lam TT, Wu T, Bjornson RD, Bruce C, Nairn AC, Rinehart J, Miller PL, Williams KR.

Genomics Proteomics Bioinformatics. 2015 Feb;13(1):25-35. doi: 10.1016/j.gpb.2014.11.002. Epub 2015 Feb 21.

14.

The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results.

Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R.

BMC Bioinformatics. 2008 Dec 9;9:529. doi: 10.1186/1471-2105-9-529.

15.

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.

Müller SA, Findeiß S, Pernitzsch SR, Wissenbach DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S.

J Proteomics. 2013 Jun 28;86:27-42. doi: 10.1016/j.jprot.2013.04.036. Epub 2013 May 9.

PMID:
23665149
16.
17.

Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides.

Heller M, Ye M, Michel PE, Morier P, Stalder D, Jünger MA, Aebersold R, Reymond F, Rossier JS.

J Proteome Res. 2005 Nov-Dec;4(6):2273-82.

PMID:
16335976
18.

Survey of the camel urinary proteome by shotgun proteomics using a multiple database search strategy.

Alhaider AA, Bayoumy N, Argo E, Gader AG, Stead DA.

Proteomics. 2012 Nov;12(22):3403-6. doi: 10.1002/pmic.201100631. Epub 2012 Oct 19.

PMID:
23001906
19.

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.

PMID:
15080748
20.

pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana.

Baerenfaller K, Hirsch-Hoffmann M, Svozil J, Hull R, Russenberger D, Bischof S, Lu Q, Gruissem W, Baginsky S.

Integr Biol (Camb). 2011 Mar;3(3):225-37. doi: 10.1039/c0ib00078g. Epub 2011 Jan 24.

PMID:
21264403

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