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Items: 1 to 20 of 35

1.

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.

Eng JK, McCormack AL, Yates JR.

J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89. doi: 10.1016/1044-0305(94)80016-2.

PMID:
24226387
2.

Assigning significance to peptides identified by tandem mass spectrometry using decoy databases.

Käll L, Storey JD, MacCoss MJ, Noble WS.

J Proteome Res. 2008 Jan;7(1):29-34. Epub 2007 Dec 8. Review.

PMID:
18067246
3.

Whole genome searching with shotgun proteomic data: applications for genome annotation.

Sevinsky JR, Cargile BJ, Bunger MK, Meng F, Yates NA, Hendrickson RC, Stephenson JL Jr.

J Proteome Res. 2008 Jan;7(1):80-8. Epub 2007 Dec 7.

PMID:
18062665
4.

Posterior error probabilities and false discovery rates: two sides of the same coin.

Käll L, Storey JD, MacCoss MJ, Noble WS.

J Proteome Res. 2008 Jan;7(1):40-4. Epub 2007 Dec 4. Review.

PMID:
18052118
5.

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ.

Nat Methods. 2007 Nov;4(11):923-5. Epub 2007 Oct 21.

PMID:
17952086
6.

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.

Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA.

Genome Res. 2007 Sep;17(9):1362-77. Epub 2007 Aug 9.

7.

Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway.

Mayor T, Graumann J, Bryan J, MacCoss MJ, Deshaies RJ.

Mol Cell Proteomics. 2007 Nov;6(11):1885-95. Epub 2007 Jul 20.

8.

A high-quality catalog of the Drosophila melanogaster proteome.

Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R.

Nat Biotechnol. 2007 May;25(5):576-83. Epub 2007 Apr 22.

PMID:
17450130
9.

Computational prediction of proteotypic peptides for quantitative proteomics.

Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R.

Nat Biotechnol. 2007 Jan;25(1):125-31. Epub 2006 Dec 31.

PMID:
17195840
10.

Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae.

Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP.

J Proteome Res. 2006 Sep;5(9):2339-47.

PMID:
16944946
11.

Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries.

Frewen BE, Merrihew GE, Wu CC, Noble WS, MacCoss MJ.

Anal Chem. 2006 Aug 15;78(16):5678-84.

PMID:
16906711
12.

The PeptideAtlas project.

Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D655-8.

13.

Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins.

Anderson L, Hunter CL.

Mol Cell Proteomics. 2006 Apr;5(4):573-88. Epub 2005 Dec 6.

14.
15.

The complete genome and proteome of Mycoplasma mobile.

Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, Butler J, Calvo S, Elkins T, FitzGerald MG, Hafez N, Kodira CD, Major J, Wang S, Wilkinson J, Nicol R, Nusbaum C, Birren B, Berg HC, Church GM.

Genome Res. 2004 Aug;14(8):1447-61.

16.

A model for random sampling and estimation of relative protein abundance in shotgun proteomics.

Liu H, Sadygov RG, Yates JR 3rd.

Anal Chem. 2004 Jul 15;76(14):4193-201.

PMID:
15253663
17.

Proteogenomic mapping as a complementary method to perform genome annotation.

Jaffe JD, Berg HC, Church GM.

Proteomics. 2004 Jan;4(1):59-77.

PMID:
14730672
18.

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH.

PLoS Biol. 2003 Nov;1(2):E45. Epub 2003 Nov 17.

19.

Statistical significance for genomewide studies.

Storey JD, Tibshirani R.

Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5. Epub 2003 Jul 25.

20.

C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression.

Reboul J, Vaglio P, Rual JF, Lamesch P, Martinez M, Armstrong CM, Li S, Jacotot L, Bertin N, Janky R, Moore T, Hudson JR Jr, Hartley JL, Brasch MA, Vandenhaute J, Boulton S, Endress GA, Jenna S, Chevet E, Papasotiropoulos V, Tolias PP, Ptacek J, Snyder M, Huang R, Chance MR, Lee H, Doucette-Stamm L, Hill DE, Vidal M.

Nat Genet. 2003 May;34(1):35-41.

PMID:
12679813
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