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The metabolomics quality assurance and quality control consortium (mQACC) evolved from the recognized need for a community-wide consensus on improving and systematizing quality assurance (QA) and quality control (QC) practices for untargeted metabolomics. In this work, we sought to identify and share the common and divergent QA and QC practices amongst mQACC members and collaborators who use liquid chromatography-mass spectrometry (LC-MS) in untargeted metabolomics. All authors voluntarily participated in this collaborative research project by providing the details of and insights into the QA and QC practices used in their laboratories. This sharing was enabled via a six-page questionnaire composed of over 120 questions and comment fields which was developed as part of this work and has proved the basis for ongoing mQACC outreach. For QA, many laboratories reported documenting maintenance, calibration and tuning (82%); having established data storage and archival processes (71%); depositing data in public repositories (55%); having standard operating procedures (SOPs) in place for all laboratory processes (68%) and training staff on laboratory processes (55%). For QC, universal practices included using system suitability procedures (100%) and using a robust system of identification (Metabolomics Standards Initiative level 1 identification standards) for at least some of the detected compounds. Most laboratories used QC samples (>86%); used internal standards (91%); used a designated analytical acquisition template with randomized experimental samples (91%); and manually reviewed peak integration following data acquisition (86%). A minority of laboratories included technical replicates of experimental samples in their workflows (36%). Although the 23 contributors were researchers with diverse and international backgrounds from academia, industry and government, they are not necessarily representative of the worldwide pool of practitioners due to the recruitment method for participants and its voluntary nature. However, both questionnaire and the findings presented here have already informed and led other data gathering efforts by mQACC at conferences and other outreach activities and will continue to evolve in order to guide discussions for recommendations of best practices within the community and to establish internationally agreed upon reporting standards. We very much welcome further feedback from readers of this article.
Anne M. Evans; Claire O’Donovan; Mary Playdon; Chris Beecher; Richard D. Beger; John A. Bowden; David Broadhurst; Clary B. Clish; Surendra Dasari; Warwick B. Dunn; Julian L. Griffin; Thomas Hartung; Ping- Ching Hsu; Tao Huan; Judith Jans; Christina M. Jones; Maureen Kachman; Andre Kleensang; Matthew R. Lewis; María Eugenia Monge; Jonathan D. Mosley; Eric Taylor; Fariba Tayyari; Georgios Theodoridis; Federico Torta; Baljit K. Ubhi; Dajana Vuckovic. Dissemination and analysis of the quality assurance (QA) and quality control (QC) practices of LC–MS based untargeted metabolomics practitioners. Metabolomics 2020, 16, 113 .
AMA StyleAnne M. Evans, Claire O’Donovan, Mary Playdon, Chris Beecher, Richard D. Beger, John A. Bowden, David Broadhurst, Clary B. Clish, Surendra Dasari, Warwick B. Dunn, Julian L. Griffin, Thomas Hartung, Ping- Ching Hsu, Tao Huan, Judith Jans, Christina M. Jones, Maureen Kachman, Andre Kleensang, Matthew R. Lewis, María Eugenia Monge, Jonathan D. Mosley, Eric Taylor, Fariba Tayyari, Georgios Theodoridis, Federico Torta, Baljit K. Ubhi, Dajana Vuckovic. Dissemination and analysis of the quality assurance (QA) and quality control (QC) practices of LC–MS based untargeted metabolomics practitioners. Metabolomics. 2020; 16 (10):113.
Chicago/Turabian StyleAnne M. Evans; Claire O’Donovan; Mary Playdon; Chris Beecher; Richard D. Beger; John A. Bowden; David Broadhurst; Clary B. Clish; Surendra Dasari; Warwick B. Dunn; Julian L. Griffin; Thomas Hartung; Ping- Ching Hsu; Tao Huan; Judith Jans; Christina M. Jones; Maureen Kachman; Andre Kleensang; Matthew R. Lewis; María Eugenia Monge; Jonathan D. Mosley; Eric Taylor; Fariba Tayyari; Georgios Theodoridis; Federico Torta; Baljit K. Ubhi; Dajana Vuckovic. 2020. "Dissemination and analysis of the quality assurance (QA) and quality control (QC) practices of LC–MS based untargeted metabolomics practitioners." Metabolomics 16, no. 10: 113.
The ratio between reduced and oxidized thiols, mainly glutathione and oxidized glutathione, is one of the biomarkers for the evaluation of oxidative stress. The accurate measurement of thiol concentrations is challenging because reduced thiols are easily oxidized during sample manipulation. Derivatization is commonly used to protect thiols from oxidation. The objective of this work was to systematically compare two cell-permeable derivatizing agents: N-ethyl maleimide (NEM) and (R)-(+)-N-(1-phenylethyl)maleimide (NPEM) in terms of derivatization efficiency, ionization enhancement, side product formation, reaction selectivity for thiols, pH dependence of the reaction, and derivative stability. All thiol measurements and the characterization of side products were performed using a biphenyl reversed phase liquid chromatography–high-resolution mass spectrometry (LC-HRMS). Four thiols, cysteine (CYS), homocysteine, N-acetylcysteine (NAC), and glutathione (GSH), were used for the evaluation. Using 1:10 ratio of thiol:derivatizing agent, complete derivatization was obtained within 30 min for both agents tested with the exception of CYS-NEM, where 97% efficiency was obtained. The more hydrophobic NPEM provided better ionization of the thiols, with enhancement ranging from 2.1x for GSH to 5.7x for CYS in comparison to NEM. NPEM derivatization led to more extensive side reactions, such as double derivatization and ring opening, which hindered the accurate measurement of the thiol concentrations. Both NEM and NPEM also showed poor stability of CYS derivative due to its time-dependent conversion to cyclic cysteine-maleimide derivative. Both reagents also showed significant reactivity with amine-containing metabolites depending on the pH used during derivatization, but overall NEM was found to be more selective towards thiol group than NPEM. Taking into account all evaluation criteria, NEM was selected as a more suitable reagent for the thiol protection and derivatization, but strict control of pH 7.0 is recommended to minimize the side reactions. This work illustrates the importance of the characterization of side products and derivative stability during the evaluation of thiol derivatizing agents and contributes fundamental understanding to improve the accuracy of thiol determinations. The key sources of errors during maleimide derivatization include the derivatization of amine-containing metabolites, poor derivative stability of certain thiols (CYS and NAC), and the side reactions especially if ring opening of the reagent is not minimized.
Mariana S. T. Russo; Alexander Napylov; Alexandra Paquet; Dajana Vuckovic. Comparison of N-ethyl maleimide and N-(1-phenylethyl) maleimide for derivatization of biological thiols using liquid chromatography-mass spectrometry. Analytical and Bioanalytical Chemistry 2020, 412, 1639 -1652.
AMA StyleMariana S. T. Russo, Alexander Napylov, Alexandra Paquet, Dajana Vuckovic. Comparison of N-ethyl maleimide and N-(1-phenylethyl) maleimide for derivatization of biological thiols using liquid chromatography-mass spectrometry. Analytical and Bioanalytical Chemistry. 2020; 412 (7):1639-1652.
Chicago/Turabian StyleMariana S. T. Russo; Alexander Napylov; Alexandra Paquet; Dajana Vuckovic. 2020. "Comparison of N-ethyl maleimide and N-(1-phenylethyl) maleimide for derivatization of biological thiols using liquid chromatography-mass spectrometry." Analytical and Bioanalytical Chemistry 412, no. 7: 1639-1652.
To increase metabolome coverage in global LC-MS metabolomics, often both reversed-phase liquid chromatography (RPLC) and hydrophilic-interaction liquid chromatography (HILIC) are implemented in parallel. However, there is a lack of consensus in the literature on the best HILIC stationary phase to employ for global metabolomics of human biological fluids. The objective of this study was to compare in detail the performance of two commonly employed HILIC phases: zwitterionic sulfobetaine ZIC-HILIC stationary phase and an underivatized silica HILIC stationary phase. During method development, the effect of salt concentration in the mobile phase was also investigated, and 5 mM ammonium acetate was selected. The stationary phases were evaluated using a mixture of 37 polar standards covering a range of logP values (-10 to 3.73), molecular weights (59-776 Da), charges (15 anions, 11 cations, and 11 neutral) as well as 17 lipid standards to understand phospholipid behaviour on the two stationary phases. The criteria used for the comparison included the quality of the chromatographic peak shape, adequate analyte retention, peak separation capability, and metabolite coverage. The zwitterionic ZIC-HILIC column provided better chromatographic performance over the silica stationary phase with 14 standards achieving good quality peaks compared to the 7 with the silica column. Only 2 standards were undetected with the ZIC-HILIC column compared to the 14 undetected with the silica column. In human plasma, 1966 and 1650 metabolites were observed on the ZIC-HILIC column in positive and negative electrospray ionization (ESI) respectively. On the silica HILIC column, 1773 and 2028 metabolites were observed in positive and negative ESI respectively, showing comparable performance of the two phases. Next, the effect of adding 10 mM ammonium phosphate to the samples to improve the analyte peak shape and metabolite coverage was investigated for both ZIC-HILIC and silica HILIC. In contrast with recently reported results for pZIC-HILIC, there was no clear evidence that ammonium phosphate addition was beneficial for human plasma samples. In conclusion, ZIC-HILIC provided better chromatographic performance for polar plasma metabolomics than underivatized silica in terms of chromatographic peak shape and chromatographic resolution, while maintaining comparable metabolite coverage. The addition of ammonium phosphate to human plasma was not beneficial for either of the two stationary phases.
Rosalynde Ann Sonnenberg; Shama Naz; Lise Cougnaud; Dajana Vuckovic. Comparison of underivatized silica and zwitterionic sulfobetaine hydrophilic interaction liquid chromatography stationary phases for global metabolomics of human plasma. Journal of Chromatography A 2019, 1608, 460419 .
AMA StyleRosalynde Ann Sonnenberg, Shama Naz, Lise Cougnaud, Dajana Vuckovic. Comparison of underivatized silica and zwitterionic sulfobetaine hydrophilic interaction liquid chromatography stationary phases for global metabolomics of human plasma. Journal of Chromatography A. 2019; 1608 ():460419.
Chicago/Turabian StyleRosalynde Ann Sonnenberg; Shama Naz; Lise Cougnaud; Dajana Vuckovic. 2019. "Comparison of underivatized silica and zwitterionic sulfobetaine hydrophilic interaction liquid chromatography stationary phases for global metabolomics of human plasma." Journal of Chromatography A 1608, no. : 460419.
Oxylipins are key lipid mediators of important brain processes, including pain, sleep, oxidative stress and inflammation. For the first‐time, an in‐depth profile of up to 52 oxylipins can be obtained from the brains of awake moving animals using in vivo solid‐phase microextraction (SPME) chemical biopsy tool in combination with liquid chromatography – high resolution mass spectrometry. Among these, 23 oxylipins are detectable in the majority of healthy wildtype samples. This new approach successfully eliminates the changes in oxylipin concentrations routinely observed during the analysis of post‐mortem samples, allows time‐course monitoring of their concentrations with high spatial resolution in specific brain regions of interest and can be performed using the same experimental set‐up as in vivo microdialysis (MD) thus providing a new and exciting tool in neuroscience and drug discovery.
Alexander Napylov; Nathaly Reyes‐Garces; German Gomez‐Rios; Mariola Olkowicz; Sofia Lendor; Cian Monnin; Barbara Bojko; Clement Hamani; Janusz Pawliszyn; Dajana Vuckovic. In Vivo Solid‐Phase Microextraction for Sampling of Oxylipins in Brain of Awake, Moving Rats. Angewandte Chemie International Edition 2019, 59, 2392 -2398.
AMA StyleAlexander Napylov, Nathaly Reyes‐Garces, German Gomez‐Rios, Mariola Olkowicz, Sofia Lendor, Cian Monnin, Barbara Bojko, Clement Hamani, Janusz Pawliszyn, Dajana Vuckovic. In Vivo Solid‐Phase Microextraction for Sampling of Oxylipins in Brain of Awake, Moving Rats. Angewandte Chemie International Edition. 2019; 59 (6):2392-2398.
Chicago/Turabian StyleAlexander Napylov; Nathaly Reyes‐Garces; German Gomez‐Rios; Mariola Olkowicz; Sofia Lendor; Cian Monnin; Barbara Bojko; Clement Hamani; Janusz Pawliszyn; Dajana Vuckovic. 2019. "In Vivo Solid‐Phase Microextraction for Sampling of Oxylipins in Brain of Awake, Moving Rats." Angewandte Chemie International Edition 59, no. 6: 2392-2398.
Oxylipins are key lipid mediators of important brain processes, including pain, sleep, oxidative stress and inflammation. For the first‐time, an in‐depth profile of up to 52 oxylipins can be obtained from the brains of awake moving animals using in vivo solid‐phase microextraction (SPME) chemical biopsy tool in combination with liquid chromatography – high resolution mass spectrometry. Among these, 23 oxylipins are detectable in the majority of healthy wildtype samples. This new approach successfully eliminates the changes in oxylipin concentrations routinely observed during the analysis of post‐mortem samples, allows time‐course monitoring of their concentrations with high spatial resolution in specific brain regions of interest and can be performed using the same experimental set‐up as in vivo microdialysis (MD) thus providing a new and exciting tool in neuroscience and drug discovery.
Alexander Napylov; Nathaly Reyes Garces; German Gomez-Rios; Mariola Olkowicz; Sofia Lendor; Cian Monnin; Barbara Bojko; Clement Hamani; Janusz Pawliszyn; Dajana Vuckovic. In Vivo Solid‐Phase Microextraction for Sampling of Oxylipins in Brain of Awake, Moving Rats. Angewandte Chemie 2019, 132, 2413 -2419.
AMA StyleAlexander Napylov, Nathaly Reyes Garces, German Gomez-Rios, Mariola Olkowicz, Sofia Lendor, Cian Monnin, Barbara Bojko, Clement Hamani, Janusz Pawliszyn, Dajana Vuckovic. In Vivo Solid‐Phase Microextraction for Sampling of Oxylipins in Brain of Awake, Moving Rats. Angewandte Chemie. 2019; 132 (6):2413-2419.
Chicago/Turabian StyleAlexander Napylov; Nathaly Reyes Garces; German Gomez-Rios; Mariola Olkowicz; Sofia Lendor; Cian Monnin; Barbara Bojko; Clement Hamani; Janusz Pawliszyn; Dajana Vuckovic. 2019. "In Vivo Solid‐Phase Microextraction for Sampling of Oxylipins in Brain of Awake, Moving Rats." Angewandte Chemie 132, no. 6: 2413-2419.
Background and Purpose The 5‐lipoxygenase product 5‐oxo‐6,8,11,14‐eicosatetraenoic acid (5‐oxo‐ETE), acting through the OXE receptor, is a potent eosinophil chemoattractant that may be an important proinflammatory mediator in eosinophilic diseases such as asthma. We previously identified a series of indole‐based OXE receptor antagonists that rapidly appear in the blood following oral administration but have limited lifetimes. The objective of this study was to increase the potency and plasma half‐lives of these compounds and thereby identify the optimal candidate for future preclinical studies in monkeys, since rodents do not have an OXE receptor ortholog. Experimental Approach We synthesized a series of substituted phenylalkyl indoles and compared their antagonist potencies, pharmacokinetics, and metabolism to those of our earlier compounds. The potencies of some of their metabolites were also investigated. Key Results Among the compounds tested, the S‐enantiomer of the m‐chlorophenyl compound (S‐Y048) was the most potent, with an pIC50 of about 10.8 for inhibition of 5‐oxo‐ETE‐induced calcium mobilization in human neutrophils. When administered orally to cynomolgus monkeys, S‐Y048 rapidly appeared in the blood and had a half‐life in plasma of over 7 h, considerably longer than any of the other OXE analogs tested. A major hydroxylated metabolite, with a potency close to that of its precursor, was identified in plasma. Conclusion and Implications Because of its highly potent antagonist activity and its long lifetime in vivo, S‐Y048 may be a useful anti‐inflammatory agent for the treatment of eosinophilic diseases such as asthma, allergic rhinitis, and atopic dermatitis.
Qiuji Ye; Shishir Chourey; Chintam Nagendra Reddy; Rui Wang; Chantal Cossette; Sylvie Gravel; Irina Slobodchikova; Dajana Vuckovic; Joshua Rokach; William S. Powell. Novel highly potent OXE receptor antagonists with prolonged plasma lifetimes that are converted to active metabolites in vivo in monkeys. Journal of Cerebral Blood Flow & Metabolism 2019, 177, 388 -401.
AMA StyleQiuji Ye, Shishir Chourey, Chintam Nagendra Reddy, Rui Wang, Chantal Cossette, Sylvie Gravel, Irina Slobodchikova, Dajana Vuckovic, Joshua Rokach, William S. Powell. Novel highly potent OXE receptor antagonists with prolonged plasma lifetimes that are converted to active metabolites in vivo in monkeys. Journal of Cerebral Blood Flow & Metabolism. 2019; 177 (2):388-401.
Chicago/Turabian StyleQiuji Ye; Shishir Chourey; Chintam Nagendra Reddy; Rui Wang; Chantal Cossette; Sylvie Gravel; Irina Slobodchikova; Dajana Vuckovic; Joshua Rokach; William S. Powell. 2019. "Novel highly potent OXE receptor antagonists with prolonged plasma lifetimes that are converted to active metabolites in vivo in monkeys." Journal of Cerebral Blood Flow & Metabolism 177, no. 2: 388-401.
Routine mycotoxin biomonitoring methods do not include many mycotoxin phase I and phase II metabolites, which may significantly underestimate mycotoxin exposure especially for heavily metabolized mycotoxins. Additional research efforts are also needed to measure metabolites in vivo after exposure and to establish which mycotoxin metabolites should be prioritized for the inclusion during large-scale biomonitoring efforts. The objective of this study was to perform human in vitro microsomal incubations of 17 mycotoxins and systematically characterize all resulting metabolites using liquid chromatography-high-resolution mass spectrometry (LC-HRMS). The results obtained were then used to build a comprehensive LC-MS library and expand a validated 17-mycotoxin method for exposure monitoring to screening of additional 188 metabolites, including 100 metabolites reported for the first time. The final method represents one of the most comprehensive LC-HRMS methods for mycotoxin biomonitoring or metabolism/fate studies.
Irina Slobodchikova; Reajean Sivakumar; Samiur Rahman; Dajana Vuckovic. Characterization of Phase I and Glucuronide Phase II Metabolites of 17 Mycotoxins Using Liquid Chromatography-High-Resolution Mass Spectrometry. Toxins 2019, 11, 433 .
AMA StyleIrina Slobodchikova, Reajean Sivakumar, Samiur Rahman, Dajana Vuckovic. Characterization of Phase I and Glucuronide Phase II Metabolites of 17 Mycotoxins Using Liquid Chromatography-High-Resolution Mass Spectrometry. Toxins. 2019; 11 (8):433.
Chicago/Turabian StyleIrina Slobodchikova; Reajean Sivakumar; Samiur Rahman; Dajana Vuckovic. 2019. "Characterization of Phase I and Glucuronide Phase II Metabolites of 17 Mycotoxins Using Liquid Chromatography-High-Resolution Mass Spectrometry." Toxins 11, no. 8: 433.
5-Oxo-6,8,11,14-eicosatetraenoic acid (5-oxo-ETE) is a potent lipid mediator that induces tissue eosinophilia via the selective OXE receptor (OXE-R), which is an attractive therapeutic target in eosinophilic diseases. We previously identified indole OXE-R antagonists that block 5-oxo-ETE-induced primate eosinophil activation. Although these compounds possess good oral absorption, their plasma levels decline rapidly due to extensive oxidation of their hexyl side chain. We have now succeeded in dramatically increasing antagonist potency and resistance to metabolism by replacing the hexyl group with phenylpentyl or phenylhexyl side chains. Compared with our previous lead compound S-230, our most potent antagonist, S-C025, has an IC50 (120 pM) over 80 times lower and a substantially longer plasma half-life. A single major metabolite, which retains antagonist activity (IC50, 690 pM) and has a prolonged lifetime in plasma was observed. These new highly potent OXE-R antagonists may provide a novel strategy for the treatment of eosinophilic disorders like asthma.
Shishir Chourey; Qiuji Ye; Chintam Nagendra Reddy; Rui Wang; Chantal Cossette; Sylvie Gravel; Irina Slobodchikova; Dajana Vuckovic; Joshua Rokach; William S. Powell. Novel Highly Potent and Metabolically Resistant Oxoeicosanoid (OXE) Receptor Antagonists That Block the Actions of the Granulocyte Chemoattractant 5-Oxo-6,8,11,14-Eicosatetraenoic Acid (5-oxo-ETE). Journal of Medicinal Chemistry 2018, 61, 5934 -5948.
AMA StyleShishir Chourey, Qiuji Ye, Chintam Nagendra Reddy, Rui Wang, Chantal Cossette, Sylvie Gravel, Irina Slobodchikova, Dajana Vuckovic, Joshua Rokach, William S. Powell. Novel Highly Potent and Metabolically Resistant Oxoeicosanoid (OXE) Receptor Antagonists That Block the Actions of the Granulocyte Chemoattractant 5-Oxo-6,8,11,14-Eicosatetraenoic Acid (5-oxo-ETE). Journal of Medicinal Chemistry. 2018; 61 (14):5934-5948.
Chicago/Turabian StyleShishir Chourey; Qiuji Ye; Chintam Nagendra Reddy; Rui Wang; Chantal Cossette; Sylvie Gravel; Irina Slobodchikova; Dajana Vuckovic; Joshua Rokach; William S. Powell. 2018. "Novel Highly Potent and Metabolically Resistant Oxoeicosanoid (OXE) Receptor Antagonists That Block the Actions of the Granulocyte Chemoattractant 5-Oxo-6,8,11,14-Eicosatetraenoic Acid (5-oxo-ETE)." Journal of Medicinal Chemistry 61, no. 14: 5934-5948.
Separation and analytical sciences can help to advance metabolomics by improving metabolite coverage, accuracy of quantitation and data quality.
Dajana Vuckovic. Improving metabolome coverage and data quality: advancing metabolomics and lipidomics for biomarker discovery. Chemical Communications 2018, 54, 6728 -6749.
AMA StyleDajana Vuckovic. Improving metabolome coverage and data quality: advancing metabolomics and lipidomics for biomarker discovery. Chemical Communications. 2018; 54 (50):6728-6749.
Chicago/Turabian StyleDajana Vuckovic. 2018. "Improving metabolome coverage and data quality: advancing metabolomics and lipidomics for biomarker discovery." Chemical Communications 54, no. 50: 6728-6749.
Mycotoxins are secondary metabolites produced by filamentous fungi. Primary route of human exposure to mycotoxins is the intake of the contaminated food. Minimizing mycotoxin exposure is important for population health, as their chronic toxic effects have been associated with kidney and liver diseases, some types of cancer and immunosuppression. The objective of this work was to develop and validate a multi-class mycotoxin method suitable for exposure monitoring of mycotoxins in human plasma. A sensitive liquid chromatography – mass spectrometry method was developed for 17 mycotoxins: nivalenol (NIV), deoxynivalenol, fusarenon X, 3-acetyldeoxynivalenol, 15-acetyldeoxynivalenol, T-2 toxin, HT-2 toxin, aflatoxin B1, aflatoxin B2, aflatoxin G1, aflatoxin G2, zearalenone, α-zearalenol (α-ZOL), β-zearalenol, zearalanone, α-zeranoland, and β-zeranol. The method relies on three-step liquid-liquid extraction with ethyl acetate to eliminate the need for immunoaffinity extraction and minimize ionization matrix effects. Chromatographic separation of mycotoxins, including all isomers, was achieved with pentafluorophenyl column and water/methanol mobile phase. Mycotoxin detection and quantitation were performed using high-resolution mass spectrometry on LTQ Velos Orbitrap, in both positive and negative electrospray ionization (ESI(+) and (ESI(−)). The use of 0.02% acetic acid as mobile phase additive for ESI(−) resulted in significant increase in ionization efficiency ranging from 1.7 to 26 times for mycotoxins that ionize better in ESI(−). The optimized method was validated according to FDA guidance procedures. LOQs of all mycotoxins ranged from 0.1 to 0.5 ng/ml, except NIV which resulted in LOQ of 3 ng/ml because of low extraction recovery of this highly polar mycotoxin. Mean intra-day accuracy ranged from 85.8% to 116.4%, and intra-day precision (n = 6) ranged from 1.6% to 12.5% RSD for all mycotoxins except α-ZOL where mean accuracy ranged from 72.9% to 97.2%. Inter-day accuracy and precision were 85.6% to 111.5% and 2.7 to 15.6% RSD respectively, showing good analytical performance of the method for biomonitoring.
Irina Slobodchikova; Dajana Vuckovic. Liquid chromatography – high resolution mass spectrometry method for monitoring of 17 mycotoxins in human plasma for exposure studies. Journal of Chromatography A 2018, 1548, 51 -63.
AMA StyleIrina Slobodchikova, Dajana Vuckovic. Liquid chromatography – high resolution mass spectrometry method for monitoring of 17 mycotoxins in human plasma for exposure studies. Journal of Chromatography A. 2018; 1548 ():51-63.
Chicago/Turabian StyleIrina Slobodchikova; Dajana Vuckovic. 2018. "Liquid chromatography – high resolution mass spectrometry method for monitoring of 17 mycotoxins in human plasma for exposure studies." Journal of Chromatography A 1548, no. : 51-63.
Dajana Vuckovic. Bioanalytical techniques in lipidomics. Bioanalysis 2018, 10, 273 -274.
AMA StyleDajana Vuckovic. Bioanalytical techniques in lipidomics. Bioanalysis. 2018; 10 (5):273-274.
Chicago/Turabian StyleDajana Vuckovic. 2018. "Bioanalytical techniques in lipidomics." Bioanalysis 10, no. 5: 273-274.
Mobile phase additives in LC-MS are used to improve peak shape, analyte ionization efficiency and method coverage. Both basic and acidic mobile phases have been used successfully for negative ESI, but very few systematic investigations exist to date to justify the choice of mobile phase. Acetic acid was previously shown to improve ionization in untargeted metabolomics of urine, but has not been investigated in lipidomics. The goal of this study was to systematically compare the performance of acetic acid to other commonly employed additives in negative ESI-LC-MS lipidomics. The performance of acetic acid was compared to commonly utilized mobile phase additives in lipidomics: ammonium acetate, ammonium acetate with acetic acid and ammonium hydroxide using lipid standard solutions containing representatives of major mammalian lipid subclasses and isopropanol-precipitated human plasma. This design allowed comparison of the influence of additive and additive concentration on lipid signal intensity, lipid peak shape and lipid coverage in both simple and complex biological matrices using both Orbitrap and quadrupole-time-of-flight MS platforms with different ESI source designs. Ammonium hydroxide caused 2- to 1000-fold signal suppression of all lipid classes in comparison to acetic acid. In comparison to ammonium acetate, acetic acid increased lipid signal intensity from 2 to 19-fold for 11 lipid subclasses, and decreased ionization efficiency only for ceramide and phosphatidylcholine lipid classes which can be effectively ionized in positive ESI mode. The improved ionization efficiency using acetic acid also increased lipid coverage by 21-50% versus ammonium acetate additive. Acetic acid at a concentration 0.02% (v/v) is the suggested choice as a mobile phase additive for lipidomics and targeted lipid profiling with negative ESI-LC-MS based on signal enhancement and improved lipid coverage compared to ammonium acetate, ammonium acetate with acetic acid, and ammonium hydroxide mobile phases.
Cian Monnin; Parsram Ramrup; Carolann Daigle-Young; Dajana Vuckovic. Improving negative liquid chromatography/electrospray ionization mass spectrometry lipidomic analysis of human plasma using acetic acid as a mobile-phase additive. Rapid Communications in Mass Spectrometry 2018, 32, 201 -211.
AMA StyleCian Monnin, Parsram Ramrup, Carolann Daigle-Young, Dajana Vuckovic. Improving negative liquid chromatography/electrospray ionization mass spectrometry lipidomic analysis of human plasma using acetic acid as a mobile-phase additive. Rapid Communications in Mass Spectrometry. 2018; 32 (3):201-211.
Chicago/Turabian StyleCian Monnin; Parsram Ramrup; Carolann Daigle-Young; Dajana Vuckovic. 2018. "Improving negative liquid chromatography/electrospray ionization mass spectrometry lipidomic analysis of human plasma using acetic acid as a mobile-phase additive." Rapid Communications in Mass Spectrometry 32, no. 3: 201-211.
We have developed a selective indole antagonist (230) targeting the OXE receptor for the potent eosinophil chemoattractant 5-oxo-ETE (5-oxo-6,8,11,14-eicosatetraenoic acid), that may be useful for the treatment of eosinophilic diseases such as asthma. In previous studies we identified ω2-oxidation of the hexyl side chain of racemic 230 as a major metabolic route in monkeys, but also obtained evidence for another pathway that appeared to involve hydroxylation of the hexyl side chain close to the indole. The present study was designed to investigate the metabolism of the active S-enantiomer of 230 (S230) and to identify the novel hydroxy metabolite and its chirality. Following oral administration, S230 rapidly appeared in the blood along with metabolites formed by a novel and highly stereospecific α-hydroxylation pathway, resulting in the formation of αS-hydroxy-S230. The chirality of α-hydroxy-S230 was determined by the total synthesis of the relevant diastereomers. Of the four possible diastereomers of α-hydroxy-230 only αS-hydroxy-S230 has significant OXE receptor antagonist activity and only this diastereomer was found in significant amounts in blood following oral administration of S230. Other novel metabolites of S230 identified in plasma by LC–MS/MS were αS,ω2-dihydroxy-S230 and glucuronides of S230 and ω2-hydroxy-S230. Thus the alkyl side chain of S230, which is essential for its antagonist activity, is also the major target of the metabolic enzymes that terminate its antagonist activity. Modification of this side chain might result in the development of related antagonists with improved metabolic stability and efficacy.
Shishir Chourey; Qiuji Ye; Chintam Nagendra Reddy; Chantal Cossette; Sylvie Gravel; Matthias Zeller; Irina Slobodchikova; Dajana Vuckovic; Joshua Rokach; William S. Powell. In vivo α-hydroxylation of a 2-alkylindole antagonist of the OXE receptor for the eosinophil chemoattractant 5-oxo-6,8,11,14-eicosatetraenoic acid in monkeys. Biochemical Pharmacology 2017, 138, 107 -118.
AMA StyleShishir Chourey, Qiuji Ye, Chintam Nagendra Reddy, Chantal Cossette, Sylvie Gravel, Matthias Zeller, Irina Slobodchikova, Dajana Vuckovic, Joshua Rokach, William S. Powell. In vivo α-hydroxylation of a 2-alkylindole antagonist of the OXE receptor for the eosinophil chemoattractant 5-oxo-6,8,11,14-eicosatetraenoic acid in monkeys. Biochemical Pharmacology. 2017; 138 ():107-118.
Chicago/Turabian StyleShishir Chourey; Qiuji Ye; Chintam Nagendra Reddy; Chantal Cossette; Sylvie Gravel; Matthias Zeller; Irina Slobodchikova; Dajana Vuckovic; Joshua Rokach; William S. Powell. 2017. "In vivo α-hydroxylation of a 2-alkylindole antagonist of the OXE receptor for the eosinophil chemoattractant 5-oxo-6,8,11,14-eicosatetraenoic acid in monkeys." Biochemical Pharmacology 138, no. : 107-118.
The comparison of extraction methods for global metabolomics is usually executed in biofluids only and focuses on metabolite coverage and method repeatability. This limits our detailed understanding of extraction parameters such as recovery and matrix effects and prevents side-by-side comparison of different sample preparation strategies. To address this gap in knowledge, seven solvent-based and solid-phase extraction methods were systematically evaluated using standard analytes spiked into both buffer and human plasma. We compared recovery, coverage, repeatability, matrix effects, selectivity and orthogonality of all methods tested for non-lipid metabolome in combination with reversed-phased and mixed-mode liquid chromatography mass spectrometry analysis (LC-MS). Our results confirmed wide selectivity and excellent precision of solvent precipitations, but revealed their high susceptibility to matrix effects. The use of all seven methods showed high overlap and redundancy which resulted in metabolite coverage increases of 34–80% depending on LC-MS method employed as compared to the best single extraction protocol (methanol/ethanol precipitation) despite 7x increase in MS analysis time and sample consumption. The most orthogonal methods to methanol-based precipitation were ion-exchange solid-phase extraction and liquid-liquid extraction using methyl-tertbutyl ether. Our results help facilitate rational design and selection of sample preparation methods and internal standards for global metabolomics.
Dmitri G. Sitnikov; Cian Monnin; Dajana Vuckovic. Systematic Assessment of Seven Solvent and Solid-Phase Extraction Methods for Metabolomics Analysis of Human Plasma by LC-MS. Scientific Reports 2016, 6, 38885 .
AMA StyleDmitri G. Sitnikov, Cian Monnin, Dajana Vuckovic. Systematic Assessment of Seven Solvent and Solid-Phase Extraction Methods for Metabolomics Analysis of Human Plasma by LC-MS. Scientific Reports. 2016; 6 (1):38885.
Chicago/Turabian StyleDmitri G. Sitnikov; Cian Monnin; Dajana Vuckovic. 2016. "Systematic Assessment of Seven Solvent and Solid-Phase Extraction Methods for Metabolomics Analysis of Human Plasma by LC-MS." Scientific Reports 6, no. 1: 38885.
This chapter briefly discusses how solid-phase microextraction (SPME) can be successfully implemented to accurately measure ligand–receptor binding constants, % plasma protein binding, blood-to-plasma distribution ratios, and free versus total analyte concentrations. The main practical considerations and assumptions to successfully apply SPME to binding studies are discussed in detail, including the effect of significant versus negligible depletion, extraction time, pH, and fiber fouling. The binding results obtained with SPME are compared to literature values and to other techniques used for binding determinations, and the advantages and disadvantages of different methods are clearly discussed. Recent applications of SPME in binding studies are highlighted, with the primary focus on binding studies in biological fluids and tissues since this application area is where SPME has been most extensively applied. Highlighted examples show that SPME has been successfully applied for ligands with both low and high binding affinities, for ligands with different affinities to multiple sites on a given receptor, to study differences in inter-species binding as well as partitioning coefficients for various tissue types. The importance of studying inter-individual variability of free concentrations in future studies is highlighted and can contribute to the development of personalized medicine.
Dajana Vuckovic. Solid-Phase Microextraction in Binding Studies. Solid Phase Microextraction 2016, 287 -308.
AMA StyleDajana Vuckovic. Solid-Phase Microextraction in Binding Studies. Solid Phase Microextraction. 2016; ():287-308.
Chicago/Turabian StyleDajana Vuckovic. 2016. "Solid-Phase Microextraction in Binding Studies." Solid Phase Microextraction , no. : 287-308.
The potent eosinophil chemoattractant 5-oxo-6,8,11,14-eicosatetraenoic acid (5-oxo-ETE) is a 5-lipoxygenase product that acts via the selective OXE receptor, which is present in many species, but not rodents. We previously reported that the indole 230 is a potent human OXE receptor antagonist. The objective of the present study was to determine whether the monkey would be a suitable animal model to investigate its pharmaceutical potential. We found that monkey leukocytes synthesize and respond to 5-oxo-ETE and that 230 is a potent antagonist of the OXE receptor in monkey eosinophils. Pharmacokinetic studies revealed that 230 appears rapidly in the blood following oral administration. Using chemically synthesized standards, we identified the major microsomal and plasma metabolites of 230 as products of ω2-hydroxylation of the alkyl side chain. These studies demonstrate that the monkey is a promising animal model to investigate the drug potential of OXE receptor antagonists.
Chantal Cossette; Shishir Chourey; Qiuji Ye; Chintam Nagendra Reddy; Vivek Gore; Sylvie Gravel; Irina Slobodchikova; Dajana Vuckovic; Joshu Rokach; William S. Powell. Pharmacokinetics and Metabolism of Selective Oxoeicosanoid (OXE) Receptor Antagonists and Their Effects on 5-Oxo-6,8,11,14-eicosatetraenoic Acid (5-Oxo-ETE)-Induced Granulocyte Activation in Monkeys. Journal of Medicinal Chemistry 2016, 59, 10127 -10146.
AMA StyleChantal Cossette, Shishir Chourey, Qiuji Ye, Chintam Nagendra Reddy, Vivek Gore, Sylvie Gravel, Irina Slobodchikova, Dajana Vuckovic, Joshu Rokach, William S. Powell. Pharmacokinetics and Metabolism of Selective Oxoeicosanoid (OXE) Receptor Antagonists and Their Effects on 5-Oxo-6,8,11,14-eicosatetraenoic Acid (5-Oxo-ETE)-Induced Granulocyte Activation in Monkeys. Journal of Medicinal Chemistry. 2016; 59 (22):10127-10146.
Chicago/Turabian StyleChantal Cossette; Shishir Chourey; Qiuji Ye; Chintam Nagendra Reddy; Vivek Gore; Sylvie Gravel; Irina Slobodchikova; Dajana Vuckovic; Joshu Rokach; William S. Powell. 2016. "Pharmacokinetics and Metabolism of Selective Oxoeicosanoid (OXE) Receptor Antagonists and Their Effects on 5-Oxo-6,8,11,14-eicosatetraenoic Acid (5-Oxo-ETE)-Induced Granulocyte Activation in Monkeys." Journal of Medicinal Chemistry 59, no. 22: 10127-10146.
Puzhen Li; Pascale Chevallier; Parsarm Ramrup; Depannita Biswas; Dajana Vuckovic; Marc-André Fortin; Jung Kwon Oh. Correction to “Mussel-Inspired Multidentate Block Copolymer to Stabilize Ultrasmall Superparamagnetic Fe3O4 for Magnetic Resonance Imaging Contrast Enhancement and Excellent Colloidal Stability”. Chemistry of Materials 2016, 28, 1243 -1243.
AMA StylePuzhen Li, Pascale Chevallier, Parsarm Ramrup, Depannita Biswas, Dajana Vuckovic, Marc-André Fortin, Jung Kwon Oh. Correction to “Mussel-Inspired Multidentate Block Copolymer to Stabilize Ultrasmall Superparamagnetic Fe3O4 for Magnetic Resonance Imaging Contrast Enhancement and Excellent Colloidal Stability”. Chemistry of Materials. 2016; 28 (4):1243-1243.
Chicago/Turabian StylePuzhen Li; Pascale Chevallier; Parsarm Ramrup; Depannita Biswas; Dajana Vuckovic; Marc-André Fortin; Jung Kwon Oh. 2016. "Correction to “Mussel-Inspired Multidentate Block Copolymer to Stabilize Ultrasmall Superparamagnetic Fe3O4 for Magnetic Resonance Imaging Contrast Enhancement and Excellent Colloidal Stability”." Chemistry of Materials 28, no. 4: 1243-1243.
Apoptosis is a hallmark of multiple etiologies of heart failure, including dilated cardiomyopathy. Since microRNAs are master regulators of cardiac development and key effectors of intracellular signaling, they represent novel candidates for understanding the mechanisms driving the increased dysfunction and loss of cardiomyocytes during cardiovascular disease progression. To determine the role of cardiac miRNAs in the apoptotic response, we used microarray technology to monitor miRNA levels in a validated murine phospholambam mutant model of dilated cardiomyopathy. 24 miRNAs were found to be differentially expressed, most of which have not been previously linked to dilated cardiomyopathy. We showed that individual silencing of 7 out of 8 significantly down-regulated miRNAs (mir-1, -29c, -30c, -30d, -149, -486, -499) led to a strong apoptotic phenotype in cell culture, suggesting they repress pro-apoptotic factors. To identify putative miRNA targets most likely relevant to cell death, we computationally integrated transcriptomic, proteomic and functional annotation data. We showed the dependency of prioritized target abundance on miRNA expression using RNA interference and quantitative mass spectrometry. We concluded that down regulation of key pro-survival miRNAs causes up-regulation of apoptotic signaling effectors that contribute to cardiac cell loss, potentially leading to system decompensation and heart failure.
Ruth Isserlin; Daniele Merico; Dingyan Wang; Dajana Vuckovic; Nicolas Bousette; Anthony O. Gramolini; Gary D. Bader; Andrew Emili. Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy. Molecular BioSystems 2014, 11, 239 -51.
AMA StyleRuth Isserlin, Daniele Merico, Dingyan Wang, Dajana Vuckovic, Nicolas Bousette, Anthony O. Gramolini, Gary D. Bader, Andrew Emili. Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy. Molecular BioSystems. 2014; 11 (1):239-51.
Chicago/Turabian StyleRuth Isserlin; Daniele Merico; Dingyan Wang; Dajana Vuckovic; Nicolas Bousette; Anthony O. Gramolini; Gary D. Bader; Andrew Emili. 2014. "Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy." Molecular BioSystems 11, no. 1: 239-51.
This review summarizes different formats of high-throughput, multi-well, solid-phase microextraction (SPME), including fiber, thin-film and in-tip configurations, with the particular focus on its fit within regulated analysis.\ud \ud New developments of the devices, such as monolithic and biocompatible extraction phases, are covered. Finally, selected applications of the technique, including the analysis of whole-blood samples and automated binding studies, are presented
Dajana Vuckovic. High-throughput solid-phase microextraction in multi-well-plate format. TrAC Trends in Analytical Chemistry 2013, 45, 136 -153.
AMA StyleDajana Vuckovic. High-throughput solid-phase microextraction in multi-well-plate format. TrAC Trends in Analytical Chemistry. 2013; 45 ():136-153.
Chicago/Turabian StyleDajana Vuckovic. 2013. "High-throughput solid-phase microextraction in multi-well-plate format." TrAC Trends in Analytical Chemistry 45, no. : 136-153.
Membrane proteins (MPs) play diverse biologically important structural and functional roles including molecular transport, cell communication, and signal transduction. The dysfunctions of many are linked to deleterious human diseases and thus are of utmost importance in drug discovery. MPs comprise approximately 20–30% of all open reading frames (ORFs), however they are typically under‐represented in many LC‐MS proteomics experiments due to their low abundance and poor solubility. To address these analytical challenges, various MP enrichment, solubilization, digestion, and fractionation strategies have been employed to further improve the coverage of the membrane systems while maintaining compatibility with MS detection. This review discusses both established and emerging high‐throughput gel‐free analytical workflows in membrane proteomics, and the inherent advantages, disadvantages, and orthogonality of the various approaches. The issues of critical importance for successful LC‐MS/MS detection such as detergent selection and minimizing ion suppression in detergent‐based workflows are discussed in detail. Recent studies comparing the performance of different analytical strategies are highlighted in order to provide practical insight into the choice of the most appropriate method for membrane‐centric applications ranging from cell surface biomarker discovery to MP interaction network mapping.
Dajana Vuckovic; Laura F. Dagley; Anthony W. Purcell; Andrew Emili. Membrane proteomics by high performance liquid chromatography-tandem mass spectrometry: Analytical approaches and challenges. PROTEOMICS 2013, 13, 404 -423.
AMA StyleDajana Vuckovic, Laura F. Dagley, Anthony W. Purcell, Andrew Emili. Membrane proteomics by high performance liquid chromatography-tandem mass spectrometry: Analytical approaches and challenges. PROTEOMICS. 2013; 13 (3-4):404-423.
Chicago/Turabian StyleDajana Vuckovic; Laura F. Dagley; Anthony W. Purcell; Andrew Emili. 2013. "Membrane proteomics by high performance liquid chromatography-tandem mass spectrometry: Analytical approaches and challenges." PROTEOMICS 13, no. 3-4: 404-423.