Proteomics Facility

LC-ESI-MS/MS Instrumentation:



Thermo Orbitrap Elite hybrid linear ion trap FT-MS with Dionex 3000 nanospray UPLC (MBB 1.420)

Thermo LTQ Velos Pro linear ion trap with Proxeon easyLC nanospray LC (MBB 1.420)

AB Sciex 4000 QTrap hybrid triple quadrupole-linear ion trap with Shimadzu Prominence analytical LC (PHR 1.110)

Proteomics Software:

Proteome Discoverer 1.3, MASCOT, and X!Tandem database search algorithms Scaffold 3 Q+ and Scaffold PTM data visualization and validation software


Protein and peptide MW determination. MS/MS and MSn of peptides with CID and/or HCD Protein identification from gel bands, gel sections, and complex mixtures Protein quantitation from spectral counting or stable isotope labeling Protein modification analysis for phosphorylation, methylation, acetylation, ubiquitination, and chemical modifications


Maria Person
Marvin Mercado
Chia-fang Lee

Internal Rates:

MS $46/sample
Protein identification $80/sample, bill 2x for protein complexes or modification analysis
For external rate, go to charges page.


Instructions for downloading the Scaffold Viewer and using it to view proteinidentification results.
View digest protocol
View representative data.

Recent publications:

Cullen TW, Madsen JA, Ivanov PL, Brodbelt JS, Trent MS. Characterization of a unique modification of the flagellar rod protein FlgG by the Campylobacter jejuni lipid A phosphoethanolamine transferase, linking bacterial locomotion and antimicrobial peptide resistance. J Biol Chem. 2011 Dec 9. PMID: 22158617 PMAF Usage: ESI of protein MW

Thomas PW, Zheng M, Wu S, Guo H, Liu D, Xu D, Fast W. Characterization of purified New Delhi metallo-Ī²-lactamase-1. Biochemistry. 2011;50(46):10102-13 PMID: 22029287 PMAF Usage: ESI of protein MW

Lee S, Warthaka M, Yan C, Kaoud TS, Ren P, Dalby KN. Examining docking interactions on ERK2 with modular peptide substrates. Biochemistry. 2011;50(44):9500-10. PMID: 21955038 PMAF Usage: ESI of peptide MW

Johnson CM, Monzingo AF, Ke Z, Yoon DW, Linsky TW, Guo H, Robertus JD, Fast W. On the mechanism of dimethylarginine dimethylaminohydrolase inactivation by 4-halopyridines. J Am Chem Soc. 2011;133(28):10951-9. PMID: 21630706 PMAF Usage: ESI of protein MW

Kaoud TS, Devkota AK, Harris R, Rana MS, Abramczyk O, Warthaka M, Lee S, Girvin ME, Riggs AF, Dalby KN. Activated ERK2 is a monomer in vitro with or without divalent cations and when complexed to the cytoplasmic scaffold PEA-15. Biochemistry. 2011;50(21):4568-78. PMID: 21506533 PMAF Usage: ESI of protein MW

Lee S, Warthaka M, Yan C, Kaoud TS, Piserchio A, Ghose R, Ren P, Dalby KN. A model of a MAPKā€¢substrate complex in an active conformation: a computational and experimental approach. PLoS One. 2011;6(4):e18594. PMID: 21494553 PMAF Usage: ESI of peptide MW

Johnson CM, Linsky TW, Yoon DW, Person MD, Fast W. Discovery of halopyridines as quiescent affinity labels: Inactivation of dimethylarginine dimethylaminohydrolase. J Am Chem Soc. 2011;133(5):1553-62. PMID: 21222447 PMAF Usage: ESI of protein MW

Veeravalli K, Boyd D, Iverson BL, Beckwith J, Georgiou G. Laboratory evolution of glutathione biosynthesis reveals natural compensatory pathways. Nat Chem Biol. 2011;7(2):101-5. PMID: 21186348 PMAF Usage: ESI of peptide MW

Thomas PW, Fast W. Heterologous overexpression, purification, and in vitro characterization of AHL lactonases. Methods Mol Biol. 2011;692:275-90. PMID: 21031319 PMAF Usage: ESI of lactones

Lluis M, Wang Y, Monzingo AF, Fast W, Robertus JD. Characterization of C-Alkyl Amidines as Bioavailable Covalent Reversible Inhibitors of Human DDAH-1. ChemMedChem. 2010;6(1):81-8. PMID: 20979083. PMAF Usage: ESI of protein MW

Liu J, Powell KL, Thames HD, MacLeod MC. Detoxication of sulfur half-mustards by nucleophilic scavengers: robust activity of thiopurines. Chem Res Toxicol. 2010;23(3):488-96. PMCID: 2838965. PMID: 20050632. PMAF Usage: ESI-MS of mustard-purine adducts

Abel EL, Angel JM, Riggs PK, Langfield L, Lo HH, Person MD, Awasthi YC, Wang LE, Strom SS, Wei Q, DiGiovanni J. Evidence that Gsta4 modifies susceptibility to skin tumor development in mice and humans. J Natl Cancer Inst. 2010;102(21):1663-75. PMCID: 2970579. PMID: 20966433 PMAF Usage: MRM metabolite quantitation

Cullen TW, Trent MS. A link between the assembly of flagella and lipooligosaccharide of the Gram-negative bacterium Campylobacter jejuni. Proc Natl Acad Sci U S A. 2010;107(11):5160-5. PMCID: 2841920. PMID: 20194750. PMAF Usage: ESI of protein MW

Callaway K, Waas WF, Rainey MA, Ren P, Dalby KN. Phosphorylation of the transcription factor Ets-1 by ERK2: rapid dissociation of ADP and phospho-Ets-1. Biochemistry. 2010;49(17):3619-30. PMCID: 2868174. PMID: 20361728. PMAF Usage: ESI of protein MW and phosphopeptides

Momb J, Yoon DW, Fast W. Enzymic disruption of N-aroyl-L-homoserine lactone-based quorum sensing. Chembiochem. 2010;11(11):1535-7. PMID: 20544776. PMAF Usage: ESI of protein MW

Burks EA, Fleming CD, Mesecar AD, Whitman CP, Pegan SD. Kinetic and structural characterization of a heterohexamer 4-oxalocrotonate tautomerase from Chloroflexus aurantiacus J-10-fl: implications for functional and structural diversity in the tautomerase superfamily. Biochemistry. 2010;49(24):5016-27. PMCID: 2913408. PMID: 20465238. PMAF Usage: ESI of protein MW

Borisova SA, Liu HW. Characterization of glycosyltransferase DesVII and its auxiliary partner protein DesVIII in the methymycin/picromycin biosynthetic pathway. Biochemistry. 2010;49(37):8071-84. PMCID: 2939310. PMID: 20695498. PMAF Usage: ESI of protein MW

Wang Y, Monzingo AF, Hu S, Schaller TH, Robertus JD, Fast W. Developing dual and specific inhibitors of dimethylarginine dimethylaminohydrolase-1 and nitric oxide synthase: toward a targeted polypharmacology to control nitric oxide. Biochemistry. 2009;48(36):8624-35. PMCID: 2746464. PMID: 19663506. PMAF Usage: ESI of protein MW

Robertson BA, Schroeder GK, Jin Z, Johnson KA, Whitman CP. Pre-steady-state kinetic analysis of cis-3-chloroacrylic acid dehalogenase: analysis and implications. Biochemistry. 2009;48(49):11737-44. PMCID: 2790542. PMID: 19856961. PMAF Usage: ESI of protein MW

Tolman JA, Nelson NA, Bosselmann S, Peters JI, Coalson JJ, Wiederhold NP, et al. Dose tolerability of chronically inhaled voriconazole solution in rodents. Int J Pharm. 2009;379(1):25-31. PMID: 19524030. PMAF Usage: MRM quantitation of voriconazole

Labenski MT, Fisher AA, Lo HH, Monks TJ, Lau SS. Protein electrophile-binding motifs: lysine-rich proteins are preferential targets of quinones. Drug Metab Dispos. 2009;37(6):1211-8 PMID: 19251821 PMAF Usage:ESI of glutathione conjugates, LC-MS/MS protein identification

Li J, Kaoud TS, Laroche C, Dalby KN, Kerwin SM. Synthesis and biological evaluation of p38alpha kinase-targeting dialkynylimidazoles. Bioorg Med Chem Lett. 2009;19(22):6293-7. PMCID: 2789032. PMID: 19822424. PMAF Usage: ESI of protein MW

Robertson BA, Johnson WH, Lo HH, Jr., Whitman CP. Inactivation of Cg10062, a cis-3-chloroacrylic acid dehalogenase homologue in Corynebacterium glutamicum, by (R)- and (S)-oxirane-2-carboxylate: analysis and implications. Biochemistry. 2008;47(33):8796-803. PMCID: 2646761. PMID: 18646866. PMAF Usage: ESI of protein MW

Poelarends GJ, Serrano H, Person MD, Johnson WH, Jr., Whitman CP. Characterization of Cg10062 from Corynebacterium glutamicum: implications for the evolution of cis-3-chloroacrylic acid dehalogenase activity in the tautomerase superfamily. Biochemistry. 2008;47(31):8139-47. PMCID: 2659011. PMID: 18598055. PMAF Usage: ESI of protein MW

Linsky TW, Monzingo AF, Stone EM, Robertus JD, Fast W. Promiscuous partitioning of a covalent intermediate common in the pentein superfamily. Chem Biol. 2008;15(5):467-75. PMCID: 2601531. PMID: 18482699. PMAF Usage: ESI-MS of reaction products

Giles TN, Graham DE. Crenarchaeal arginine decarboxylase evolved from an S-adenosylmethionine decarboxylase enzyme. J Biol Chem. 2008;283(38):25829-38. PMCID: 2533785. PMID: 18650422. PMAF Usage: ESI of protein MW

Wang SC, Johnson WH, Jr., Czerwinski RM, Stamps SL, Whitman CP. Kinetic and stereochemical analysis of YwhB, a 4-oxalocrotonate tautomerase homologue in Bacillus subtilis: mechanistic implications for the YwhB- and 4-oxalocrotonate tautomerase-catalyzed reactions. Biochemistry. 2007;46(42):11919-29. PMCID: 2531070. PMID: 17902707. PMAF Usage: ESI of protein MW

Waas WF, Dalby KN. The expression and purification of the N-terminal activation domain of the transcription factor c-Myc: a model substrate for exploring ERK2 docking interactions. Protein Expr Purif. 2007;53(1):80-6. PMID: 17251036. PMAF Usage: ESI of protein MW, phosphopeptide MS/MS

Morrison AJ, Kim JA, Person MD, Highland J, Xiao J, Wehr TS, et al. Mec1/Tel1 phosphorylation of the INO80 chromatin remodeling complex influences DNA damage checkpoint responses. Cell. 2007;130(3):499-511. PMID: 17693258. PMAF Usage: LC-ESI-MS separation and purification of proteins and MW determination, ESI of protein MW

Lu C, Zhu J, Wang Y, Umeda A, Cowmeadow RB, Lai E, et al. Staphylococcus aureus sortase A exists as a dimeric protein in vitro. Biochemistry. 2007;46(32):9346-54. PMID: 17658894. PMAF Usage: ESI of protein MW

Hong L, Fast W. Inhibition of human dimethylarginine dimethylaminohydrolase-1 by S-nitroso-L-homocysteine and hydrogen peroxide. Analysis, quantification, and implications for hyperhomocysteinemia. J Biol Chem. 2007;282(48):34684-92. PMID: 17895252. PMAF Usage: ESI of protein MW

Giles TN, Graham DE. Characterization of an acid-dependent arginine decarboxylase enzyme from Chlamydophila pneumoniae. J Bacteriol. 2007;189(20):7376-83. PMCID: 2168457. PMID: 17693492. PMAF Usage: LCQ ESI of protein MW

de Jong RM, Bazzacco P, Poelarends GJ, Johnson WH, Jr., Kim YJ, Burks EA, et al. Crystal structures of native and inactivated cis-3-chloroacrylic acid dehalogenase. Structural basis for substrate specificity and inactivation by (R)-oxirane-2-carboxylate. J Biol Chem. 2007;282(4):2440-9. PMID: 17121835. PMAF Usage: ESI of protein MW

Last Reviewed: February 13, 2012

Maria D. Person

Michelle V. Gadush

Andre Bui

Delivery Address:

Proteomics Facility
The University of Texas
at Austin
2500 Speedway MBB 1.420
Stop A4800
Austin, TX, USA

Email Address: pmaf


Institute for Cellular and Molecular Biology (ICMB)

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