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Julian Watts

2009
Mirzaei H, Brusniak MY, Mueller LN, Letarte S, Watts J, Aebersold R.  2009.  Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry. Mol Cell Proteomics. 8:1934-46.
Wollscheid B, Bausch-Fluck D, Henderson C, O'Brien R, Bibel M, Schiess R, Aebersold R, Watts J.  2009.  Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat Biotechnol. 27:378-86.
Teckchandani A, Toida N, Goodchild J, Henderson C, Watts J, Wollscheid B, Cooper JA.  2009.  Quantitative proteomics identifies a Dab2/integrin module regulating cell migration. J Cell Biol. 186:99-111.
2008
Mirzaei H, McBee JK, Watts J, Aebersold R.  2008.  Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Mol Cell Proteomics. 7:813-23.
Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V et al..  2008.  Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics. 9:542.
Letarte S, Brusniak MY, Campbell D, Eddes J, Kemp CJ, Lau H, Mueller L, Schmidt A, Shannon P, Kelly-Spratt KS et al..  2008.  Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform. Clin Proteomics. 4:105.
2007
Prakash A, Piening B, Whiteaker J, Zhang H, Shaffer SA, Martin D, Hohmann L, Cooke K, Olson JM, Hansen S et al..  2007.  Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics. Mol Cell Proteomics. 6:1741-8.
Whiteaker JR, Zhang H, Eng JK, Fang R, Piening BD, Feng LC, Lorentzen TD, Schoenherr RM, Keane JF, Holzman T et al..  2007.  Head-to-head comparison of serum fractionation techniques. J Proteome Res. 6:828-36.
Zhang H, Liu AY, Loriaux P, Wollscheid B, Zhou Y, Watts J, Aebersold R.  2007.  Mass spectrometric detection of tissue proteins in plasma. Mol Cell Proteomics. 6:64-71.
2006
Gupta N, Wollscheid B, Watts J, Scheer B, Aebersold R, DeFranco AL.  2006.  Quantitative proteomic analysis of B cell lipid rafts reveals that ezrin regulates antigen receptor-mediated lipid raft dynamics. Nat Immunol. 7:625-33.
2005
Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S et al..  2005.  Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 6:R9.
Tao WA, Wollscheid B, O'Brien R, Eng JK, Li XJ, Bodenmiller B, Watts J, Hood L, Aebersold R.  2005.  Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods. 2:591-8.
2004
Wollscheid B, von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR et al..  2004.  Lipid raft proteins and their identification in T lymphocytes. Subcell Biochem. 37:121-52.
Wollscheid B, Watts J, Aebersold R.  2004.  Proteomics/genomics and signaling in lymphocytes. Curr Opin Immunol. 16:337-44.
Sozio MS, Mathis MA, Young JA, Walchli S, Pitcher LA, Wrage PC, Bartok B, Campbell A, Watts J, Aebersold R et al..  2004.  PTPH1 is a predominant protein-tyrosine phosphatase capable of interacting with and dephosphorylating the T cell receptor zeta subunit. J Biol Chem. 279:7760-9.
2003
von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R et al..  2003.  The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of s. Mol Cell Proteomics. 2:428-42.
von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R et al..  2003.  The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and t. Mol Cell Proteomics. 2:426-7.
2002
Aebersold R, Watts J.  2002.  The need for national centers for proteomics. Nat Biotechnol. 20:651.
Zhou H, Ranish JA, Watts J, Aebersold R.  2002.  Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat Biotechnol. 20:512-5.
2001
Heller M, Watts J, Aebersold R.  2001.  CD28 stimulation regulates its association with N-ethylmaleimide-sensitive fusion protein and other proteins involved in vesicle sorting. Proteomics. 1:70-8.
Goodlett DR, Keller A, Watts J, Newitt R, Yi EC, Purvine S, Eng JK, von Haller P, Aebersold R, Kolker E.  2001.  Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation. Rapid Commun Mass Spectrom. 15:1214-21.
von Haller PD, Donohoe S, Goodlett DR, Aebersold R, Watts J.  2001.  Mass spectrometric characterization of proteins extracted from Jurkat T cell detergent-resistant membrane domains. Proteomics. 1:1010-21.
Zhou H, Watts J, Aebersold R.  2001.  A systematic approach to the analysis of protein phosphorylation. Nat Biotechnol. 19:375-8.
2000
Heller M, Goodlett DR, Watts J, Aebersold R.  2000.  A comprehensive characterization of the T-cell antigen receptor complex composition by microcapillary liquid chromatography-tandem mass spectrometry. Electrophoresis. 21:2180-95.
Aebersold R, Hood LE, Watts J.  2000.  Equipping scientists for the new biology. Nat Biotechnol. 18:359.
Goodlett DR, Aebersold R, Watts J.  2000.  Quantitative in vitro kinase reaction as a guide for phosphoprotein analysis by mass spectrometry. Rapid Commun Mass Spectrom. 14:344-8.
Ostrowski J, Schullery DS, Denisenko ON, Higaki Y, Watts J, Aebersold R, Stempka L, Gschwendt M, Bomsztyk K.  2000.  Role of tyrosine phosphorylation in the regulation of the interaction of heterogenous nuclear ribonucleoprotein K protein with its protein and RNA partners. J Biol Chem. 275:3619-28.

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