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O. Krokhin’s publications

Papers in refereed journals during residence in Manitoba (proteomics 2003-present):

2022

  1. Shuvo, S. R.; Motnenko, A.; Krokhin, O. V.; Spicer, V.; Court, D. A., Proteomic Shifts Reflecting Oxidative Stress and Reduced Capacity for Protein Synthesis, and Alterations to Mitochondrial Membranes in Neurospora crassa Lacking VDAC. Microorganisms 2022, 10 (2) 198.
  2. Mizero, B.; Villacres, C.; Spicer, V.; Viner, R.; Saba, J.; Patel, B.; Snovida, S.; Jensen, P.; Huhmer, A.; Krokhin, O. V., Retention Time Prediction for TMT-Labeled Peptides in Proteomic LC-MS Experiments. J Proteome Res. 2022. doi:10.1021/acs.jproteome.1c00833.

2021

  1. Mizero, B.; Yeung, D.; Spicer, V.; Krokhin, O. V., Peptide retention time prediction for peptides with post-translational modifications: N-terminal (alpha-amine) and lysine (epsilon-amine) acetylation. J Chromatogr A 2021, 1657, 462584.
  2. Chang, C. H.; Yeung, D.; Spicer, V.; Ogata, K.; Krokhin, O.; Ishihama, Y., Sequence-Specific Model for Predicting Peptide Collision Cross Section Values in Proteomic Ion Mobility Spectrometry. J Proteome Res 2021. doi: 10.1021/acs.jproteome.1c00185
  3. Piyadasa, H.; Hemshekhar, M.; Osawa, N.; Lloyd, D.; Altieri, A.; Basu, S.; Krokhin, O. V.; Halayko, A. J.; Mookherjee, N., Disrupting Tryptophan in the Central Hydrophobic Region Selectively Mitigates Immunomodulatory Activities of the Innate Defence Regulator Peptide IDR-1002. J Med Chem 2021, 64 (10), 6696-6705.
  4. Sestric, R.; Spicer, V.; Krokhin, O. V.; Sparling, R.; Levin, D. B., Analysis of the Yarrowia lipolytica proteome reveals subtle variations in expression levels between lipogenic and non-lipogenic conditions. FEMS Yeast Res 2021, 21 (2).
  5. Villacres, C.; Spicer, V.; Krokhin, O. V., Confident Identification of Citrullination and Carbamylation Assisted by Peptide Retention Time Prediction. J Proteome Res 2021, 20 (3), 1571-1581.

2020

  1. Yeung, D.; Mizero, B.; Gussakovsky, D.; Klaassen, N.; Lao, Y.; Spicer, V.; Krokhin, O. V., Separation Orthogonality in Liquid Chromatography-Mass Spectrometry for Proteomic Applications: Comparison of 16 Different Two-Dimensional Combinations. Anal Chem 2020, 92 (5), 3904-3912.
  2. Yeung, D.; Klaassen, N.; Mizero, B.; Spicer, V.; Krokhin, O. V., Peptide retention time prediction in hydrophilic interaction liquid chromatography: Zwitter-ionic sulfoalkylbetaine and phosphorylcholine stationary phases. J Chromatogr A 2020, 460909.
  3. Gussakovsky, D.; Anderson, G.; Spicer, V.; Krokhin, O. V., Peptide separation selectivity in proteomics LC-MS experiments: Comparison of formic and mixed formic/heptafluorobutyric acids ion-pairing modifiers. J Sep Sci 2020, 43 (20), 3830-3839.

2019

  1. Chen, D.; Ludwig, K. R.; Krokhin, O. V.; Spicer, V.; Yang, Z.; Shen, X.; Hummon, A. B.; Sun, L., Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Large-Scale Phosphoproteomics with the Production of over 11,000 Phosphopeptides from the Colon Carcinoma HCT116 Cell Line. Anal Chem 2019, 91 (3), 2201-2208.
  2. Klaassen, N.; Spicer, V.; Krokhin, O. V., Universal retention standard for peptide separations using various modes of high-performance liquid chromatography. J Chromatogr A 2019, 1588, 163-168.
  3. Wushke, S.; Froese, A.; Fristensky, B.; Zhang, X. L.; Spicer, V.; Krokhin, O. V.; Levin, D. B.; Sparling, R., Genomic comparison of facultatively anaerobic and obligatory aerobic Caldibacillus debilis strains GB1 and Tf helps explain physiological differences. Can J Microbiol 2019, 65 (6), 421-428.
  4. Rody, W. J., Jr.; Chamberlain, C. A.; Emory-Carter, A. K.; McHugh, K. P.; Wallet, S. M.; Spicer, V.; Krokhin, O.; Holliday, L. S., The proteome of extracellular vesicles released by clastic cells differs based on their substrate. PLoS One 2019, 14 (7), e0219602.
  5. Hemshekhar, M.; Faiyaz, S.; Choi, K. G.; Krokhin, O. V.; Mookherjee, N., Immunomodulatory Functions of the Human Cathelicidin LL-37 (aa 13-31)-Derived Peptides are Associated with Predicted alpha-Helical Propensity and Hydrophobic Index. Biomolecules 2019, 9 (9).
  6. Ang, E.; Neustaeter, H.; Spicer, V.; Perreault, H.; Krokhin, O., Retention Time Prediction for Glycopeptides in Reversed-Phase Chromatography for Glycoproteomic Applications. Anal Chem 2019, 91 (21), 13360-13366.

2018

  1. Wushke, S.; Jin, Z.; Spicer, V.; Zhang, X. L.; Fristensky, B.; Krokhin, O. V.; Levin, D. B.; Sparling, R., Description of a cryptic thermophilic (pro)phage, CBP1 from Caldibacillus debilis strain GB1. Extremophiles 2018, 22 (2), 203-209.
  2. Spicer, V.; Krokhin, O. V., Peptide retention time prediction in hydrophilic interaction liquid chromatography. Comparison of separation selectivity between bare silica and bonded stationary phases. J Chromatogr A 2018, 1534, 75-84.
  3. Roy, R.; Ang, E.; Komatsu, E.; Domalaon, R.; Bosseboeuf, A.; Harb, J.; Hermouet, S.; Krokhin, O.; Schweizer, F.; Perreault, H., Absolute Quantitation of Glycoforms of Two Human IgG Subclasses Using Synthetic Fc Peptides and Glycopeptides. J Am Soc Mass Spectrom 2018, 29 (6), 1086-1098.
  4. Ogata, K.; Krokhin, O. V.; Ishihama, Y., Retention Order Reversal of Phosphorylated and Unphosphorylated Peptides in Reversed-Phase LC/MS. Anal Sci 2018, 34 (9), 1037-1041.
  5. Gussakovsky, D.; Neustaeter, H.; Spicer, V.; Krokhin, O. V. Peptide retention time prediction for immobilized artificial membrane phosphatidylcholine stationary phase: method development and preliminary observations ADMET&DMPK 2018, 6 (2) 190-199.
  6. Wushke, S.; Fristensky, B.; Zhang, X. L.; Spicer, V.; Krokhin, O. V.; Levin, D. B.; Stott, M. B.; Sparling, R., A metabolic and genomic assessment of sugar fermentation profiles of the thermophilic Thermotogales, Fervidobacterium pennivorans. Extremophiles 2018, 22 (6), 965-974.

2017

  1. Ferens, F. G.; Spicer, V.; Krokhin, O. V.; Motnenko, A.; Summers, W. A.; Court, D. A., A deletion variant partially complements a porin-less strain of Neurospora crassa. Biochem Cell Biol 2017, 95 (2), 318-327.
  2. Krokhin, O. V.; Anderson, G.; Spicer, V.; Sun, L.; Dovichi, N. J., Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis. Anal Chem 2017, 89 (3), 2000-2008.
  3. Hughes, C. S.; Spicer, V.; Krokhin, O. V.; Morin, G. B., Investigating Acquisition Performance on the Orbitrap Fusion When Using Tandem MS/MS/MS Scanning with Isobaric Tags. J Proteome Res 2017, 16 (5), 1839-1846.
  4. Hughes, C. S.; Zhu, C.; Spicer, V.; Krokhin, O. V.; Morin, G. B., Evaluating the Characteristics of Reporter Ion Signal Acquired in the Orbitrap Analyzer for Isobaric Mass Tag Proteome Quantification Experiments. J Proteome Res 2017, 16 (5), 1831-1838.
  5. Krokhin, O. V.; Ezzati, P.; Spicer, V., Peptide Retention Time Prediction in Hydrophilic Interaction Liquid Chromatography: Data Collection Methods and Features of Additive and Sequence-Specific Models. Anal Chem 2017, 89 (10), 5526-5533.
  6. Krokhin, O. V., Comparison of peptide retention prediction algorithm in reversed-phase chromatography. Comment on "Predictive chromatography of peptides and proteins as a complementary tool for proteomics", by I. A. Tarasova, C. D. Masselon, A. V. Gorshkov and M. V. Gorshkov, Analyst, 2016, 141, 4816. Analyst 2017, 142 (11), 2050-2051.
  7. Guan, Q.; Ezzati, P.; Spicer, V.; Krokhin, O.; Wall, D.; Wilkins, J. A., Interferon gamma induced compositional changes in human bone marrow derived mesenchymal stem/stromal cells. Clin Proteomics 2017, 14, 26.
  8. Rody, W. J., Jr.; Krokhin, O.; Spicer, V.; Chamberlain, C. A.; Chamberlain, M.; McHugh, K. P.; Wallet, S. M.; Emory, A. K.; Crull, J. D.; Holliday, L. S., The use of cell culture platforms to identify novel markers of bone and dentin resorption. Orthod Craniofac Res 2017, 20 Suppl 1, 89-94.
  9. Wushke, S.; Spicer, V.; Zhang, X. L.; Fristensky, B.; Krokhin, O. V.; Levin, D. B.; Cicek, N.; Sparling, R., Understanding aerobic/anaerobic metabolism in Caldibacillus debilis through a comparison with model organisms. Syst Appl Microbiol 2017, 40 (5), 245-253.
  10. Gussakovsky, D.; Neustaeter, H.; Spicer, V.; Krokhin, O. V., Sequence-Specific Model for Peptide Retention Time Prediction in Strong Cation Exchange Chromatography. Anal Chem 2017, 89 (21), 11795-11802.

2016

  1. Dwivedi, R. C.; Krokhin, O. V.; El-Gabalawy, H. S.; Wilkins, J. A., Development of an SRM method for absolute quantitation of MYDGF/C19orf10 protein. Proteomics Clin Appl 2016, 10 (6), 663-70.
  2. Ho, J.; Rush, D. N.; Krokhin, O.; Antonovici, M.; Gao, A.; Bestland, J.; Wiebe, C.; Hiebert, B.; Rigatto, C.; Gibson, I. W.; Wilkins, J. A.; Nickerson, P. W., Elevated Urinary Matrix Metalloproteinase-7 Detects Underlying Renal Allograft Inflammation and Injury. Transplantation 2016, 100 (3), 648-54.
  3. Spicer, V.; Ezzati, P.; Neustaeter, H.; Beavis, R. C.; Wilkins, J. A.; Krokhin, O. V., 3D HPLC-MS with Reversed-Phase Separation Functionality in All Three Dimensions for Large-Scale Bottom-Up Proteomics and Peptide Retention Data Collection. Anal Chem 2016, 88 (5), 2847-55.
  4. Sharma, P. K.; Fu, J.; Spicer, V.; Krokhin, O. V.; Cicek, N.; Sparling, R.; Levin, D. B., Global changes in the proteome of Cupriavidus necator H16 during poly-(3-hydroxybutyrate) synthesis from various biodiesel by-product substrates. AMB Express 2016, 6 (1), 36.
  5. Munir, R. I.; Spicer, V.; Krokhin, O. V.; Shamshurin, D.; Zhang, X.; Taillefer, M.; Blunt, W.; Cicek, N.; Sparling, R.; Levin, D. B., Transcriptomic and proteomic analyses of core metabolism in Clostridium termitidis CT1112 during growth on alpha-cellulose, xylan, cellobiose and xylose. BMC Microbiol 2016, 16, 91.
  6. Dwivedi, R. C.; Navarrete, M.; Choi, N.; Spicer, V.; Rigatto, C.; Arora, R. C.; Krokhin, O.; Ho, J.; Wilkins, J. A., A proteomic evaluation of urinary changes associated with cardiopulmonary bypass. Clin Proteomics 2016, 13, 17.
  7. Krokhin, O. V.; Spicer, V., Generation of accurate peptide retention data for targeted and data independent quantitative LC-MS analysis: Chromatographic lessons in proteomics. Proteomics 2016, 16 (23), 2931-2936.

2015

  1. McQueen, P.; Spicer, V.; Schellenberg, J.; Krokhin, O.; Sparling, R.; Levin, D.; Wilkins, J. A., Whole cell, label free protein quantitation with data independent acquisition: quantitation at the MS2 level. Proteomics 2015, 15 (1), 16-24.
  2. Munir, R. I.; Spicer, V.; Shamshurin, D.; Krokhin, O. V.; Wilkins, J.; Ramachandran, U.; Sparling, R.; Levin, D. B., Quantitative proteomic analysis of the cellulolytic system of Clostridium termitidis CT1112 reveals distinct protein expression profiles upon growth on alpha-cellulose and cellobiose. J Proteomics 2015, 125, 41-53.
  3. Fu, J.; Sharma, P.; Spicer, V.; Krokhin, O. V.; Zhang, X.; Fristensky, B.; Wilkins, J. A.; Cicek, N.; Sparling, R.; Levin, D. B., Effects of impurities in biodiesel-derived glycerol on growth and expression of heavy metal ion homeostasis genes and gene products in Pseudomonas putida LS46. Appl Microbiol Biotechnol 2015, 99 (13), 5583-92.
  4. Lao, Y. W.; Gungormusler-Yilmaz, M.; Shuvo, S.; Verbeke, T.; Spicer, V.; Krokhin, O. V., Chromatographic behavior of peptides containing oxidized methionine residues in proteomic LC-MS experiments: Complex tale of a simple modification. J Proteomics 2015, 125, 131-9.
  5. Abate-Pella, D.; Freund, D. M.; Ma, Y.; Simon-Manso, Y.; Hollender, J.; Broeckling, C. D.; Huhman, D. V.; Krokhin, O. V.; Stoll, D. R.; Hegeman, A. D.; Kind, T.; Fiehn, O.; Schymanski, E. L.; Prenni, J. E.; Sumner, L. W.; Boswell, P. G., Retention projection enables accurate calculation of liquid chromatographic retention times across labs and methods. J Chromatogr A 2015, 1412, 43-51.
  6. Fu, J.; Sharma, P.; Spicer, V.; Krokhin, O. V.; Zhang, X.; Fristensky, B.; Cicek, N.; Sparling, R.; Levin, D. B., Quantitative 'Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids. PLoS One 2015, 10 (11), e0142322.

2014

  1. Verbeke, T. J.; Spicer, V.; Krokhin, O. V.; Zhang, X.; Schellenberg, J. J.; Fristensky, B.; Wilkins, J. A.; Levin, D. B.; Sparling, R., Thermoanaerobacter thermohydrosulfuricus WC1 shows protein complement stability during fermentation of key lignocellulose-derived substrates. Appl Environ Microbiol 2014, 80 (5), 1602-15.
  2. Lao, Y. W.; Mackenzie, K.; Vincent, W.; Krokhin, O. V., Characterization and complete separation of major cyclolinopeptides in flaxseed oil by reversed-phase chromatography. J Sep Sci 2014, 37 (14), 1788-96.
  3. Rydzak, T.; Grigoryan, M.; Cunningham, Z. J.; Krokhin, O. V.; Ezzati, P.; Cicek, N.; Levin, D. B.; Wilkins, J. A.; Sparling, R., Insights into electron flux through manipulation of fermentation conditions and assessment of protein expression profiles in Clostridium thermocellum. Appl Microbiol Biotechnol 2014, 98 (14), 6497-510.
  4. Rody, W. J., Jr.; Holliday, L. S.; McHugh, K. P.; Wallet, S. M.; Spicer, V.; Krokhin, O., Mass spectrometry analysis of gingival crevicular fluid in the presence of external root resorption. Am J Orthod Dentofacial Orthop 2014, 145 (6), 787-98.
  5. Schellenberg, J. J.; Verbeke, T. J.; McQueen, P.; Krokhin, O. V.; Zhang, X.; Alvare, G.; Fristensky, B.; Thallinger, G. G.; Henrissat, B.; Wilkins, J. A.; Levin, D. B.; Sparling, R., Enhanced whole genome sequence and annotation of Clostridium stercorarium DSM8532T using RNA-seq transcriptomics and high-throughput proteomics. BMC Genomics 2014, 15, 567.
  6. Vanee, N.; Brooks, J. P.; Spicer, V.; Shamshurin, D.; Krokhin, O.; Wilkins, J. A.; Deng, Y.; Fong, S. S., Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca. BMC Syst Biol 2014, 8, 86.
  7. Gungormusler-Yilmaz, M.; Shamshurin, D.; Grigoryan, M.; Taillefer, M.; Spicer, V.; Krokhin, O. V.; Sparling, R.; Levin, D. B., Reduced catabolic protein expression in Clostridium butyricum DSM 10702 correlate with reduced 1,3-propanediol synthesis at high glycerol loading. AMB Express 2014, 4, 63.
  8. Shamshurin, D.; Krokhin, O.V.; Levin, D.B.; Sparling, R,; Wilkins, J.A. In situ activity-based protein profiling of serine hydrolases in E. coli. EuPA Open Proteomics 2014, 4, 18-24.
  9. Spicer, V.; Lao, Y. W.; Shamshurin, D.; Ezzati, P.; Wilkins, J. A.; Krokhin, O. V., N-capping motifs promote interaction of amphipathic helical peptides with hydrophobic surfaces and drastically alter hydrophobicity values of individual amino acids. Anal Chem 2014, 86 (23), 11498-502.

2013

  1. Jiang, X.; Shamshurin, D.; Spicer, V.; Krokhin, O. V., The effect of various S-alkylating agents on the chromatographic behavior of cysteine-containing peptides in reversed-phase chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2013, 915-916, 57-63.
  2. Verbeke, T. J.; Zhang, X.; Henrissat, B.; Spicer, V.; Rydzak, T.; Krokhin, O. V.; Fristensky, B.; Levin, D. B.; Sparling, R., Genomic evaluation of Thermoanaerobacter spp. for the construction of designer co-cultures to improve lignocellulosic biofuel production. PLoS One 2013, 8 (3), e59362.
  3. Grigoryan, M.; Shamshurin, D.; Spicer, V.; Krokhin, O. V., Unifying expression scale for peptide hydrophobicity in proteomic reversed phase high-pressure liquid chromatography experiments. Anal Chem 2013, 85 (22), 10878-86.
  4. Navarrete, M.; Ho, J.; Krokhin, O.; Ezzati, P.; Rigatto, C.; Reslerova, M.; Rush, D. N.; Nickerson, P.; Wilkins, J. A., Proteomic characterization of serine hydrolase activity and composition in normal urine. Clin Proteomics 2013, 10 (1), 17.

2012

  1. Krokhin, O., Peptide retention prediction in reversed-phase chromatography: proteomic applications. Expert Rev Proteomics 2012, 9 (1), 1-4.
  2. McQueen, P.; Krokhin, O., Optimal selection of 2D reversed-phase-reversed-phase HPLC separation techniques in bottom-up proteomics. Expert Rev Proteomics 2012, 9 (2), 125-8.
  3. McQueen, P.; Spicer, V.; Rydzak, T.; Sparling, R.; Levin, D.; Wilkins, J. A.; Krokhin, O., Information-dependent LC-MS/MS acquisition with exclusion lists potentially generated on-the-fly: case study using a whole cell digest of Clostridium thermocellum. Proteomics 2012, 12 (8), 1160-9.
  4. Reimer, J.; Spicer, V.; Krokhin, O. V., Application of modern reversed-phase peptide retention prediction algorithms to the Houghten and DeGraw dataset: peptide helicity and its effect on prediction accuracy. J Chromatogr A 2012, 1256, 160-8.
  5. Rydzak, T.; McQueen, P. D.; Krokhin, O. V.; Spicer, V.; Ezzati, P.; Dwivedi, R. C.; Shamshurin, D.; Levin, D. B.; Wilkins, J. A.; Sparling, R., Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression. BMC Microbiol 2012, 12, 214.
  6. Berard, A. R.; Cortens, J. P.; Krokhin, O.; Wilkins, J. A.; Severini, A.; Coombs, K. M., Quantification of the host response proteome after mammalian reovirus T1L infection. PLoS One 2012, 7 (12), e51939.

2011

  1. Andreev, V. P.; Dwivedi, R. C.; Paz-Filho, G.; Krokhin, O. V.; Wong, M. L.; Wilkins, J. A.; Licinio, J., Dynamics of plasma proteome during leptin-replacement therapy in genetically based leptin deficiency. Pharmacogenomics J 2011, 11 (3), 174-90.
  2. Azoulay-Shemer, T.; Harpaz-Saad, S.; Cohen-Peer, R.; Mett, A.; Spicer, V.; Lovat, N.; Krokhin, O.; Brand, A.; Gidoni, D.; Standing, K. G.; Goldschmidt, E. E.; Eyal, Y., Dual N- and C-terminal processing of citrus chlorophyllase precursor within the plastid membranes leads to the mature enzyme. Plant Cell Physiol 2011, 52 (1), 70-83.
  3. Reimer, J.; Shamshurin, D.; Harder, M.; Yamchuk, A.; Spicer, V.; Krokhin, O. V., Effect of cyclization of N-terminal glutamine and carbamidomethyl-cysteine (residues) on the chromatographic behavior of peptides in reversed-phase chromatography. J Chromatogr A 2011, 1218 (31), 5101-7.
  4. McCubbin, J. A.; Voth, S.; Krokhin, O. V., Mild and tunable benzoic acid catalysts for rearrangement reactions of allylic alcohols. J Org Chem 2011, 76 (20), 8537-42.
  5. Shamshurin, D.; Spicer, V.; Krokhin, O. V., Defining intrinsic hydrophobicity of amino acids' side chains in random coil conformation. Reversed-phase liquid chromatography of designed synthetic peptides vs. random peptide data sets. J Chromatogr A 2011, 1218 (37), 6348-55.

2010

  1. Dwivedi, R. C.; Krokhin, O. V.; Cortens, J. P.; Wilkins, J. A., Assessment of the reproducibility of random hexapeptide peptide library-based protein normalization. J Proteome Res 2010, 9 (2), 1144-9.
  2. Ghosh, D.; Lippert, D.; Krokhin, O.; Cortens, J. P.; Wilkins, J. A., Defining the membrane proteome of NK cells. J Mass Spectrom 2010, 45 (1), 1-25.
  3. McCubbin, J. A.; Hosseini, H.; Krokhin, O. V., Boronic Acid catalyzed friedel-crafts reactions of allylic alcohols with electron-rich arenes and heteroarenes. J Org Chem 2010, 75 (3), 959-62.
  4. Vu, H.; Spicer, V.; Gotfrid, A.; Krokhin, O. V., A model for predicting slopes S in the basic equation for the linear-solvent-strength theory of peptide separation by reversed-phase high-performance liquid chromatography. J Chromatogr A 2010, 1217 (4), 489-97.
  5. McCubbin, J.A.; Krokhin, O.V., Organocatalyzed Friedel-Crafts arylation of benzylic alcohols. Tetrahedron letters 2010, 51 (18), 2447-2449.
  6. Coombs, K. M.; Berard, A.; Xu, W.; Krokhin, O.; Meng, X.; Cortens, J. P.; Kobasa, D.; Wilkins, J.; Brown, E. G. Quantitative Proteomic Analyses of Influenza virus-Infected Cultured Human Lung Cells. J Virol. 2010 84 (20), 10888-10906.
  7. Spicer, V.; Grigoryan, M.; Gotfrid, A.; Standing, K. G.; Krokhin, O. V., Predicting retention time shifts associated with variation of the gradient slope in peptide RP-HPLC. Anal Chem 2010, 82 (23), 9678-85.
  8. Krokhin, O. V.; Spicer, V., Predicting peptide retention times for proteomics. Curr Protoc Bioinformatics 2010, Chapter 13, Unit 13 14.

2009

  1. Seifers, D. L.; Martin, T. J.; Harvey, T. L.; Haber, S.; Krokhin, O.; Spicer, V.; Ying, S.; Standing, K. G., Identification of Variants of the High Plains virus Infecting Wheat in Kansas. Plant Dis 2009, 93 (12), 1265-1274.
  2. Dwivedi, R. C.; Dhindsa, N.; Krokhin, O. V.; Cortens, J.; Wilkins, J. A.; El-Gabalawy, H. S., The effects of infliximab therapy on the serum proteome of rheumatoid arthritis patients. Arthritis Res Ther 2009, 11 (2), R32.
  3. Ho, J.; Lucy, M.; Krokhin, O.; Hayglass, K.; Pascoe, E.; Darroch, G.; Rush, D.; Nickerson, P.; Rigatto, C.; Reslerova, M., Mass spectrometry-based proteomic analysis of urine in acute kidney injury following cardiopulmonary bypass: a nested case-control study. Am J Kidney Dis 2009, 53 (4), 584-95.
  4. Krokhin, O. V.; Spicer, V., Peptide retention standards and hydrophobicity indexes in reversed-phase high-performance liquid chromatography of peptides. Anal Chem 2009, 81 (22), 9522-30.

2008

  1. Azoulay Shemer, T.; Harpaz-Saad, S.; Belausov, E.; Lovat, N.; Krokhin, O.; Spicer, V.; Standing, K. G.; Goldschmidt, E. E.; Eyal, Y., Citrus chlorophyllase dynamics at ethylene-induced fruit color-break: a study of chlorophyllase expression, posttranslational processing kinetics, and in situ intracellular localization. Plant Physiol 2008, 148 (1), 108-18.
  2. Qian, Y.; Preston, K.; Krokhin, O.; Mellish, J.; Ens, W., Characterization of wheat gluten proteins by HPLC and MALDI TOF mass spectrometry. J Am Soc Mass Spectrom 2008, 19 (10), 1542-50.
  3. Dwivedi, R. C.; Spicer, V.; Harder, M.; Antonovici, M.; Ens, W.; Standing, K. G.; Wilkins, J. A.; Krokhin, O. V., Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics. Anal Chem 2008, 80 (18), 7036-42.
  4. Seifers, D. L.; Martin, T. J.; Harvey, T. L.; Fellers, J. P.; Stack, J. P.; Ryba-White, M.; Haber, S.; Krokhin, O.; Spicer, V.; Lovat, N.; Yamchuk, A.; Standing, K. G., Triticum mosaic virus: A New Virus Isolated from Wheat in Kansas. Plant Dis 2008, 92 (5), 808-817.

2007

  1. Tripet, B.; Cepeniene, D.; Kovacs, J. M.; Mant, C. T.; Krokhin, O. V.; Hodges, R. S., Requirements for prediction of peptide retention time in reversed-phase high-performance liquid chromatography: hydrophilicity/hydrophobicity of side-chains at the N- and C-termini of peptides are dramatically affected by the end-groups and location. J Chromatogr A 2007, 1141 (2), 212-25.
  2. Meng, X.; Krokhin, O.; Cheng, K.; Ens, W.; Wilkins, J. A., Characterization of IQGAP1-containing complexes in NK-like cells: evidence for Rac 2 and RACK1 association during homotypic adhesion. J Proteome Res 2007, 6 (2), 744-50.
  3. Moore, D. F.; Krokhin, O. V.; Beavis, R. C.; Ries, M.; Robinson, C.; Goldin, E.; Brady, R. O.; Wilkins, J. A.; Schiffmann, R., Proteomics of specific treatment-related alterations in Fabry disease: a strategy to identify biological abnormalities. Proc Natl Acad Sci U S A 2007, 104 (8), 2873-8.
  4. Weiler, T.; Du, Q.; Krokhin, O.; Ens, W.; Standing, K.; El-Gabalawy, H.; Wilkins, J. A., The identification and characterization of a novel protein, c19orf10, in the synovium. Arthritis Res Ther 2007, 9 (2), R30.
  5. She, Y. M.; Krokhin, O.; Spicer, V.; Loboda, A.; Garland, G.; Ens, W.; Standing, K. G.; Westmore, J. B., Formation of (bn-1 + H2O) ions by collisional activation of MALDI-formed peptide [M + H]+ ions in a QqTOF mass spectrometer. J Am Soc Mass Spectrom 2007, 18 (6), 1024-37.
  6. Falzarano, D.; Krokhin, O.; Van Domselaar, G.; Wolf, K.; Seebach, J.; Schnittler, H. J.; Feldmann, H., Ebola sGP--the first viral glycoprotein shown to be C-mannosylated. Virology 2007, 368 (1), 83-90.
  7. Spicer, V.; Yamchuk, A.; Cortens, J.; Sousa, S.; Ens, W.; Standing, K. G.; Wilkins, J. A.; Krokhin, O. V., Sequence-specific retention calculator. A family of peptide retention time prediction algorithms in reversed-phase HPLC: applicability to various chromatographic conditions and columns. Anal Chem 2007, 79 (22), 8762-8.

2007

  1. Tripet, B.; Cepeniene, D.; Kovacs, J. M.; Mant, C. T.; Krokhin, O. V.; Hodges, R. S., Requirements for prediction of peptide retention time in reversed-phase high-performance liquid chromatography: hydrophilicity/hydrophobicity of side-chains at the N- and C-termini of peptides are dramatically affected by the end-groups and location. J Chromatogr A 2007, 1141 (2), 212-25.
  2. Meng, X.; Krokhin, O.; Cheng, K.; Ens, W.; Wilkins, J. A., Characterization of IQGAP1-containing complexes in NK-like cells: evidence for Rac 2 and RACK1 association during homotypic adhesion. J Proteome Res 2007, 6 (2), 744-50.
  3. Moore, D. F.; Krokhin, O. V.; Beavis, R. C.; Ries, M.; Robinson, C.; Goldin, E.; Brady, R. O.; Wilkins, J. A.; Schiffmann, R., Proteomics of specific treatment-related alterations in Fabry disease: a strategy to identify biological abnormalities. Proc Natl Acad Sci U S A 2007, 104 (8), 2873-8.
  4. Weiler, T.; Du, Q.; Krokhin, O.; Ens, W.; Standing, K.; El-Gabalawy, H.; Wilkins, J. A., The identification and characterization of a novel protein, c19orf10, in the synovium. Arthritis Res Ther 2007, 9 (2), R30.
  5. She, Y. M.; Krokhin, O.; Spicer, V.; Loboda, A.; Garland, G.; Ens, W.; Standing, K. G.; Westmore, J. B., Formation of (bn-1 + H2O) ions by collisional activation of MALDI-formed peptide [M + H]+ ions in a QqTOF mass spectrometer. J Am Soc Mass Spectrom 2007, 18 (6), 1024-37.
  6. Falzarano, D.; Krokhin, O.; Van Domselaar, G.; Wolf, K.; Seebach, J.; Schnittler, H. J.; Feldmann, H., Ebola sGP--the first viral glycoprotein shown to be C-mannosylated. Virology 2007, 368 (1), 83-90.
  7. Spicer, V.; Yamchuk, A.; Cortens, J.; Sousa, S.; Ens, W.; Standing, K. G.; Wilkins, J. A.; Krokhin, O. V., Sequence-specific retention calculator. A family of peptide retention time prediction algorithms in reversed-phase HPLC: applicability to various chromatographic conditions and columns. Anal Chem 2007, 79 (22), 8762-8.

2006

  1. Krokhin, O.; Wilkins, J. A.; Standing, K.G. A novel sequence-specific algorithm for peptide retention prediction in ion-pair RP-HPLC: applications in proteomics. Laboratory Focus 2006, 1, 10-11.
  2. Bykova, N. V.; Rampitsch, C.; Krokhin, O.; Standing, K. G.; Ens, W., Determination and characterization of site-specific N-glycosylation using MALDI-Qq-TOF tandem mass spectrometry: case study with a plant protease. Anal Chem 2006, 78 (4), 1093-103.
  3. Lattova, E.; Kapkova, P.; Krokhin, O.; Perreault, H., Method for investigation of oligosaccharides from glycopeptides: direct determination of glycosylation sites in proteins. Anal Chem 2006, 78 (9), 2977-84.
  4. Krokhin, O. V.; Antonovici, M.; Ens, W.; Wilkins, J. A.; Standing, K. G., Deamidation of -Asn-Gly- sequences during sample preparation for proteomics: Consequences for MALDI and HPLC-MALDI analysis. Anal Chem 2006, 78 (18), 6645-50.
  5. Krokhin, O. V.; Ying, S.; Cortens, J. P.; Ghosh, D.; Spicer, V.; Ens, W.; Standing, K. G.; Beavis, R. C.; Wilkins, J. A., Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS. Anal Chem 2006, 78 (17), 6265-9.
  6. Snovida, S. I.; Chen, V. C.; Krokhin, O.; Perreault, H., Isolation and identification of sialylated glycopeptides from bovine alpha1-acid glycoprotein by off-line capillary electrophoresis MALDI-TOF mass spectrometry. Anal Chem 2006, 78 (18), 6556-63.
  7. Falzarano, D.; Krokhin, O.; Wahl-Jensen, V.; Seebach, J.; Wolf, K.; Schnittler, H. J.; Feldmann, H., Structure-function analysis of the soluble glycoprotein, sGP, of Ebola virus. Chembiochem 2006, 7 (10), 1605-11.
  8. Krokhin, O. V., Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: application to 300- and 100-A pore size C18 sorbents. Anal Chem 2006, 78 (22), 7785-95.

2005

  1. Hasinoff, B. B.; Wu, X.; Krokhin, O. V.; Ens, W.; Standing, K. G.; Nitiss, J. L.; Sivaram, T.; Giorgianni, A.; Yang, S.; Jiang, Y.; Yalowich, J. C., Biochemical and proteomics approaches to characterize topoisomerase IIalpha cysteines and DNA as targets responsible for cisplatin-induced inhibition of topoisomerase IIalpha. Mol Pharmacol 2005, 67 (3), 937-47.
  2. Ethier, M.; Krokhin, O.; Ens, W.; Standing, K. G.; Wilkins, J. A.; Perreault, H., Global and site-specific detection of human integrin alpha 5 beta 1 glycosylation using tandem mass spectrometry and the StrOligo algorithm. Rapid Commun Mass Spectrom 2005, 19 (5), 721-7.
  3. Schaub, S.; Wilkins, J. A.; Antonovici, M.; Krokhin, O.; Weiler, T.; Rush, D.; Nickerson, P., Proteomic-based identification of cleaved urinary beta2-microglobulin as a potential marker for acute tubular injury in renal allografts. Am J Transplant 2005, 5 (4 Pt 1), 729-38.
  4. Lattova, E.; Snovida, S.; Perreault, H.; Krokhin, O., Influence of the labeling group on ionization and fragmentation of carbohydrates in mass spectrometry. J Am Soc Mass Spectrom 2005, 16 (5), 683-96.
  5. Meng, X.; Cheng, K.; Krohkin, O.; Mould, A. P.; Humphries, M. J.; Ens, W.; Standing, K.; Wilkins, J. A., Evidence for the presence of a low-mass beta1 integrin on the cell surface. J Cell Sci 2005, 118 (Pt 17), 4009-16.
  6. Krokhin, O. V.; Ens, W.; Standing, K. G., MALDI QqTOF MS combined with off-line HPLC for characterization of protein primary structure and post-translational modifications. J Biomol Tech 2005, 16 (4), 429-40.

2004

  1. Lattova, E.; Perreault, H.; Krokhin, O., Matrix-assisted laser desorption/ionization tandem mass spectrometry and post-source decay fragmentation study of phenylhydrazones of N-linked oligosaccharides from ovalbumin. J Am Soc Mass Spectrom 2004, 15 (5), 725-35.
  2. Krokhin, O. V.; Craig, R.; Spicer, V.; Ens, W.; Standing, K. G.; Beavis, R. C.; Wilkins, J. A., An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its application to protein peptide mapping by off-line HPLC-MALDI MS. Mol Cell Proteomics 2004, 3 (9), 908-19.
  3. Ghosh, D.; Krokhin, O.; Antonovici, M.; Ens, W.; Standing, K. G.; Beavis, R. C.; Wilkins, J. A., Lectin affinity as an approach to the proteomic analysis of membrane glycoproteins. J Proteome Res 2004, 3 (4), 841-50.
  4. Krokhin, O.; Ens, W.; Standing, K. G.; Wilkins, J.; Perreault, H., Site-specific N-glycosylation analysis: matrix-assisted laser desorption/ionization quadrupole-quadrupole time-of-flight tandem mass spectral signatures for recognition and identification of glycopeptides. Rapid Commun Mass Spectrom 2004, 18 (18), 2020-30.

2003

  1. Krokhin, O.; Li, Y.; Andonov, A.; Feldmann, H.; Flick, R.; Jones, S.; Stroeher, U.; Bastien, N.; Dasuri, K. V.; Cheng, K.; Simonsen, J. N.; Perreault, H.; Wilkins, J.; Ens, W.; Plummer, F.; Standing, K. G., Mass spectrometric characterization of proteins from the SARS virus: a preliminary report. Mol Cell Proteomics 2003, 2 (5), 346-56.
  2. Donald, L. J.; Krokhin, O. V.; Duckworth, H. W.; Wiseman, B.; Deemagarn, T.; Singh, R.; Switala, J.; Carpena, X.; Fita, I.; Loewen, P. C., Characterization of the catalase-peroxidase KatG from Burkholderia pseudomallei by mass spectrometry. J Biol Chem 2003, 278 (37), 35687-92.
  3. Krokhin, O. V.; Ens, W.; Standing, K. G., Characterizing degradation products of peptides containing N-terminal Cys residues by (off-line high-performance liquid chromatography)/matrix-assisted laser desorption/ionization quadrupole time-of-flight measurements. Rapid Commun Mass Spectrom 2003, 17 (22), 2528-34.
  4. Craig, R.; Krokhin, O.; Wilkins, J.; Beavis, R. C., Implementation of an algorithm for modeling disulfide bond patterns using mass spectrometry. J Proteome Res 2003, 2 (6), 657-61.
  5. Krokhin, O. V.; Cheng, K.; Sousa, S. L.; Ens, W.; Standing, K. G.; Wilkins, J. A., Mass spectrometric based mapping of the disulfide bonding patterns of integrin alpha chains. Biochemistry 2003, 42 (44), 12950-9.
  6. Ethier, M.; Saba, J. A.; Spearman, M.; Krokhin, O.; Butler, M.; Ens, W.; Standing, K. G.; Perreault, H., Application of the StrOligo algorithm for the automated structure assignment of complex N-linked glycans from glycoproteins using tandem mass spectrometry. Rapid Commun Mass Spectrom 2003, 17 (24), 2713-20.

Papers in refereed journals (chromatography/inorganic analytical chemistry):

1992-2002

  1. Krokhin, O. V.; Pirogov, A. V.; Obrezkov, O. N.; Shpigun, O. A., Flow-Injection Determination of Boric-Acid. J Anal Chem+ (russ). 1992, 47 (5), 561-562.
  2. Krokhin, O. V.; Elefterov, A. I.; Obrezkov, O. N.; Shpigun, O. A., Increase in the Sensitivity of the Ion-Chromatographic Determination of Strongly Retained Anions. J Anal Chem+ (russ). 1993, 48 (1), 82-86.
  3. Krokhin, O. V.; Obrezkov, O. N.; Shpigun, O. A., Use of Aromatic Sulfonic-Acids as Eluents in Ion Chromatography. J Anal Chem+ (russ). 1993, 48 (7), 827-831.
  4. Obrezkov, O. N.; Krokhin, O. V.; Pirogov, A. V.; Semenova, S. N.; Shpigun, O. A., Determination of Transition-Metals on Dynamically Modified Cation-Exchangers. Zh Fiz Khim+ (russ). 1994, 68 (10), 1880-1883.
  5. Krokhin, O. V.; Smolenkov, A. D.; Svintsova, N. V.; Obrezkov, O. N.; Shpigun, O. A., Modified Silica as a Stationary-Phase for Ion Chromatography. Journal of Chromatography A 1995, 706 (1-2), 93-98.
  6. Krokhin, O. V.; Xu, W. Z.; Hoshino, H.; Shpigun, O. A.; Yotsuyanagi, T., Simultaneous determination of inorganic anions and equally charged complexes of transition metals with polyaminocarboxylic acids by capillary electrophoresis. Chem Lett 1996, (12), 1095-1096.
  7. O.I. Martynova, V.I. Kashinsky, A.Yu. Petrov, L.V. Makarova, O.V. Krokhin. "The use of ion chromatography for the control of water quality at electric power stations". Teploenergetika (russ). 1996, 8, 39-42.
  8. Krokhin, O. V.; Hoshino, H.; Shpigun, O. A.; Yotsuyanagi, T., Use of cationic polymers for the simultaneous determination of inorganic anions and metal-4-(2-pyridylazo)resorcinolato chelates in kinetic differentiation-mode capillary electrophoresis. Journal of Chromatography A 1997, 776 (2), 329-336.
  9. Krokhin, O. V.; Hoshino, H.; Shpigun, O. A.; Yotsuyanagi, T., Influence of cationic polymers on separation selectivity in kinetic differentiation mode capillary electrophoresis of metal-4-(2-pyridylazo)resorcinolato chelates. Journal of Chromatography A 1997, 772 (1-2), 339-346.
  10. Krokhin, O. V.; Svintsova, N. V.; Obrezkov, O. N.; Shpigun, O. A., Modified silica gel for the determination of anions by single-column ion chromatography. J Anal Chem+ (russ). 1997, 52 (11), 1066-1068.
  11. Obrezkov, O. N.; Tolkacheva, V. A.; Zaikanova, G. I.; Yamnikov, V. A.; Krokhin, O. V.; Shpigun, O. A., Application of ion chromatography in distillery production. Determination of inorganic anions. Ind Lab+ (russ). 1997, 63 (2), 71-73.
  12. O.V. Krokhin. "Ion Chromatographs of Dionex company". Bull. of Russ. Chem. Soc. (russ). 1997 3, 61-64.
  13. Krokhin, O. V.; Obrezkov, O. N.; Shpigun, O. A., Analytical potentialities of an AI-05 instrument for capillary electrophoresis in the determination of metal cations. J Anal Chem+ (russ). 1998, 53 (4), 372-374.
  14. Obrezkov, O. N.; Krokhin, O. V.; Makarov, A. Y.; Guglya, E. B.; Shpigun, O. A., Determination of phosphorous and phosphoric acids in air by ion chromatography and capillary isotachophoresys. J Anal Chem+ (russ). 1998, 53 (6), 557-560.
  15. Pirogov, A. V.; Svintsova, N. V.; Kuzina, O. V.; Krokhin, O. V.; Platonov, M. M.; Shpigun, O. A., Silicas modified by polyelectrolyte complexes for the ion chromatography of anionic complexes of transition metals. Fresen J Anal Chem 1998, 361 (3), 288-293.
  16. Svintsova, N. V.; Smolenkov, A. D.; Krokhin, O. V.; Pirogov, A. V.; Obrezkov, O. N.; Shpigun, O. A., Use of new surface-modified sorbents based on silica gel for the determination of anionic transition metal complexes by ion chromatography. J Anal Chem+ (russ). 1998, 53 (4), 347-350.
  17. Krokhin, O. V.; Adamov, A. V.; Hoshino, H.; Shpigun, O. A.; Yotsuyanagi, T., Separation selectivity of some ethylenediaminetetraacetic acid and cyclohexane-1,2-diaminetetraacetic acid complexes in column and ion electrokinetic chromatography. Journal of Chromatography A 1999, 850 (1-2), 269-276.
  18. Krokhin, O. V.; Hoshino, H.; Shpigun, O. A.; Yotsuyanagi, T., The use of N,N-bis(hydroxybenzyl)ethylenediamine-N,N-diacetic acid (HBED) for the determination of trivalent metal ions by capillary electrophoresis. Chem Lett 1999, (9), 903-904.
  19. Krokhin, O. V.; Hoshino, H.; Shpigun, O. A.; Yotsuyanagi, T., Separation selectivity of anionic metal complexes of N,N'-bis(hydroxybenzyl)ethylenediamine-N,N'-diacetic acid in ion and ion electrokinetic chromatography. J Chromatogr A 2000, 895 (1-2), 255-61.
  20. Krokhin, O. V.; Kuzina, O. V.; Hoshino, H.; Shpigun, O. A.; Yotsuyanagi, T., Potential of ethylenediaminedi(o-hydroxyphenylacetic acid) and N,N'-bis(hydroxybenzyl)ethylenediamine-N,N'-diacetic acid for the determination of metal ions by capillary electrophoresis. J Chromatogr A 2000, 890 (2), 363-9.
  21. Obrezkov, O. N.; Tolkacheva, V. A.; Zaikanova, G. I.; Yamnikov, V. A.; Krokhin, O. V.; Zhukov, S. P.; Shpigun, O. A., The use of ion chromatography in vodka and liqueur production. Determination of transition metals. Ind Lab+ (russ). 2000, 66 (1), 18-21.
  22. Pirogov, A. V.; Krokhin, O. V.; Platonov, M. M.; Deryugina, Y. I.; Shpigun, O. A., Ion-chromatographic selectivity of polyelectrolyte sorbents based on some aliphatic and aromatic ionenes. Journal of Chromatography A 2000, 884 (1-2), 31-39.
  23. Shapovalov, V. L.; Rokitskaya, T. I.; Kotova, E. A.; Krokhin, O. V.; Antonenko, Y. N., Effect of fluoride anions on gramicidin photoinactivation sensitized by sulfonated aluminum phthalocyanines. Photochemistry and Photobiology 2001, 74 (1), 1-7.
  24. Krokhin, O. V.; Pirogov, A. V.; Shpigun, O. A., New high-performance techniques for ion-exchange separation. J Anal Chem+ (russ). 2002, 57 (10), 920-927.
  25. Tikhomirova, T. I.; Krokhin, O. V.; Dubovik, D. B.; Ivanov, A. V.; Shpigun, O. A., Chromatographic determination of silicon and phosphorus as molybdic heteropoly acids with preconcentration. J Anal Chem+ (russ). 2002, 57 (1), 18-23.