Publications

60. Kostas JC, Greguš M, Schejbal J, Ray S, Ivanov AR*.

Simple and efficient micro-SPE tip-based sample preparation workflow to enable sensitive proteomic profiling of limited samples (200 to 10,000 cells). J. Proteome Res.,  Dec. 2020: Accepted for publication.

59.   Tošić I, Heppler LN, Egusquiaguirre SP, Boehnke N, Correa S, Costa DF, Grossman Moore EA, Pal S, Richardson D, Ivanov AR, Haas-Kogan DA, Nomura D, Hammond PT, and Frank DA

Lipidome-based Targeting of STAT3-driven Breast Cancer Cells Using Poly-L-glutamic acid-coated Layer-by-Layer Nanoparticles. Mol Cancer Ther, 2021 Feb 3:molcanther.0505.2020. doi: 10.1158/1535-7163.MCT-20-0505. Online ahead of print. PMID: 33536189

58. Bhattacharya B, Xiao S, Chatterjee S, Urbanowski ME, Ordonez AA, Ihms EA, Agrahari G, Lun S, Berland R, Pichugin A, Gao Y, Connor JH, Ivanov AR, Yan BS, Kobzik L, Koo BB, Jain SK, Bishai WR, Kramnik I.

The integrated stress response mediates necrosis in murine Mycobacterium tuberculosis granulomas. J Clin Invest. 2020 Dec 10:130319. doi: 10.1172/JCI130319. Online ahead of print. PMID: 33301427

57. Marie AL, Ray R, Lu S, Jones J, Ghiran I, and Ivanov AR*.

High-Sensitivity Glycan Profiling of Blood-Derived Immunoglobulin G, Plasma, and Extracellular Vesicle Isolates with Capillary Zone Electrophoresis-Mass Spectrometry. Anal Chem., 2021 Jan 12.  doi: 10.1021/acs.analchem.0c03102. Online ahead of print. doi: 10.1021/acs.analchem.0c03102. PMID: 33433994

56. Greguš M, Kostas JC, Ray S, Abbatiello SE, Ivanov AR*.

Improved Sensitivity of Ultralow Flow LC-MS-Based Proteomic Profiling of Limited Samples Using Monolithic Capillary Columns and FAIMS Technology. Anal Chem. 2020 Nov 3;92(21):14702-14712. doi: 10.1021/acs.analchem.0c03262. Epub 2020 Oct 15. PMID: 33054160

55. Peng Y, Jain S, Li YF, Greguš M, Ivanov AR, Vitek O, and Radivojac P.

New mixture models for decoy-free false discovery rate estimation in mass-spectrometry proteomics. Bioinformatics, Bioinformatics. 2020 Dec 0;36(Supplement_2):i745-i753. doi: 10.1093/bioinformatics/btaa807. PMID: 33381824

54. Sarkar S, Kang W, Jiang S, Li K, Ray S, Luther E, Ivanov AR, Fu Y, Konry T.

Machine learning-aided quantification of antibody-based cancer immunotherapy by natural killer cells in microfluidic droplets Lab Chip. 2020 Jun 30;20(13):2317-2327. doi: 10.1039/d0lc00158a. PMID: 32458907

53. Gandham S, Su X, Wood J, Nocera AL, Alli SC, Milane L, Zimmerman A, Amiji M, and Ivanov AR*.

Technologies and Standardization in Research of Extracellular Vesicles. Trends in Biotechnology. 2020 Jun 18:S0167-7799(20)30163-3. doi: 10.1016/j.tibtech.2020.05.012. Online ahead of print. PMID: 32564882

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

Multi-Omics Reveals Impact of Cysteine Feed Concentration and Resulting Redox Imbalance on Cellular Energy Metabolism and Specific Productivity in CHO Cell Bioprocessing.  Biotechnol J. 2020 Mar 13:e1900565. doi: 10.1002/biot.201900565. [Epub ahead of print] PMID: 32170810

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

A nanoscale, multi-parametric flow cytometry-based platform to study mitochondrial heterogeneity and mitochondrial DNA dynamics. Communications Biology. 2019, Jul 11;2(1):258. PMID: 31925087.

50.  Donnelly DP, Rawlins CM, DeHart CJ, Fornelli L, Schachner LF, Lin Z, Lippens JL, Aluri JL, Sarin R, Chen B, Lantz C, Jung W, Johnson KR, Koller A, Wolff JJ, Campuzano I.D.G., 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

Best Practices and Benchmarks for Intact Protein Analysis for Top-down Mass Spectrometry. Nature Methods. 2019 Jul;16(7):587-594. PMID: 31249407.

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

Genetically Encoded Fluorescent Proteins Enable High-Throughput Assignment of Cell Cohorts Directly from MALDI-MS Images. Anal Chem. 2019 Mar 19;91(6):3810-3817. PMID: 30839199.

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

Multi-Omics Study on the Impact of Cysteine Feed Level on Cell Viability and mAb Production in a CHO Bioprocess.  Biotechnol J. 2019 Apr;14(4):e1800352. doi: 10.1002/biot.201800352. PMID: 30485675

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

Complementary middle-down and intact monoclonal antibody proteoform characterization by capillary zone electrophoresis – mass spectrometry. Electrophoresis. 2018 Aug, 39(16) 2069-2082. PMID: 29749064 (Cover Story)

46.  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.

How many human proteoforms are there?  Nature Chemical Biology, 2018 14(3):206-214. PMID: 29443976.

45.  Belov AM, Viner R, Santos MR, Horn DM, Bern M, Karger BL, Ivanov AR.  Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis – Native Mass Spectrometry. J Am Soc Mass Spectrom. 2017 Dec; 28(12):2614-2634. PMID: 28875426

44.  Kreimer S, Ivanov AR.  Rapid Isolation of Extracellular Vesicles from Blood Plasma with Size-Exclusion Chromatography Followed by Mass Spectrometry-Based Proteomic Profiling. Methods Mol Biol. 2017; 1660: 295-302. doi: 10.1007/978-1-4939-7253-1_24. PMID: 28828666

43.  Kreimer S, Gao Y, Ray S, Jin M, Tan Z, Mussa NA, Tao L, Li Z, Ivanov AR, Karger BL.  Host Cell Protein Profiling by Targeted and Untargeted Analysis of Data Independent Acquisition Mass Spectrometry Data with Parallel Reaction Monitoring Verification. Anal Chem. 2017 May 16;89(10):5294-5302. PMID: 28402653

42.  Mallipeddi S, Kreimer S, Zvonok N, Vemuri K, Karger BL, Ivanov AR, Makriyannis A.  Binding Site Characterization of AM1336, a Novel Covalent Inverse Agonist at Human Cannabinoid 2 Receptor, Using Mass Spectrometric Analysis. J Proteome Res. 2017 Jul 7;16(7):2419-2428. PMID: 28374590

41.  Kreimer S, Belov ME, Danielson WF, Levitsky LI, Gorshkov MV, Karger BL, and Ivanov AR.  Advanced Precursor Ion Selection Algorithms for Increased Depth of Bottom-Up Proteomic Profiling. J Proteome Res. 2016, Oct 7;15(10):3563-3573. PMID: 27569903.

40.   Gao Y, Ray S, Dai S, Ivanov AR, Abu-Absi NR, Lewis AM, Huang Z, Xing Z, Borys MC, Li ZJ, Karger BL.  Combined metabolomics and proteomics reveals hypoxia as a cause of lower productivity on scale-up to a 5000-liter CHO bioprocess. Biotechnol J., 2016, Sep;11(9):1190-200. PMID: 27213298.

39.   Moskovets EV and Ivanov AR, Comparative studies on peak intensities and chromatographic separation of proteolytic digests, PTMs, and intact proteins obtained in the nanoLC-ESI MS analysis at room and elevated temperatures. Anal and Bioanal Chem, 2016, Jun;408(15):3953-68. PMID: 26898204.

38.   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.  Ligation of Glycophorin A Generates Reactive Oxygen Species Leading to Decreased Red Blood Cell Function. PLoS One. 2016 Jan 19;11(1). PMID: 26784696.

37.   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. Diurnal Variations of Circulating Extracellular Vesicles Measured by Nano Flow Cytometry. PLoS One. 2016 Jan 8;11(1). PMID: 26745887

36.   Bush DR, Zang L, Belov AM, Ivanov AR, Karger BL. High Resolution CZE-MS Quantitative Characterization of Intact Biopharmaceutical Proteins: Proteoforms of Interferon-β1. Anal Chem. 2016 Jan 19;88(2):1138-46. PMID: 26641950

35.  Tarasova IA, Goloborodko AA, Perlova TY, Pridatchenko ML, Gorshkov AV, Evreinov VV, Ivanov AR, Gorshkov MV. Application of Statistical Thermodynamics to Predict the Adsorption Properties of Polypeptides in Reversed-Phase HPLC. Anal Chem. 2015 Jul 7;87(13):6562-9. doi: 10.1021/acs.analchem.5b00595. Epub 2015 Jun 10. PMID: 26023813.

34.   Yeh JE, Kreimer S, Walker SR, Emori MM, Krystal H, Richardson A, Ivanov AR, Frank DA. Granulin, a novel STAT3-interacting protein, enhances STAT3 transcriptional function and correlates with poorer prognosis in breast cancer. Genes Cancer. 2015 Mar;6(3-4):153-68. PMID: 26000098.

33.   Kreimer S, Belov AM, Ghiran I, Murthy SK, Frank DA, Ivanov AR.  Mass-spectrometry-based molecular characterization of extracellular vesicles: lipidomics and proteomics. J Proteome Res. 2015 Jun 5;14(6):2367-84. doi: 10.1021/pr501279t. Epub 2015 May 14. PMID: 25927954.

32.   Li S, Plouffe BD, Belov AM, Ray S, Wang X, Murthy SK, Karger BL, Ivanov AR.  An Integrated Platform for Isolation, Processing and Mass Spectrometry-based Proteomic Profiling of Rare Cells in Whole Blood. Mol Cell Proteomics. 2015. Jun;14(6):1672-83. doi: 10.1074/mcp.M114.045724.  PMID: 25755294. (Cover Story)

31.   Keskin DB, Reinhold BB, Zhang GL, Ivanov AR, Karger BL, Reinherz EL.  Physical detection of influenza A epitopes identifies a stealth subset on human lung epithelium evading natural CD8 immunity.  Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):2151-6.  PMID: 25646416.

30.     Sun J, Zhang G, Li S, Ivanov AR, Fenyo D, Lisacek F, Murthy SK, Karger BL, Brusic V.  Pathway Analysis and Transcriptomics Improve Protein Identification by Shotgun Proteomics from Samples Comprising Small Numbers of Cells: A Benchmarking Study.  BMC Genomics 2014, Dec 8;15, S1  PMID: 25521637.

29.   Mantel PY, Hoang AN, Goldowitz I, Potashnikova D, Hamza B, Vorobjev I, Ghiran I, Toner M, Irimia D, Ivanov AR, Barteneva N, Marti M. Malaria-infected erythrocyte-derived microvesicles mediate cellular communication within the parasite population and with the host immune system. Cell Host Microbe. 2013 May 15;13(5):521-34 PMID: 23684304

28.   Ivanov AR, Colangelo CM, Dufresne CP, Friedman DB, Lilley KS, Mechtler K, Phinney BS, Rose KL, Rudnick PA, Searle BC, Shaffer SA, Weintraub ST. Interlaboratory studies and initiatives developing standards for proteomics. Proteomics. 2013 Mar;13(6):904-9. doi: 10.1002/pmic.201200532. Epub 2013 Feb 19. PMID: 23319436.

27.   Momen-Heravi F, Balaj L, Alian S, Tigges J, Toxavidis V, Ericsson M, Distel RJ, Ivanov AR, Skog J, Kuo WP. Alternative methods for characterization of extracellular vesicles. Front Physiol. 2012 Sep 7;3:354. PMID: 22973237.

26.   Jafari M, Primo V, Smejkal GB, Moskovets EV, Kuo WP, Ivanov AR. Comparison of in-gel protein separation techniques commonly used for fractionation in mass spectrometry-based proteomic profiling. Electrophoresis. 2012 Aug;33(16):2516-26. PMID: 22899259.

24.   Powell BS, Lazarev AV, Carlson G, Ivanov AR, Rozak DA. Pressure cycling technology in systems biology. Methods Mol Biol. 2012; 881:27-62. PMID: 22639209.

23.   Fu S, Li P, Yang L, Hofmann O, Dicker L, Hide W, Lin X, Watkins SM, Ivanov AR, and Hotamisligil GS, Aberrant lipid metabolism disrupts calcium homeostasis causing liver endoplasmic reticulum stress in obesity. Nature. 2011. May 26;473(7348):528-31.PMID: 21532591.

22.   Smejkal G, Rivas-Morello C, Chang RG, Freeman E, Trachtenberg A, Lazarev A, Ivanov AR, Kuo WP, Stabilization of Tissues and the Preservation of Protein Phosphorylation States for Two-Dimensional Gel Electrophoresis. Electrophoresis. 2011. Aug;32(16):2206-15. PMID: 21792998.

21.   Freeman E, Ivanov AR, Proteomics under pressure: searching for effective alternatives for sample preparation in proteomics. J Proteome Res. 2011. Dec 2;10(12):5536-46. PMID: 22029901.

21.   Dicker L, Lin X, Ivanov AR, Increased Power for the Analysis of Label-Free LC-MS/MS Proteomic Data by Combining Spectral Counts and Peptide Peak Attributes. Molecular Cell. Proteomics. 2010 Dec;9(12):2704-18. PMID: 20823122

20.   T.Y. Perlova; A.A. Goloborodko; Y. Margolin; M.L. Pridatchenko, I.A. Tarasova; A.V. Gorshkov; E. Moskovets; A.R. Ivanov; M.V. Gorshkov. Retention time prediction using the model of liquid chromatography of biomacromolecules at critical conditions in LC-MS phosphopeptide analysis. Proteomics. 2010 Oct;10(19):3458-68. PMID: 20815086.

19.   Ivanov AR, The state of proteome research at the Harvard School of Public Health Proteomics Resource. Expert Rev. Proteomics 2010 7(4S): 31.

18.   Freeman E, Ivanov AR, Development of essential sample preparation techniques in proteomics using ultra-high pressure. Expert Rev. Proteomics 2010 7(4S): 18.

17.   Renard BY, Kirchner M, Monigatti F, Ivanov AR, Rappsilber J, Winter D, Steen JA, Hamprecht FA, Steen H. When Less Can Yield More – Computational Preprocessing of MS/MS Spectra for Peptide Identification. Proteomics. 2009 Nov;9(21):4978-84.

16.   Jones MR, Quinton LJ, Blahna MT, Fu S, Ivanov AR, Wolf DA, Mizgerd JP, Zcchc11 Directs cytokine expression by microRNA uridylation, Nature Cell Biology, 2009, 11(9):1157-63.

15.   Albè E, Chang JH, Azar NF, Ivanov AR, Azar DT. Proteomic Analysis of the Hyaloid Vascular System Regression during Ocular Development. J Proteome Res. 2008 Nov 7;7(11):4904-4913.

14.   Clements RT, Smejkal G, Sodha NR, Ivanov AR, Asara JM, Feng J, Lazarev A, Gautam S, Senthilnathan V, Khabbaz KR, Bianchi C, Sellke FW. Pilot proteomic profile of differentially regulated proteins in right atrial appendage before and after cardiac surgery using cardioplegia and cardiopulmonary bypass. Circulation. 2008, 118 (14 Suppl):S24-31.

13.   Gross V, Carlson G, Kwan AT, Smejkal G, Freeman E, Ivanov AR, Lazarev A, Tissue Fractionation by Hydrostatic Pressure Cycling Technology: The Unified Sample Preparation Technique for Systems Biology Studies. J Biomol Tech. 2008, 19(3): 189–199

12.   Schmidt MW, Houseman A, Ivanov AR, Wolf DA, Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe, Molecular Systems Biology, 2007, 3:79.

11.    Heilig EA, Thompson KJ, Molina RM, Ivanov AR, Brain JD, Wessling-Resnick M. Manganese and Iron Transport Across Pulmonary Epithelium. Am J Physiol Lung Cell Mol Physiol. 2006, 290(6):L1247-59

10.    Zhou C, Arslan F, Wee S, Krishnan S, Ivanov AR, Oliva A, Leatherwood J, Wolf DA, PCI Proteins eIF3e and eIF3m Define Distinct Translation Initiation Factor 3 Complexes, BioMed Central Biology, 2005, 3:14.

9.   Baczek T, Bucinski A, Ivanov AR, Kaliszan R. Artificial neural network analysis for evaluation of peptide MS/MS spectra in proteomics. Anal Chem. 2004, 76, 1726-1732.

8.    Andreev VP, Rejtar T, Chen H-S, Moscovets, EV, Ivanov AR, Karger BL. A universal denoising and peak picking algorithm for LC-MS based on matched filtration in the chromatographic time domain. Anal Chem. 2003, 75, 6314-6326.

7.   Ivanov AR, Horvath C, Karger BL. High-efficiency peptide analysis on monolithic multi-mode capillary columns: pressure assisted CEC/CE coupled to UV and ESI-MS. Electrophoresis. 2003, 24 No. 21, 3663-3673.

6.   Ivanov AR, Zang L, Karger BL. Low Attomole ESI-MS/MS Analysis of tryptic peptides using 20-μm I.D. monolithic capillary columns. Anal Chem. 2003, 75, 5306-5316.

5.    Ivanov AR, Nazimov IV, Baratova LA. Determination of biologically active low-molecular-mass thiols in human blood. II. High-performance capillary electrophoresis with photometric detection. J Chromatogr A 2000; 20: 895(1-2):167-171.

4.   Ivanov AR, Nazimov IV, Baratova LA. Determination of biologically active low-molecular-mass thiols in human blood. I. Fast qualitative and quantitative, gradient and isocratic reversed-phase high-performance liquid chromatography with photometric and fluorescence detection.  J Chromatogr A 2000; 20:895(1-2):157-166.

3.   Ivanov AR, Nazimov IV. Identification of unusual (modified and non-encoded) amino acid residues in peptides by combinations of high-performance liquid chromatography and high-performance capillary electrophoresis with matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J Chromatogr A 2000; 18:870(1-2):255-269.

2.   Ivanov AR, Nazimov IV, Baratova LA. Qualitative and quantitative determination of biologically active low-molecular-mass thiols in human blood by reversed-phase high-performance liquid chromatography with photometry and fluorescence detection. J Chromatogr A 2000;18:870(1-2):433-442.

1.   Ivanov AR, Nazimov IV, Lobazov AP, Popkovich GB. Direct determination of amino acids and carbohydrates by high-performance capillary electrophoresis with refractometric detection. J Chromatogr A 2000;13:894(1-2):253-257.

Books:

Sample Preparation in Biological Mass Spectrometry. Eds.: Lazarev A, Ivanov AR, Springer. 2011, ISBN: 978-94-007-0758-0. (As of January 2015: over 60,000 downloads, which placed the book sales in the top 5% of all Springer’s book portfolio on Biomedicine, Life Sciences and Clinical Medicine).

Book Chapters:

5.   P.S. Powell, A.V. Lazarev, G. Carlson, A.R. Ivanov, D.A. Rozak, Pressure Cycling Technology in Systems Biology. In Microbial Systems Biology: Methods and Protocols. In Methods in Molecular Biology, Humana. Press, Springer, New York. Ed.: Ali Navid, Chapter 17, 2013.

4.   E. Freeman, V. Gross, I. Romanovsky, A. Lazarev, A.R. Ivanov, Adipose Tissue Lysis and Protein Extraction Followed by MS-based Proteomic Profiling Reveals Constituents of Oxidative Stress in Obesity. In Sample Preparation in Biological Mass Spectrometry. Eds.: Lazarev A, Ivanov AR, Springer, Chapter 30, 2011, ISBN: 978-94-007-0758-0.

3.   E. Freeman, Y. Margolin, A.R. Ivanov, Pressure-Assisted Lysis of Mammalian Cell Cultures Prior to Proteomic Analysis. In Sample Preparation in Biological Mass Spectrometry. Eds.: Lazarev A, Ivanov AR, Springer, Chapter 5, 2011, ISBN: 978-94-007-0758-0.

2.   A.V.Lazarev, A.R. Ivanov, Materialistic Dualism of Sample Preparation: Boring but Important! In Sample Preparation in Biological Mass Spectrometry. Eds.: Lazarev A, Ivanov AR, Springer, Chapter 1, 2011, ISBN: 978-94-007-0758-0.

1.   Ivanov AR, Polymeric Monolithic Capillary Columns in Proteomics. In Separation Methods in Proteomics. Eds.: Smejkal GB, Lazarev A, Apex Publishing, LLC, Chapter 22, 419-435, 2005.

Patents Granted:

Ivanov AR, Zang L, Karger BL.  Narrow I.D. (50-µm I.D. or less) Monolithic capillary columns coupled to electrospray ionization mass spectrometry for high-efficiency separation and high-sensitive analysis of biomolecules. US patent # US 8,691,088.

Moskovets E, Ivanov AR, Doroshenko V. A thermo-stabilized nano- and micro-flow LC/ESI-MS interface and a method thereof. US Patent # US 8,410,434 B1.