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Phosphorylation of NS5A Serine-235 is essential to hepatitis C virus RNA replication and normal replication compartment formation.

Eyre NS, Hampton-Smith RJ, Aloia AL, Eddes JS, Simpson KJ, Hoffmann P, Beard MR.

Virology. 2016 Apr;491:27-44. doi: 10.1016/j.virol.2016.01.018. Epub 2016 Feb 10.


Matrix-assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin-fixed tissue.

Gustafsson OJ, Eddes JS, Meding S, McColl SR, Oehler MK, Hoffmann P.

Rapid Commun Mass Spectrom. 2013 Mar 30;27(6):655-70. doi: 10.1002/rcm.6488.


Tryptic peptide reference data sets for MALDI imaging mass spectrometry on formalin-fixed ovarian cancer tissues.

Meding S, Martin K, Gustafsson OJ, Eddes JS, Hack S, Oehler MK, Hoffmann P.

J Proteome Res. 2013 Jan 4;12(1):308-15. doi: 10.1021/pr300996x. Epub 2012 Dec 13.


Internal calibrants allow high accuracy peptide matching between MALDI imaging MS and LC-MS/MS.

Gustafsson JO, Eddes JS, Meding S, Koudelka T, Oehler MK, McColl SR, Hoffmann P.

J Proteomics. 2012 Aug 30;75(16):5093-105. doi: 10.1016/j.jprot.2012.04.054. Epub 2012 May 23.


Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N.

Hohmann L, Sherwood C, Eastham A, Peterson A, Eng JK, Eddes JS, Shteynberg D, Martin DB.

J Proteome Res. 2009 Mar;8(3):1415-22. doi: 10.1021/pr800774h.


Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.

Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD.

BMC Bioinformatics. 2008 Dec 16;9:542. doi: 10.1186/1471-2105-9-542.


Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform.

Letarte S, Brusniak MY, Campbell D, Eddes J, Kemp CJ, Lau H, Mueller L, Schmidt A, Shannon P, Kelly-Spratt KS, Vitek O, Zhang H, Aebersold R, Watts JD.

Clin Proteomics. 2008 Dec 1;4(3-4):105.


Building consensus spectral libraries for peptide identification in proteomics.

Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R.

Nat Methods. 2008 Oct;5(10):873-5. doi: 10.1038/nmeth.1254. Epub 2008 Sep 21.


The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools.

Klimek J, Eddes JS, Hohmann L, Jackson J, Peterson A, Letarte S, Gafken PR, Katz JE, Mallick P, Lee H, Schmidt A, Ossola R, Eng JK, Aebersold R, Martin DB.

J Proteome Res. 2008 Jan;7(1):96-103. Epub 2007 Aug 21.


Development and validation of a spectral library searching method for peptide identification from MS/MS.

Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R.

Proteomics. 2007 Mar;7(5):655-67.


Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas.

King NL, Deutsch EW, Ranish JA, Nesvizhskii AI, Eddes JS, Mallick P, Eng J, Desiere F, Flory M, Martin DB, Kim B, Lee H, Raught B, Aebersold R.

Genome Biol. 2006;7(11):R106.


Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing.

Seebacher J, Mallick P, Zhang N, Eddes JS, Aebersold R, Gelb MH.

J Proteome Res. 2006 Sep;5(9):2270-82.


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.


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.


Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database.

Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H, Paik YK, Yoo JS, Ping P, Pounds J, Adkins J, Qian X, Wang R, Wasinger V, Wu CY, Zhao X, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher DW, Hanash SM.

Proteomics. 2005 Aug;5(13):3226-45.


Application of 2-D free-flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-abundance proteins.

Moritz RL, Clippingdale AB, Kapp EA, Eddes JS, Ji H, Gilbert S, Connolly LM, Simpson RJ.

Proteomics. 2005 Aug;5(13):3402-13.


Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation.

Kapp EA, Sch├╝tz F, Reid GE, Eddes JS, Moritz RL, O'Hair RA, Speed TP, Simpson RJ.

Anal Chem. 2003 Nov 15;75(22):6251-64.


CHOMPER: a bioinformatic tool for rapid validation of tandem mass spectrometry search results associated with high-throughput proteomic strategies.

Eddes JS, Kapp EA, Frecklington DF, Connolly LM, Layton MJ, Moritz RL, Simpson RJ.

Proteomics. 2002 Sep;2(9):1097-103.


Proteomic analysis of the human colon carcinoma cell line (LIM 1215): development of a membrane protein database.

Simpson RJ, Connolly LM, Eddes JS, Pereira JJ, Moritz RL, Reid GE.

Electrophoresis. 2000 May;21(9):1707-32.

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