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Items: 1 to 50 of 110

1.

Retention Time Prediction for Glycopeptides in Reversed-Phase Chromatography for Glycoproteomic Applications.

Ang E, Neustaeter H, Spicer V, Perreault H, Krokhin O.

Anal Chem. 2019 Nov 5;91(21):13360-13366. doi: 10.1021/acs.analchem.9b02584. Epub 2019 Oct 14.

PMID:
31566965
2.

Immunomodulatory Functions of the Human Cathelicidin LL-37 (aa 13-31)-Derived Peptides are Associated with Predicted α-Helical Propensity and Hydrophobic Index.

Hemshekhar M, Faiyaz S, Choi KG, Krokhin OV, Mookherjee N.

Biomolecules. 2019 Sep 18;9(9). pii: E501. doi: 10.3390/biom9090501.

3.

The proteome of extracellular vesicles released by clastic cells differs based on their substrate.

Rody WJ Jr, Chamberlain CA, Emory-Carter AK, McHugh KP, Wallet SM, Spicer V, Krokhin O, Holliday LS.

PLoS One. 2019 Jul 10;14(7):e0219602. doi: 10.1371/journal.pone.0219602. eCollection 2019.

4.

Genomic comparison of facultatively anaerobic and obligatory aerobic Caldibacillus debilis strains GB1 and Tf helps explain physiological differences.

Wushke S, Froese A, Fristensky B, Zhang XL, Spicer V, Krokhin OV, Levin DB, Sparling R.

Can J Microbiol. 2019 Jun;65(6):421-428. doi: 10.1139/cjm-2018-0464. Epub 2019 Jan 29.

PMID:
30694700
5.

Universal retention standard for peptide separations using various modes of high-performance liquid chromatography.

Klaassen N, Spicer V, Krokhin OV.

J Chromatogr A. 2019 Mar 15;1588:163-168. doi: 10.1016/j.chroma.2018.12.057. Epub 2018 Dec 26.

PMID:
30626502
6.

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.

Chen D, Ludwig KR, Krokhin OV, Spicer V, Yang Z, Shen X, Hummon AB, Sun L.

Anal Chem. 2019 Feb 5;91(3):2201-2208. doi: 10.1021/acs.analchem.8b04770. Epub 2019 Jan 23.

PMID:
30624053
7.

A metabolic and genomic assessment of sugar fermentation profiles of the thermophilic Thermotogales, Fervidobacterium pennivorans.

Wushke S, Fristensky B, Zhang XL, Spicer V, Krokhin OV, Levin DB, Stott MB, Sparling R.

Extremophiles. 2018 Nov;22(6):965-974. doi: 10.1007/s00792-018-1053-4. Epub 2018 Sep 4.

PMID:
30182148
8.

Retention Order Reversal of Phosphorylated and Unphosphorylated Peptides in Reversed-Phase LC/MS.

Ogata K, Krokhin OV, Ishihama Y.

Anal Sci. 2018 Sep 10;34(9):1037-1041. doi: 10.2116/analsci.18SCP11. Epub 2018 Jul 27.

9.

Absolute Quantitation of Glycoforms of Two Human IgG Subclasses Using Synthetic Fc Peptides and Glycopeptides.

Roy R, Ang E, Komatsu E, Domalaon R, Bosseboeuf A, Harb J, Hermouet S, Krokhin O, Schweizer F, Perreault H.

J Am Soc Mass Spectrom. 2018 Jun;29(6):1086-1098. doi: 10.1007/s13361-018-1900-7. Epub 2018 May 23.

PMID:
29796736
10.

Description of a cryptic thermophilic (pro)phage, CBP1 from Caldibacillus debilis strain GB1.

Wushke S, Jin Z, Spicer V, Zhang XL, Fristensky B, Krokhin OV, Levin DB, Sparling R.

Extremophiles. 2018 Mar;22(2):203-209. doi: 10.1007/s00792-017-0988-1. Epub 2018 Jan 30.

PMID:
29380170
11.

Peptide retention time prediction in hydrophilic interaction liquid chromatography. Comparison of separation selectivity between bare silica and bonded stationary phases.

Spicer V, Krokhin OV.

J Chromatogr A. 2018 Jan 26;1534:75-84. doi: 10.1016/j.chroma.2017.12.046. Epub 2017 Dec 18.

PMID:
29306631
12.

Sequence-Specific Model for Peptide Retention Time Prediction in Strong Cation Exchange Chromatography.

Gussakovsky D, Neustaeter H, Spicer V, Krokhin OV.

Anal Chem. 2017 Nov 7;89(21):11795-11802. doi: 10.1021/acs.analchem.7b03436. Epub 2017 Oct 17.

PMID:
28971681
13.

Interferon γ induced compositional changes in human bone marrow derived mesenchymal stem/stromal cells.

Guan Q, Ezzati P, Spicer V, Krokhin O, Wall D, Wilkins JA.

Clin Proteomics. 2017 Jul 6;14:26. doi: 10.1186/s12014-017-9161-1. eCollection 2017.

14.

The use of cell culture platforms to identify novel markers of bone and dentin resorption.

Rody WJ Jr, Krokhin O, Spicer V, Chamberlain CA, Chamberlain M, McHugh KP, Wallet SM, Emory AK, Crull JD, Holliday LS.

Orthod Craniofac Res. 2017 Jun;20 Suppl 1:89-94. doi: 10.1111/ocr.12162.

PMID:
28643914
16.

Understanding aerobic/anaerobic metabolism in Caldibacillus debilis through a comparison with model organisms.

Wushke S, Spicer V, Zhang XL, Fristensky B, Krokhin OV, Levin DB, Cicek N, Sparling R.

Syst Appl Microbiol. 2017 Jul;40(5):245-253. doi: 10.1016/j.syapm.2017.03.004. Epub 2017 Apr 13.

PMID:
28527624
17.

Peptide Retention Time Prediction in Hydrophilic Interaction Liquid Chromatography: Data Collection Methods and Features of Additive and Sequence-Specific Models.

Krokhin OV, Ezzati P, Spicer V.

Anal Chem. 2017 May 16;89(10):5526-5533. doi: 10.1021/acs.analchem.7b00537. Epub 2017 Apr 26.

PMID:
28429592
18.

Investigating Acquisition Performance on the Orbitrap Fusion When Using Tandem MS/MS/MS Scanning with Isobaric Tags.

Hughes CS, Spicer V, Krokhin OV, Morin GB.

J Proteome Res. 2017 May 5;16(5):1839-1846. doi: 10.1021/acs.jproteome.7b00091. Epub 2017 Apr 20.

PMID:
28418257
19.

Evaluating the Characteristics of Reporter Ion Signal Acquired in the Orbitrap Analyzer for Isobaric Mass Tag Proteome Quantification Experiments.

Hughes CS, Zhu C, Spicer V, Krokhin OV, Morin GB.

J Proteome Res. 2017 May 5;16(5):1831-1838. doi: 10.1021/acs.jproteome.7b00092. Epub 2017 Apr 20.

PMID:
28418254
20.

Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis.

Krokhin OV, Anderson G, Spicer V, Sun L, Dovichi NJ.

Anal Chem. 2017 Feb 7;89(3):2000-2008. doi: 10.1021/acs.analchem.6b04544. Epub 2017 Jan 19.

21.

A deletion variant partially complements a porin-less strain of Neurospora crassa.

Ferens FG, Spicer V, Krokhin OV, Motnenko A, Summers WA, Court DA.

Biochem Cell Biol. 2017 Apr;95(2):318-327. doi: 10.1139/bcb-2016-0166. Epub 2016 Nov 2.

PMID:
28177769
22.

Generation of accurate peptide retention data for targeted and data independent quantitative LC-MS analysis: Chromatographic lessons in proteomics.

Krokhin OV, Spicer V.

Proteomics. 2016 Dec;16(23):2931-2936. doi: 10.1002/pmic.201600283. Epub 2016 Nov 21.

PMID:
27701844
23.

A proteomic evaluation of urinary changes associated with cardiopulmonary bypass.

Dwivedi RC, Navarrete M, Choi N, Spicer V, Rigatto C, Arora RC, Krokhin O, Ho J, Wilkins JA.

Clin Proteomics. 2016 Aug 15;13:17. doi: 10.1186/s12014-016-9118-9. eCollection 2016.

24.

Transcriptomic and proteomic analyses of core metabolism in Clostridium termitidis CT1112 during growth on α-cellulose, xylan, cellobiose and xylose.

Munir RI, Spicer V, Krokhin OV, Shamshurin D, Zhang X, Taillefer M, Blunt W, Cicek N, Sparling R, Levin DB.

BMC Microbiol. 2016 May 23;16:91. doi: 10.1186/s12866-016-0711-x.

25.

Global changes in the proteome of Cupriavidus necator H16 during poly-(3-hydroxybutyrate) synthesis from various biodiesel by-product substrates.

Sharma PK, Fu J, Spicer V, Krokhin OV, Cicek N, Sparling R, Levin DB.

AMB Express. 2016 Dec;6(1):36. doi: 10.1186/s13568-016-0206-z. Epub 2016 May 17.

26.

Elevated Urinary Matrix Metalloproteinase-7 Detects Underlying Renal Allograft Inflammation and Injury.

Ho J, Rush DN, Krokhin O, Antonovici M, Gao A, Bestland J, Wiebe C, Hiebert B, Rigatto C, Gibson IW, Wilkins JA, Nickerson PW.

Transplantation. 2016 Mar;100(3):648-54. doi: 10.1097/TP.0000000000000867.

PMID:
26906940
27.

3D HPLC-MS with Reversed-Phase Separation Functionality in All Three Dimensions for Large-Scale Bottom-Up Proteomics and Peptide Retention Data Collection.

Spicer V, Ezzati P, Neustaeter H, Beavis RC, Wilkins JA, Krokhin OV.

Anal Chem. 2016 Mar 1;88(5):2847-55. doi: 10.1021/acs.analchem.5b04567. Epub 2016 Feb 18.

PMID:
26849966
28.

Quantitative 'Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids.

Fu J, Sharma P, Spicer V, Krokhin OV, Zhang X, Fristensky B, Cicek N, Sparling R, Levin DB.

PLoS One. 2015 Nov 6;10(11):e0142322. doi: 10.1371/journal.pone.0142322. eCollection 2015.

29.

Development of an SRM method for absolute quantitation of MYDGF/C19orf10 protein.

Dwivedi RC, Krokhin OV, El-Gabalawy HS, Wilkins JA.

Proteomics Clin Appl. 2016 Jun;10(6):663-70. doi: 10.1002/prca.201500057. Epub 2015 Dec 15.

PMID:
26537655
30.

Retention projection enables accurate calculation of liquid chromatographic retention times across labs and methods.

Abate-Pella D, Freund DM, Ma Y, Simón-Manso Y, Hollender J, Broeckling CD, Huhman DV, Krokhin OV, Stoll DR, Hegeman AD, Kind T, Fiehn O, Schymanski EL, Prenni JE, Sumner LW, Boswell PG.

J Chromatogr A. 2015 Sep 18;1412:43-51. doi: 10.1016/j.chroma.2015.07.108. Epub 2015 Aug 3.

31.

Chromatographic behavior of peptides containing oxidized methionine residues in proteomic LC-MS experiments: Complex tale of a simple modification.

Lao YW, Gungormusler-Yilmaz M, Shuvo S, Verbeke T, Spicer V, Krokhin OV.

J Proteomics. 2015 Jul 1;125:131-9. doi: 10.1016/j.jprot.2015.05.018. Epub 2015 May 27.

PMID:
26025879
32.

Effects of impurities in biodiesel-derived glycerol on growth and expression of heavy metal ion homeostasis genes and gene products in Pseudomonas putida LS46.

Fu J, Sharma P, Spicer V, Krokhin OV, Zhang X, Fristensky B, Wilkins JA, Cicek N, Sparling R, Levin DB.

Appl Microbiol Biotechnol. 2015 Jul;99(13):5583-92. doi: 10.1007/s00253-015-6685-z. Epub 2015 May 23.

PMID:
26002633
33.

Quantitative proteomic analysis of the cellulolytic system of Clostridium termitidis CT1112 reveals distinct protein expression profiles upon growth on α-cellulose and cellobiose.

Munir RI, Spicer V, Shamshurin D, Krokhin OV, Wilkins J, Ramachandran U, Sparling R, Levin DB.

J Proteomics. 2015 Jul 1;125:41-53. doi: 10.1016/j.jprot.2015.04.026. Epub 2015 May 7.

PMID:
25957533
34.

Reduced catabolic protein expression in Clostridium butyricum DSM 10702 correlate with reduced 1,3-propanediol synthesis at high glycerol loading.

Gungormusler-Yilmaz M, Shamshurin D, Grigoryan M, Taillefer M, Spicer V, Krokhin OV, Sparling R, Levin DB.

AMB Express. 2014 Aug 30;4:63. doi: 10.1186/s13568-014-0063-6. eCollection 2014.

35.

N-capping motifs promote interaction of amphipathic helical peptides with hydrophobic surfaces and drastically alter hydrophobicity values of individual amino acids.

Spicer V, Lao YW, Shamshurin D, Ezzati P, Wilkins JA, Krokhin OV.

Anal Chem. 2014 Dec 2;86(23):11498-502. doi: 10.1021/ac503352h. Epub 2014 Nov 10.

PMID:
25372782
36.

Whole cell, label free protein quantitation with data independent acquisition: quantitation at the MS2 level.

McQueen P, Spicer V, Schellenberg J, Krokhin O, Sparling R, Levin D, Wilkins JA.

Proteomics. 2015 Jan;15(1):16-24. doi: 10.1002/pmic.201400188. Epub 2014 Dec 10.

PMID:
25348682
37.

Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca.

Vanee N, Brooks JP, Spicer V, Shamshurin D, Krokhin O, Wilkins JA, Deng Y, Fong SS.

BMC Syst Biol. 2014 Aug 13;8:86. doi: 10.1186/s12918-014-0086-2.

38.

Enhanced whole genome sequence and annotation of Clostridium stercorarium DSM8532T using RNA-seq transcriptomics and high-throughput proteomics.

Schellenberg JJ, Verbeke TJ, McQueen P, Krokhin OV, Zhang X, Alvare G, Fristensky B, Thallinger GG, Henrissat B, Wilkins JA, Levin DB, Sparling R.

BMC Genomics. 2014 Jul 7;15:567. doi: 10.1186/1471-2164-15-567.

39.

Mass spectrometry analysis of gingival crevicular fluid in the presence of external root resorption.

Rody WJ Jr, Holliday LS, McHugh KP, Wallet SM, Spicer V, Krokhin O.

Am J Orthod Dentofacial Orthop. 2014 Jun;145(6):787-98. doi: 10.1016/j.ajodo.2014.03.013.

PMID:
24880850
40.

Insights into electron flux through manipulation of fermentation conditions and assessment of protein expression profiles in Clostridium thermocellum.

Rydzak T, Grigoryan M, Cunningham ZJ, Krokhin OV, Ezzati P, Cicek N, Levin DB, Wilkins JA, Sparling R.

Appl Microbiol Biotechnol. 2014;98(14):6497-510. doi: 10.1007/s00253-014-5798-0. Epub 2014 May 20.

PMID:
24841118
41.

Characterization and complete separation of major cyclolinopeptides in flaxseed oil by reversed-phase chromatography.

Lao YW, Mackenzie K, Vincent W, Krokhin OV.

J Sep Sci. 2014 Jul;37(14):1788-96. doi: 10.1002/jssc.201400193.

PMID:
24788784
42.

Thermoanaerobacter thermohydrosulfuricus WC1 shows protein complement stability during fermentation of key lignocellulose-derived substrates.

Verbeke TJ, Spicer V, Krokhin OV, Zhang X, Schellenberg JJ, Fristensky B, Wilkins JA, Levin DB, Sparling R.

Appl Environ Microbiol. 2014 Mar;80(5):1602-15. doi: 10.1128/AEM.03555-13. Epub 2013 Dec 20.

43.

Proteomic characterization of serine hydrolase activity and composition in normal urine.

Navarrete M, Ho J, Krokhin O, Ezzati P, Rigatto C, Reslerova M, Rush DN, Nickerson P, Wilkins JA.

Clin Proteomics. 2013 Nov 15;10(1):17. doi: 10.1186/1559-0275-10-17.

44.

Unifying expression scale for peptide hydrophobicity in proteomic reversed phase high-pressure liquid chromatography experiments.

Grigoryan M, Shamshurin D, Spicer V, Krokhin OV.

Anal Chem. 2013 Nov 19;85(22):10878-86. doi: 10.1021/ac402310t. Epub 2013 Nov 1.

PMID:
24127634
45.

Genomic evaluation of Thermoanaerobacter spp. for the construction of designer co-cultures to improve lignocellulosic biofuel production.

Verbeke TJ, Zhang X, Henrissat B, Spicer V, Rydzak T, Krokhin OV, Fristensky B, Levin DB, Sparling R.

PLoS One. 2013;8(3):e59362. doi: 10.1371/journal.pone.0059362. Epub 2013 Mar 26.

46.

The effect of various S-alkylating agents on the chromatographic behavior of cysteine-containing peptides in reversed-phase chromatography.

Jiang X, Shamshurin D, Spicer V, Krokhin OV.

J Chromatogr B Analyt Technol Biomed Life Sci. 2013 Feb 1;915-916:57-63. doi: 10.1016/j.jchromb.2012.12.010. Epub 2012 Dec 22.

PMID:
23333779
47.

Quantification of the host response proteome after mammalian reovirus T1L infection.

Berard AR, Cortens JP, Krokhin O, Wilkins JA, Severini A, Coombs KM.

PLoS One. 2012;7(12):e51939. doi: 10.1371/journal.pone.0051939. Epub 2012 Dec 11.

48.

Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression.

Rydzak T, McQueen PD, Krokhin OV, Spicer V, Ezzati P, Dwivedi RC, Shamshurin D, Levin DB, Wilkins JA, Sparling R.

BMC Microbiol. 2012 Sep 21;12:214. doi: 10.1186/1471-2180-12-214.

49.

Application of modern reversed-phase peptide retention prediction algorithms to the Houghten and DeGraw dataset: peptide helicity and its effect on prediction accuracy.

Reimer J, Spicer V, Krokhin OV.

J Chromatogr A. 2012 Sep 21;1256:160-8. doi: 10.1016/j.chroma.2012.07.092. Epub 2012 Aug 6.

PMID:
22897865
50.

Information-dependent LC-MS/MS acquisition with exclusion lists potentially generated on-the-fly: case study using a whole cell digest of Clostridium thermocellum.

McQueen P, Spicer V, Rydzak T, Sparling R, Levin D, Wilkins JA, Krokhin O.

Proteomics. 2012 Apr;12(8):1160-9. doi: 10.1002/pmic.201100425.

PMID:
22577018

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