Extended O‑GlcNAc on HLA Class-I-Bound Peptides
J. of American Chemical Society, June 25, 2015 [Epub ahead of print]
Marino F, Bern M, Mommen G, Leney A, van Ganns-van den Brink J, Bonvin A, Becker C, van Els C, Heck, A
Glycoproteomic analysis of the secretome of human endothelial cells.
Mol Cell Proteomics. 2013 Jan 23. [Epub ahead of print]
Polylactosaminoglycan glycomics: enhancing the detection of high molecular weight N-glycans in MALDI-TOF profiles by matched filtering.
Mol Cell Proteomics. 2013 Jan 16. [Epub ahead of print]
Byonic: advanced peptide and protein identification software.
Curr Protoc Bioinformatics. 2012 Dec; Chapter 13:Unit13.20.
Bern M, Kil YJ, Becker C
http://www.ncbi.nlm.nih.gov/pubmed/23255153
Constrained de novo sequencing of conotoxins.
J Proteome Res. 2012 Aug 3;11(8):4191-200. Epub 2012 Jul 2.
Two-dimensional target decoy strategy for shotgun proteomics.
J Proteome Res. 2011 Dec 2;10(12):5296-301. Epub 2011 Nov 7.
Bern MW, Kil YJ.
http://www.ncbi.nlm.nih.gov/pubmed/22010998
Comment on “Unbiased statistical analysis for multi-stage proteomic search strategies”.
J Proteome Res. 2011 Apr 1;10(4):2123-7. Epub 2011 Feb 21.
Bern M, Kil YJ.
http://www.ncbi.nlm.nih.gov/pubmed/21288048
Preview: a program for surveying shotgun proteomics tandem mass spectrometry data.
Anal Chem. 2011 Jul 1;83(13):5259-67. Epub 2011 Jun 13
Kil YJ, Becker C, Sandoval W, Goldberg D, Bern M.
http://www.ncbi.nlm.nih.gov/pubmed/21619057
Proteomic changes in cerebrospinal fluid of presymptomatic and affected persons carrying familial Alzheimer disease mutations.
Arch Neurol. 2012 Jan;69(1):96-104.
Ringman JM, Schulman H, Becker C, Jones T, Bai Y, Immermann F, Cole G, Sokolow S, Gylys K, Geschwind DH, Cummings JL, Wan HI.
http://www.ncbi.nlm.nih.gov/pubmed/22232349
Implication of perturbed axoglial apparatus in early pediatric multiple sclerosis.
Ann Neurol. 2012 May;71(5):601-13. doi: 10.1002/ana.22693. Epub 2012 Apr 4.
Dhaunchak AS, Becker C, Schulman H, De Faria O Jr, Rajasekharan S, Banwell B, Colman DR, Bar-Or A; Canadian Pediatric.
http://www.ncbi.nlm.nih.gov/pubmed/22473675
Protein standard absolute quantification (PSAQ) method for the measurement of cellular ubiquitin pools.
Nat Methods. 2011 Jul 10;8(8):691-6. doi: 10.1038/nmeth.1649.
Kaiser SE, Riley BE, Shaler TA, Trevino RS, Becker CH, Schulman H, Kopito RR.
http://www.ncbi.nlm.nih.gov/pubmed/21743460
Recent developments in quantitative proteomics.
Mutat Res. 2011 Jun 17;722(2):171-82. Epub 2010 Jul 8.
Becker CH, Bern M.
http://www.ncbi.nlm.nih.gov/pubmed/20620221
Consistency of a two clinical site sample collection: a proteomics study.
Proteomics Clin Appl. 2010 Sep;4(8-9):726-38.
Wiesner CHannum CReckamp KFiglin RDubridge RRoy SMLin SBecker CHJones THiller JCheville JCWilson K.
http://www.ncbi.nlm.nih.gov/pubmed/21137090
Identification of tandem mass spectra of mixtures of isomeric peptides.
J Proteome Res. 2010 Jun 4;9(6):3270-9.
Chen X, Drogaris P, Bern M.
http://www.ncbi.nlm.nih.gov/pubmed/20329787
Conversion of methionine into homocysteic acid in heavily oxidized proteomics samples.
Rapid Commun Mass Spectrom. 2010 Mar;24(6):768-72.
Bern M, Saladino J, Sharp JS.
http://www.ncbi.nlm.nih.gov/pubmed/20169556
Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry.
Anal Chem. 2010 Feb 1;82(3):833-41.
Bern M, Finney G, Hoopmann MR, Merrihew G, Toth MJ, MacCoss MJ.
http://www.ncbi.nlm.nih.gov/pubmed/20039681
Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting.
Mol Cell Proteomics. 2009 Aug;8(8):1999-2010. Epub 2009 May 26.
Zhu Y, Guo T, Park JE, Li X, Meng W, Datta A, Bern M, Lim SK, Sze SK.
http://www.ncbi.nlm.nih.gov/pubmed/19473960
Glycan family analysis for deducing N-glycan topology from single MS.
Bioinformatics. 2009 Feb 1;25(3):365-71. Epub 2008 Dec 10.
Goldberg D, Bern M, North SJ, Haslam SM, Dell A.
http://www.ncbi.nlm.nih.gov/pubmed/19073587
Improved ranking functions for protein and modification-site identifications.
J Comput Biol. 2008 Sep;15(7):705-19.
Bern M, Goldberg D.
http://www.ncbi.nlm.nih.gov/pubmed/18651800
Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1.
J Am Soc Mass Spectrom. 2008 Nov;19(11):1692-705. Epub 2008 Jul 18.
Charvátová O, Foley BL, Bern MW, Sharp JS, Orlando R, Woods RJ.
http://www.ncbi.nlm.nih.gov/pubmed/18707901
Protein biomarker identification in the CSF of patients with CNS lymphoma.
J Clin Oncol. 2008 Jan 1;26(1):96-105. Epub 2007 Dec 3.
Roy S, Josephson SA, Fridlyand J, Karch J, Kadoch C, Karrim J, Damon L, Treseler P, Kunwar S, Shuman MA, Jones T, Becker CH, Schulman H, Rubenstein JL.
http://www.ncbi.nlm.nih.gov/pubmed/18056677
Automated N-glycopeptide identification using a combination of single- and tandem-MS.
J Proteome Res. 2007 Oct;6(10):3995-4005. Epub 2007 Aug 30.
Goldberg D, Bern M, Parry S, Sutton-Smith M, Panico M, Morris HR, Dell A.
http://www.ncbi.nlm.nih.gov/pubmed/17727280
Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry.
Anal Chem. 2007 Feb 15;79(4):1393-400. Epub 2007 Jan 23.
Bern M, Cai Y, Goldberg D.
http://www.ncbi.nlm.nih.gov/pubmed/17243770