Publications

2013

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins.

H. Mirzaei, T. A. Knijnenburg, B. Kim, M. Robinson, P. Picotti, G. W. Carter, S. Li, D. J. Dilworth, J. K. Eng, J. D. Aitchison, I. Shmulevich, T. Galitski, R. Aebersold and J. Ranish, PNAS, Early Edition doi: 10.1073/pnas.1216918110, 2013.

2012

Cloud CPFP: A Shotgun Proteomics Data Analysis Pipeline Using Cloud and High Performance Computing.

Trudgian DC, Mirzaei H, Journal of proteome research, 2012 Oct;

2011

Glutathione-S-transferase P1 is a critical regulator of Cdk5 kinase activity.

Sun KH, Chang KH, Clawson S, Ghosh S, Mirzaei H, Regnier F, Shah K, Journal of neurochemistry, 2011 Sep 5 (118) 1471-4159

2010

Characterizing the connectivity of poly-ubiquitin chains by selected reaction monitoring mass spectrometry.

Mirzaei H, Rogers RS, Grimes B, Eng J, Aderem A, Aebersold R, Molecular bioSystems, 2010 Oct 10 (6) 1742-2051

QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments.

Dilworth DJ, Saleem RA, Rogers RS, Mirzaei H, Boyle J, Aitchison JD, Journal of the American Society for Mass Spectrometry, 2010 Aug 8 (21) 1879-1123

Guidelines for reporting the use of column chromatography in proteomics.

Jones AR, Carroll K, Knight D, Maclellan K, Domann PJ, Legido-Quigley C, Huang L, Smallshaw L, Mirzaei H, Shofstahl J, Paton NW, Nature biotechnology, 2010 Jul 7 (28) 1546-1696

Synthesis, metabolism and in vitro cytotoxicity studies on novel lavendamycin antitumor agents.

Cai W, Hassani M, Karki R, Walter ED, Koelsch KH, Seradj H, Lineswala JP, Mirzaei H, York JS, Olang F, Sedighi M, Lucas JS, Eads TJ, Rose AS, Charkhzarrin S, Hermann NG, Beall HD, Behforouz M, Bioorganic & medicinal chemistry, 2010 Mar 5 (18) 1464-3391

2009

Proteins That Underlie Neoplastic Progression of Ulcerative Colitis.

Brentnall TA, Pan S, Bronner MP, Crispin DA, Mirzaei H, Cooke K, Tamura Y, Nikolskaya T, Jebailey L, Goodlett DR, McIntosh M, Aebersold R, Rabinovitch PS, Chen R, Proteomics. Clinical applications, 2009 Sep 11 (3) 1862-8354

Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry.

Mirzaei H, Brusniak MY, Mueller LN, Letarte S, Watts JD, Aebersold R, Molecular & cellular proteomics : MCP, 2009 Aug 8 (8) 1535-9484

Rapid optimization of MRM-MS instrument parameters by subtle alteration of precursor and product m/z targets.

Sherwood CA, Eastham A, Lee LW, Risler J, Mirzaei H, Falkner JA, Martin DB, Journal of proteome research, 2009 Jul 7 (8) 1535-3893

Quantitative proteomics investigation of pancreatic intraepithelial neoplasia.

Pan S, Chen R, Reimel BA, Crispin DA, Mirzaei H, Cooke K, Coleman JF, Lane Z, Bronner MP, Goodlett DR, McIntosh MW, Traverso W, Aebersold R, Brentnall TA, Electrophoresis, 2009 Apr 7 (30) 1522-2683

2008

A database of mass spectrometric assays for the yeast proteome.

Picotti P, Lam H, Campbell D, Deutsch EW, Mirzaei H, Ranish J, Domon B, Aebersold R, Nature methods, 2008 Nov 11 (5) 1548-7105

GAPDH is conformationally and functionally altered in association with oxidative stress in mouse models of amyotrophic lateral sclerosis.

Pierce A, Mirzaei H, Muller F, De Waal E, Taylor AB, Leonard S, Van Remmen H, Regnier F, Richardson A, Chaudhuri A, Journal of molecular biology, 2008 Oct 5 (382) 1089-8638

Protein:protein aggregation induced by protein oxidation.

Mirzaei H, Regnier F, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences, 2008 Sep 1 (873) 1570-0232

Identification of oxidized proteins in rat plasma using avidin chromatography and tandem mass spectrometry.

Mirzaei H, Baena B, Barbas C, Regnier F, Proteomics, 2008 Apr 7 (8) 1615-9861

Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics.

Mirzaei H, McBee JK, Watts J, Aebersold R, Molecular & cellular proteomics : MCP, 2008 Apr 4 (7) 1535-9484

2007

Destabilization of DJ-1 by familial substitution and oxidative modifications: implications for Parkinson's disease.

Hulleman JD, Mirzaei H, Guigard E, Taylor KL, Ray SS, Kay CM, Regnier FE, Rochet JC, Biochemistry, 2007 May 19 (46) 0006-2960

Identification of yeast oxidized proteins: chromatographic top-down approach for identification of carbonylated, fragmented and cross-linked proteins in yeast.

Mirzaei H, Regnier F, Journal of chromatography. A, 2007 Feb 1 (1141) 0021-9673

Neural network prediction of peptide separation in strong anion exchange chromatography.

Oh C, Zak SH, Mirzaei H, Buck C, Regnier FE, Zhang X, Bioinformatics (Oxford, England), 2007 Jan 1 (23) 1367-4811

2006

Protein-RNA cross-linking in the ribosomes of yeast under oxidative stress.

Mirzaei H, Regnier F, Journal of proteome research, 2006 Dec 12 (5) 1535-3893

Performance evaluation of existing de novo sequencing algorithms.

Pevtsov S, Fedulova I, Mirzaei H, Buck C, Zhang X, Journal of proteome research, 2006 Nov 11 (5) 1535-3893

Identification and quantification of protein carbonylation using light and heavy isotope labeled Girard's P reagent.

Mirzaei H, Regnier F, Journal of chromatography. A, 2006 Nov 1-2 (1134) 0021-9673

Creation of allotypic active sites during oxidative stress.

Mirzaei H, Regnier F, Journal of proteome research, 2006 Sep 9 (5) 1535-3893

Enhancement of amino acid detection and quantification by electrospray ionization mass spectrometry.

Yang WC, Mirzaei H, Liu X, Regnier FE, Analytical chemistry, 2006 Jul 13 (78) 0003-2700

Enhancing electrospray ionization efficiency of peptides by derivatization.

Mirzaei H, Regnier F, Analytical chemistry, 2006 Jun 12 (78) 0003-2700

Identification of rotenone-induced modifications in alpha-synuclein using affinity pull-down and tandem mass spectrometry.

Mirzaei H, Schieler JL, Rochet JC, Regnier F, Analytical chemistry, 2006 Apr 7 (78) 0003-2700

Enrichment of carbonylated peptides using Girard P reagent and strong cation exchange chromatography.

Mirzaei H, Regnier F, Analytical chemistry, 2006 Feb 3 (78) 0003-2700

2005

Affinity chromatographic selection of carbonylated proteins followed by identification of oxidation sites using tandem mass spectrometry.

Mirzaei H, Regnier F, Analytical chemistry, 2005 Apr 8 (77) 0003-2700

Structure specific chromatographic selection in targeted proteomics.

Mirzaei H, Regnier F, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences, 2005 Mar 1 (817) 1570-0232

2003

Evaluating immobilized metal affinity chromatography for the selection of histidine-containing peptides in comparative proteomics.

Ren D, Penner NA, Slentz BE, Mirzaei H, Regnier F, Journal of proteome research, 2003 May-Jun 3 (2) 1535-3893