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A nanoscale, multi-parametric flow cytometry-based platform to study mitochondrial heterogeneity and mitochondrial DNA dynamics.

MacDonald JA, Bothun AM, Annis SN, Sheehan H, Ray S, Gao Y, Ivanov AR, Khrapko K, Tilly JL, Woods DC.

Commun Biol. 2019 Jul 11;2:258. doi: 10.1038/s42003-019-0513-4. eCollection 2019.


Best practices and benchmarks for intact protein analysis for top-down mass spectrometry.

Donnelly DP, Rawlins CM, DeHart CJ, Fornelli L, Schachner LF, Lin Z, Lippens JL, Aluri KC, Sarin R, Chen B, Lantz C, Jung W, Johnson KR, Koller A, Wolff JJ, Campuzano IDG, Auclair JR, Ivanov AR, Whitelegge JP, Paša-Tolić L, Chamot-Rooke J, Danis PO, Smith LM, Tsybin YO, Loo JA, Ge Y, Kelleher NL, Agar JN.

Nat Methods. 2019 Jul;16(7):587-594. doi: 10.1038/s41592-019-0457-0. Epub 2019 Jun 27. Review.


Genetically Encoded Fluorescent Proteins Enable High-Throughput Assignment of Cell Cohorts Directly from MALDI-MS Images.

Schmitt ND, Rawlins CM, Randall EC, Wang X, Koller A, Auclair JR, Kowalski JM, Kowalski PJ, Luther E, Ivanov AR, Agar NYR, Agar JN.

Anal Chem. 2019 Mar 19;91(6):3810-3817. doi: 10.1021/acs.analchem.8b03454. Epub 2019 Mar 6.


Multi-Omics Study on the Impact of Cysteine Feed Level on Cell Viability and mAb Production in a CHO Bioprocess.

Ali AS, Raju R, Kshirsagar R, Ivanov AR, Gilbert A, Zang L, Karger BL.

Biotechnol J. 2019 Apr;14(4):e1800352. doi: 10.1002/biot.201800352. Epub 2018 Dec 14.


Complementary middle-down and intact monoclonal antibody proteoform characterization by capillary zone electrophoresis - mass spectrometry.

Belov AM, Zang L, Sebastiano R, Santos MR, Bush DR, Karger BL, Ivanov AR.

Electrophoresis. 2018 Aug;39(16):2069-2082. doi: 10.1002/elps.201800067. Epub 2018 Jun 5.


How many human proteoforms are there?

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B.

Nat Chem Biol. 2018 Feb 14;14(3):206-214. doi: 10.1038/nchembio.2576.


Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry.

Belov AM, Viner R, Santos MR, Horn DM, Bern M, Karger BL, Ivanov AR.

J Am Soc Mass Spectrom. 2017 Dec;28(12):2614-2634. doi: 10.1007/s13361-017-1781-1. Epub 2017 Sep 5.


Host Cell Protein Profiling by Targeted and Untargeted Analysis of Data Independent Acquisition Mass Spectrometry Data with Parallel Reaction Monitoring Verification.

Kreimer S, Gao Y, Ray S, Jin M, Tan Z, Mussa NA, Tao L, Li Z, Ivanov AR, Karger BL.

Anal Chem. 2017 May 16;89(10):5294-5302. doi: 10.1021/acs.analchem.6b04892. Epub 2017 Apr 26.


Binding Site Characterization of AM1336, a Novel Covalent Inverse Agonist at Human Cannabinoid 2 Receptor, Using Mass Spectrometric Analysis.

Mallipeddi S, Kreimer S, Zvonok N, Vemuri K, Karger BL, Ivanov AR, Makriyannis A.

J Proteome Res. 2017 Jul 7;16(7):2419-2428. doi: 10.1021/acs.jproteome.7b00023. Epub 2017 Jun 19.


Advanced Precursor Ion Selection Algorithms for Increased Depth of Bottom-Up Proteomic Profiling.

Kreimer S, Belov ME, Danielson WF, Levitsky LI, Gorshkov MV, Karger BL, Ivanov AR.

J Proteome Res. 2016 Oct 7;15(10):3563-3573. Epub 2016 Sep 7.


Combined metabolomics and proteomics reveals hypoxia as a cause of lower productivity on scale-up to a 5000-liter CHO bioprocess.

Gao Y, Ray S, Dai S, Ivanov AR, Abu-Absi NR, Lewis AM, Huang Z, Xing Z, Borys MC, Li ZJ, Karger BL.

Biotechnol J. 2016 Sep;11(9):1190-200. doi: 10.1002/biot.201600030. Epub 2016 Jun 29.


Ligation of Glycophorin A Generates Reactive Oxygen Species Leading to Decreased Red Blood Cell Function.

Khoory J, Estanislau J, Elkhal A, Lazaar A, Melhorn MI, Brodsky A, Illigens B, Hamachi I, Kurishita Y, Ivanov AR, Shevkoplyas S, Shapiro NI, Ghiran IC.

PLoS One. 2016 Jan 19;11(1):e0141206. doi: 10.1371/journal.pone.0141206. eCollection 2016.


Diurnal Variations of Circulating Extracellular Vesicles Measured by Nano Flow Cytometry.

Danielson KM, Estanislau J, Tigges J, Toxavidis V, Camacho V, Felton EJ, Khoory J, Kreimer S, Ivanov AR, Mantel PY, Jones J, Akuthota P, Das S, Ghiran I.

PLoS One. 2016 Jan 8;11(1):e0144678. doi: 10.1371/journal.pone.0144678. eCollection 2016.


High Resolution CZE-MS Quantitative Characterization of Intact Biopharmaceutical Proteins: Proteoforms of Interferon-β1.

Bush DR, Zang L, Belov AM, Ivanov AR, Karger BL.

Anal Chem. 2016 Jan 19;88(2):1138-46. doi: 10.1021/acs.analchem.5b03218. Epub 2015 Dec 24.


Application of Statistical Thermodynamics To Predict the Adsorption Properties of Polypeptides in Reversed-Phase HPLC.

Tarasova IA, Goloborodko AA, Perlova TY, Pridatchenko ML, Gorshkov AV, Evreinov VV, Ivanov AR, Gorshkov MV.

Anal Chem. 2015 Jul 7;87(13):6562-9. doi: 10.1021/acs.analchem.5b00595. Epub 2015 Jun 10.


Granulin, a novel STAT3-interacting protein, enhances STAT3 transcriptional function and correlates with poorer prognosis in breast cancer.

Yeh JE, Kreimer S, Walker SR, Emori MM, Krystal H, Richardson A, Ivanov AR, Frank DA.

Genes Cancer. 2015 Mar;6(3-4):153-68.


Mass-spectrometry-based molecular characterization of extracellular vesicles: lipidomics and proteomics.

Kreimer S, Belov AM, Ghiran I, Murthy SK, Frank DA, Ivanov AR.

J Proteome Res. 2015 Jun 5;14(6):2367-84. doi: 10.1021/pr501279t. Epub 2015 May 14. Review.


Reply to van de Sandt and Rimmelzwaan: Matching epitope display with functional avidity.

Keskin DB, Reinhold BR, Zhang GL, Ivanov AR, Karger BL, Reinherz EL.

Proc Natl Acad Sci U S A. 2015 May 12;112(19):E2418. doi: 10.1073/pnas.1503931112. Epub 2015 Apr 6. No abstract available. Erratum in: Proc Natl Acad Sci U S A. 2015 May 26;112(21):E2845.


An Integrated Platform for Isolation, Processing, and Mass Spectrometry-based Proteomic Profiling of Rare Cells in Whole Blood.

Li S, Plouffe BD, Belov AM, Ray S, Wang X, Murthy SK, Karger BL, Ivanov AR.

Mol Cell Proteomics. 2015 Jun;14(6):1672-83. doi: 10.1074/mcp.M114.045724. Epub 2015 Mar 9.


Physical detection of influenza A epitopes identifies a stealth subset on human lung epithelium evading natural CD8 immunity.

Keskin DB, Reinhold BB, Zhang GL, Ivanov AR, Karger BL, Reinherz EL.

Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):2151-6. doi: 10.1073/pnas.1423482112. Epub 2015 Feb 2.


Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study.

Sun J, Zhang GL, Li S, Ivanov AR, Fenyo D, Lisacek F, Murthy SK, Karger BL, Brusic V.

BMC Genomics. 2014;15 Suppl 9:S1. doi: 10.1186/1471-2164-15-S9-S1. Epub 2014 Dec 8.


Describing sequencing results of structural chromosome rearrangements with a suggested next-generation cytogenetic nomenclature.

Ordulu Z, Wong KE, Currall BB, Ivanov AR, Pereira S, Althari S, Gusella JF, Talkowski ME, Morton CC.

Am J Hum Genet. 2014 May 1;94(5):695-709. doi: 10.1016/j.ajhg.2014.03.020. Epub 2014 Apr 17.


Malaria-infected erythrocyte-derived microvesicles mediate cellular communication within the parasite population and with the host immune system.

Mantel PY, Hoang AN, Goldowitz I, Potashnikova D, Hamza B, Vorobjev I, Ghiran I, Toner M, Irimia D, Ivanov AR, Barteneva N, Marti M.

Cell Host Microbe. 2013 May 15;13(5):521-534. doi: 10.1016/j.chom.2013.04.009.


Interlaboratory studies and initiatives developing standards for proteomics.

Ivanov AR, Colangelo CM, Dufresne CP, Friedman DB, Lilley KS, Mechtler K, Phinney BS, Rose KL, Rudnick PA, Searle BC, Shaffer SA, Weintraub ST.

Proteomics. 2013 Mar;13(6):904-9. doi: 10.1002/pmic.201200532. Epub 2013 Feb 19.


Alternative methods for characterization of extracellular vesicles.

Momen-Heravi F, Balaj L, Alian S, Tigges J, Toxavidis V, Ericsson M, Distel RJ, Ivanov AR, Skog J, Kuo WP.

Front Physiol. 2012 Sep 7;3:354. doi: 10.3389/fphys.2012.00354. eCollection 2012.


Comparison of in-gel protein separation techniques commonly used for fractionation in mass spectrometry-based proteomic profiling.

Jafari M, Primo V, Smejkal GB, Moskovets EV, Kuo WP, Ivanov AR.

Electrophoresis. 2012 Aug;33(16):2516-26. doi: 10.1002/elps.201200031.


Pressure cycling technology in systems biology.

Powell BS, Lazarev AV, Carlson G, Ivanov AR, Rozak DA.

Methods Mol Biol. 2012;881:27-62. doi: 10.1007/978-1-61779-827-6_2.


Proteomics under pressure: development of essential sample preparation techniques in proteomics using ultrahigh hydrostatic pressure.

Freeman E, Ivanov AR.

J Proteome Res. 2011 Dec 2;10(12):5536-46. doi: 10.1021/pr200805u. Epub 2011 Nov 14.


Thermal stabilization of tissues and the preservation of protein phosphorylation states for two-dimensional gel electrophoresis.

Smejkal GB, Rivas-Morello C, Chang JH, Freeman E, Trachtenberg AJ, Lazarev A, Ivanov AR, Kuo WP.

Electrophoresis. 2011 Aug;32(16):2206-15. doi: 10.1002/elps.201100170. Epub 2011 Jul 27.


Aberrant lipid metabolism disrupts calcium homeostasis causing liver endoplasmic reticulum stress in obesity.

Fu S, Yang L, Li P, Hofmann O, Dicker L, Hide W, Lin X, Watkins SM, Ivanov AR, Hotamisligil GS.

Nature. 2011 May 26;473(7348):528-31. doi: 10.1038/nature09968. Epub 2011 May 1.


Increased power for the analysis of label-free LC-MS/MS proteomics data by combining spectral counts and peptide peak attributes.

Dicker L, Lin X, Ivanov AR.

Mol Cell Proteomics. 2010 Dec;9(12):2704-18. doi: 10.1074/mcp.M110.002774. Epub 2010 Sep 7.


Retention time prediction using the model of liquid chromatography of biomacromolecules at critical conditions in LC-MS phosphopeptide analysis.

Perlova TY, Goloborodko AA, Margolin Y, Pridatchenko ML, Tarasova IA, Gorshkov AV, Moskovets E, Ivanov AR, Gorshkov MV.

Proteomics. 2010 Oct;10(19):3458-68. doi: 10.1002/pmic.200900837.


When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification.

Renard BY, Kirchner M, Monigatti F, Ivanov AR, Rappsilber J, Winter D, Steen JA, Hamprecht FA, Steen H.

Proteomics. 2009 Nov;9(21):4978-84. doi: 10.1002/pmic.200900326.


Zcchc11-dependent uridylation of microRNA directs cytokine expression.

Jones MR, Quinton LJ, Blahna MT, Neilson JR, Fu S, Ivanov AR, Wolf DA, Mizgerd JP.

Nat Cell Biol. 2009 Sep;11(9):1157-63. doi: 10.1038/ncb1931. Epub 2009 Aug 23.


Tissue fractionation by hydrostatic pressure cycling technology: the unified sample preparation technique for systems biology studies.

Gross V, Carlson G, Kwan AT, Smejkal G, Freeman E, Ivanov AR, Lazarev A.

J Biomol Tech. 2008 Jul;19(3):189-99.


Proteomic analysis of the hyaloid vascular system regression during ocular development.

Albè E, Chang JH, Azar NF, Ivanov AR, Azar DT.

J Proteome Res. 2008 Nov;7(11):4904-13. doi: 10.1021/pr800551m. Epub 2008 Oct 8.


Pilot proteomic profile of differentially regulated proteins in right atrial appendage before and after cardiac surgery using cardioplegia and cardiopulmonary bypass.

Clements RT, Smejkal G, Sodha NR, Ivanov AR, Asara JM, Feng J, Lazarev A, Gautam S, Senthilnathan V, Khabbaz KR, Bianchi C, Sellke FW.

Circulation. 2008 Sep 30;118(14 Suppl):S24-31. doi: 10.1161/CIRCULATIONAHA.107.792747.


Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe.

Schmidt MW, Houseman A, Ivanov AR, Wolf DA.

Mol Syst Biol. 2007;3:79. Epub 2007 Feb 13.


Manganese and iron transport across pulmonary epithelium.

Heilig EA, Thompson KJ, Molina RM, Ivanov AR, Brain JD, Wessling-Resnick M.

Am J Physiol Lung Cell Mol Physiol. 2006 Jun;290(6):L1247-59. Epub 2006 Jan 20.


PCI proteins eIF3e and eIF3m define distinct translation initiation factor 3 complexes.

Zhou C, Arslan F, Wee S, Krishnan S, Ivanov AR, Oliva A, Leatherwood J, Wolf DA.

BMC Biol. 2005 May 17;3:14.


Artificial neural network analysis for evaluation of peptide MS/MS spectra in proteomics.

Baczek T, Buciński A, Ivanov AR, Kaliszan R.

Anal Chem. 2004 Mar 15;76(6):1726-32.


A universal denoising and peak picking algorithm for LC-MS based on matched filtration in the chromatographic time domain.

Andreev VP, Rejtar T, Chen HS, Moskovets EV, Ivanov AR, Karger BL.

Anal Chem. 2003 Nov 15;75(22):6314-26.


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