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2. Contributors

Author

Bystrom, Cory, primary, Clarke, Nigel J., additional, Grant, Russell P., additional, Hage, David S., additional, Heaton, Phillip, additional, Hoofnagle, Andrew N., additional, Kushnir, Mark M., additional, Patel, Robin, additional, Rappold, Brian A., additional, Rockwood, Alan L., additional, and Wells, David A., additional

Published
2018
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4. Contributors

Author

Best, D. Hunter, primary, Bystrom, Cory, additional, Chiu, Rossa W.K., additional, Dietzen, Dennis J., additional, Gettings, Katherine B., additional, Hoofnagle, Andrew N., additional, Hoon, Dave, additional, Howe, John Greg, additional, Kelley, Todd W., additional, Lianidou, Evi, additional, Lo, Y.M. Dennis, additional, Makrigiorgos, G. Mike, additional, Mardis, Elaine R., additional, McMillin, Gwendolyn A., additional, Nolte, Frederick S., additional, Park, Jason Y., additional, Patel, Jay L., additional, Podini, Daniele S., additional, Pratt, Victoria M., additional, Thatcher, Stephanie A., additional, Vnencak-Jones, Cindy L., additional, Wadelius, Mia, additional, Weedn, Victor W., additional, and Wittwer, Carl T., additional

Published
2018
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6. Textbook Contributors

Author

Aarsand, Aasne K., Abbott, April N., Abraham, Roshini S., Adeli, Khosrow, Alexander, Mariam Priya, Alix-Panabières, Catherine, Alter, David, Anderson, Neil W., Apple, Fred S., Ayling, Ruth M., Babu, Daniel, Badminton, Michael N., Badrick, Tony, Banaei, Niaz, Baudhuin, Linnea M., Bazydlo, Lindsay A.L., Bechtel, Laura K., Benco, John, Bentall, Andrew J., Berg, Marc, Bertholf, Roger L., Best, D. Hunter, Biljak, Vanja Radisic, Block, Darci R., Blum, Lee M., Bodamer, Olaf A., Boh, Benjamin, Bohn, Mary Kathryn, Bossuyt, Patrick M.M., Bossuyt, Xavier, Boyd, James Clark, Braga, Julie A., Buchan, Blake W., Buchbinder, David, Burnett, Leslie, Burnham, Carey-Ann D., Bush, Theresa Ambrose, Bystrom, Cory, Cattaneo, Marco, Caulfield, Adam J., Cervinski, Mark A., Chabot-Richards, Devon S., Chandrakasan, Shanmuganathan, Chen, Derrick J., Chen, Dong, Chiu, Rossa W.K., Clarke, Nigel J., Cole, Timothy J., Cooper, Mark, Crook, Martin, Morena, Maite de la, Delaney, Michael P., Delgado, Julio C., Deresinski, Stanley C., Dietzen, Dennis J., Dinh, Anh P., Doern, Christopher D., Dukić, Lora, Eisenhofer, Graeme, El-Khoury, Joe M., Ellervik, Christina, Florkowski, Christopher M., Fraser, William Duncan, Gandhi, Manish J., Genzen, Jonathan R., George, Tracy I., Glasziou, Paul, Grant, Russell P., Green, Ralph, Hage, David S., Halsall, David John, Hawker, Charles D., Haymond, Shannon, Heaton, Phillip, Higgins, Russell A., Higgins, Victoria, Hilmarsdóttir, Ingibjörg, Hitchcock, Matthew M., Hogan, Catherine A., Holmes, Daniel Thomas, Holstege, Christopher P., Hoofnagle, Andrew N., Horowitz, Gary, Horvath, Andrea R., Howe, John Greg, Humphries, Romney M., Infusino, Ilenia, Jaffe, Allan Stanley, Jones, Graham Ross Dallas, Jones, Patricia M., Julian, Randall K., Jr., Kavsak, Peter A., Kellogg, Mark, Khanolkar, Aaruni, Kidd, Sarah E., Kitchen, Steve, Kreuter, Justin D., Kushnir, Mark M., Lainhart, William D., Lamb, Edmund J., Landers, James P., Langman, Loralie J., Laterza, Omar Fernando, Lau, Anna F., Lázár-Molnár, Eszter, Liesman, Rachael M., Linnet, Kristian, Lo, Stanley F., Lo, Yuk Ming Dennis, Longo, Nicola, Lyon, Elaine, Ma, Edmond S.K., Mackay, Mark, Madkaikar, Manisha, Manis, John P., Mardis, Elaine R., Master, Stephen R., Mathison, Blaine A., McElvania, Erin, McMillin, Gwendolyn Appell, Meeusen, Jeffrey W., Michniacki, Thomas F., Miller, Melissa B., Miller, W. Greg, Milone, Michael C., Mochon, Brian, Moons, Karel G.M., Mostafa, Heba H., Nerenz, Robert D., Nordestgaard, Børge G., Nygaard, Birte, O’Kane, Maurice, Pagano, Monica B., Pamidi, Prasad V.A., Panteghini, Mauro, Pantel, Klaus, Park, Jason Y., Pasquali, Marzia, Patel, Jay L., Patel, Khushbu, Patel, Robin, Peake, Roy W.A., Pence, Morgan A., Perrotta, Peter L., Pillay, Tahir S., Poston, Jacqueline N., Pratt, Victoria M., Pritt, Bobbi S., Procop, Gary W., Rab, Minke A.E., Rao, Lokinendi V., Rappold, Brian A., Rashidi, Hooman H., Remaley, Alan T., Rifai, Nader, Rockwood, Alan L., Røraas, Thomas, Rosenberg, William Malcolm Charles, Sacks, David B., Sandberg, Sverre, Schifman, Ronald, Schmitt, Caroline, Sethi, Amar Akhtar, Shapiro, Howard M., Shaw, Leslie Michael, Sherwood, Roy Alan, Simundic, Ana-Maria, Snyder, Melissa R., So, Jason C.C., Sodi, Ravinder, Strathmann, Frederick G., Sturgeon, Catharine, Swinkels, Dorine W., Taly, Valérie, Tanwar, Sudeep, Tebo, Anne E., TeKippe, Michael, Thatcher, Stephanie A., Tran, Nam K., Tsongalis, Gregory J., Ueda, Masako, van Wijk, Richard, Vaught, Jim B., Vnencak-Jones, Cindy L., Wadelius, Mia, Walkovich, Kelly, Walsham, Natalie E., Wang, Ping, Wells, David A., Wengenack, Nancy L., Whatley, Sharon D., Willrich, Maria Alice Vieira, Winter, William E., Wittwer, Carl T., Wood, Timothy, Yoon, Edward J., Young, Ian, Zhang, Qian-Yun, and Zimmermann, Stefan

Published
2023
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10. Crystal structure of a complex of Escherichia coli glycerol kinase and an allosteric effector fructose 1,6-biphosphate

Author

Ormo, Mats, Bystrom, Cory E., and Remington, S. James

Subjects
Bacteria -- Physiological aspects, Binding sites (Biochemistry) -- Research, Enzymes -- Research, Escherichia coli -- Physiological aspects, Glycerol kinase -- Research, Metabolic regulation -- Research, Microbial metabolism -- Research, Biological sciences, Chemistry
Abstract

A study relating to the effect of fructose 1,6-biphosphate on Escherichia coli glycerol kinase was conducted to investigate the position and nature of the fructose 1,6-biphosphate (FBP) binding site. A new crystal form of the enzyme was obtained that permitted the analysis to proceed. The crystal structure analysis of E. coli glycerol kinase in complex with the allosteric effector FBP and a mutant form of the enzyme which conclusively shows the observed binding site to be the physiologically relevant one are described.

Published
1998

13. Development and Validation of Apolipoprotein AI-Associated Lipoprotein Proteome Panel for the Prediction of Cholesterol Efflux Capacity and Coronary Artery Disease

Author

Jin, Zhicheng, primary, Collier, Timothy S, primary, Dai, Darlene L Y, primary, Chen, Virginia, primary, Hollander, Zsuzsanna, primary, Ng, Raymond T, primary, McManus, Bruce M, primary, Balshaw, Robert, primary, Apostolidou, Sophia, primary, Penn, Marc S, primary, and Bystrom, Cory, primary

Published
2019
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18. Rapid Affinity Enrichment of Human Apolipoprotein A-I Associated Lipoproteins for Proteome Analysis

Author

Collier, Timothy S., Jin, Zhicheng, Topbas, Celalettin, and Bystrom, Cory

Abstract

Isolation of high density lipoproteins (HDL) for structural and functional studies typically relies on ultracentrifugation techniques, which are time-consuming and difficult to scale. With emerging interest in the clinical relevance of HDL structure and function to cardiovascular disease, a significant gap exists between current and desirable sample preparation throughput. To enable proteomic studies of HDL with large clinical cohorts, we have developed an affinity enrichment approach that relies on the association of histidine-tagged, lipid free ApoA-I with HDL followed by standard metal chelate chromatography. Characterization of the resulting affinity-enriched ApoA-I associated lipoprotein (AALP) pool using biochemical, electrophoretic, and proteomic analysis demonstrates that the isolated material is closely related in structural features, lipid content, protein complement, and relative protein distribution to HDL isolated by ultracentrifugation using sequential density adjustment. The simplicity of the method provides avenues for high-throughput analysis of HDL associated proteins.

Published
2024
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19. Contributors

Author

Aarsand, Aasne K., Abbott, April N., Adeli, Khosrow, Anderson, Neil W., Apple, Fred S., Ayling, Ruth M., Babady, Esther, Badminton, Michael N., Badrick, Tony, Bais, Renze, Bazydlo, Lindsay A.L., Bechtel, Laura K., Bertholf, Roger L., Best, D. Hunter, Bjarnason, Ingvar, Block, Darci R., Blum, Lee M., Bossuyt, Patrick M.M., Boyd, James C., Brown, Sarah M., Buchan, Blake W., Burnett, David, Burnett, Leslie, Bystrom, Cory, Cappellini, Maria Domenica, Caulfield, Adam J., Ceriotti, Ferruccio, Chabot-Richards, Devon, Chen, Derrick J., Chen, Dong, Cheng, Steven, Cheung, Nai-Kong V., Chiu, Rossa W.K., Clarke, Nigel J., Cole, Timothy J., Cooper, Mark, Dayspring, Thomas D., Delaney, Michael P., Dietzen, Dennis J., Doern, Christopher D., D’Orazio, Paul, Eisenhofer, Graeme, Ellervik, Christina, Florkowski, Christopher M., Forbes, Betty A., Fraser, Callum G., Fraser, William D., Freedman, Danielle B., Genzen, Jonathan R., George, Tracy I., Gettings, Katherine B., Glasziou, Paul, Goetze, Jens Peter, Grant, Russell P., Grebe, Stefan, Green, Ralph, Gronowski, Ann M., Guder, Walter G., Hage, David S., Halsall, David, Haverstick, Doris M., Hawker, Charles D., Heaton, Phillip, Higgins, Russell A., Hilmarsdóttir, Ingibjörg, Holstege, Chris, Hoofnagle, Andrew N., Hoon, Dave, Horowitz, Gary, Horvath, Andrea Rita, Howe, John Greg, Humphries, Romney M., Jaffe, Allan S., Jones, Graham R.D., Jones, Patricia M., Jungheim, Emily, Kelley, Todd W., Kitchen, Steve, Kricka, Larry J., Kushnir, Mark M., Lamb, Edmund J., Landers, James P., Langman, Loralie J., Laterza, Omar, Lau, Anna F., Lianidou, Evi, Liesman, Rachael M., Linnet, Kristian, Lo, Stanley F., Lo, Y.M. Dennis, Longo, Nicola, Mackay, Mark, Makrigiorgos, G. Mike, Manis, John P., Mardis, Elaine R., Marshall, William J., McCormack, Ann, McMillin, Gwendolyn A., Meier, Brenton M., Miller, W. Greg, Milone, Michael C., Moons, Karel G.M., Nerenz, Robert D., Nieuwesteeg, Michelle, Nikolac, Nora, Nolte, Frederick S., Panteghini, Mauro, Park, Jason Y., Pasquali, Marzia, Patel, Jay L., Patel, Robin, Podini, Daniele S., Pratt, Victoria M., Price, Christopher P., Pritt, Bobbi S., Quillen, Karen, Rappold, Brian A., Rashidi, Hooman H., Remaley, Alan T., Rifai, Nader, Roberts, Norman B., Rockwood, Alan L., Rosenberg, William, Sacks, David B., Sandberg, Sverre, Sardh, Eliane, Sarno, Mark J., Schindler, Emily I., Schuetz, Audrey N., Scott, Mitchell G., Sethi, Amar A., Shapiro, Howard M., Shaw, Leslie M., Sherwood, Roy A., Simundic, Ana-Maria, Sodi, Ravinder, St John, Andrew, Stout, Molly, Strathmann, Frederick G., Sturgeon, Catharine, Swinkels, Dorine W., Tanwar, Sudeep, Taylor, Andrew, Thatcher, Stephanie A., van Solinge, Wouter W., van Wijk, Richard, Vaught, Jim, Vnencak-Jones, Cindy L., Wadelius, Mia, Walsham, Natalie E., Warnick, G. Russell, Weedn, Victor W., Wells, David A., Wengenack, Nancy L., Whatley, Sharon D., Winter, William E., Wittwer, Carl T., Yarbrough, Melanie L., and Zhang, Qian-Yun

Published
2018
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21. The 2012/2013 PRG Study: Assessing Longitudinal Variability in Routine Peptide LC-MS/MS Analysis

Author

Andacht, Tracy M., Bennett, Keiryn L., Bystrom, Cory, Dangott, Larry, Leszyk, John, Molina, Henrik, Moritz, Robert L., Phinney, Brett S., Thompson, J. Will, Williams, Jason, Elortza, Felix, Chambers, Matthew, Tabb, David, and Bunger, Maureen

Subjects
Poster Session Abstracts
Abstract

The PRG study for 2012-2013 was intended to catalog critical parameters of variability influencing LC-MS/MS data quality within laboratories over a nine month period between March and November, 2012. This study was intended to determine intra-laboratory reproducibility and inform participants of key areas of variability in routine peptide mass spectrometry analyses. Aliquots of a dried, digested protein mixture was sent to all participants with the expectation that once per month a new vial will be reconstituted and analyzed using routine LC-MS and data-dependent MS/MS acquisition settings. Of key importance in the design of this study is the lack of a standard operating protocol. The goal was to measure the degree of reproducibility within a lab as it applies to their established HPLC and MS settings and QC measures. A survey was conducted with each sample submission to catalog individual laboratory practices, instrument configurations, acquisition settings, and routine and non-routine maintenance procedures. Over 80 participants submitted at least one data set, and 36 participants completed the study with 8 or more submissions over the 9 month period. Survey data revealed the vast majority of laboratories (>90%) perform routine QC to determine system suitability, but there was considerable variability in the type and frequency of QC analysis. Collected raw data was searched using identical parameters by the PRG and analyzed for more than 40 MS and MS/MS metrics using the software QuaMeter. The software tool generates metrics that assess multiple properties of LC-MS/MS, from extracted ion chromatogram peak width to total ion current distribution and MS sampling rates. Both identification-dependent and identification-independent metrics can be generated. The variability within these metrics across time was analyzed for each participant and correlative relationships with survey results will be presented.

Published
2013

22. The 2012 PRG Study: Assessing Longitudinal Variability in Routine Peptide LC-MS/MS Analysis

Author

Andacht, Tracy M., Bennett, Keiryn, Bystrom, Cory, Dangott, Larry, Leszyk, John, Molina, Henrik, Moritz, Robert L, Phinney, Brett S., Thompson, J. Will, Chambers, Matthew, Tabb, David, and Bunger, Maureen

Subjects
Scientific Poster Abstracts, Research Groups Presentation Abstracts
Abstract

The PRG study for 2012 is intended to catalog critical parameters of variability influencing LC-MS/MS data quality within labs over a nine month period between March and November, 2012. This study is intended to inform participant labs of key areas of variability in their routine qualitative and quantitative analyses. A dried digested protein mix is sent to labs in aliquots with the expectation that once per month a new vial will be reconstituted and analyzed using routine LC-MS and data-dependent MS/MS acquisition settings. Participants will return the raw data to a centralized server for analysis. The analysis consists of 42 MS and MS/MS metrics that have been determined through the efforts of the CPTC consortium and implemented in open source software from NIST (“MSQC”) and Vanderbilt University (“QuaMeter”). Of key importance in the design of this study is the lack of a standard operating protocol. The concept is to determine variability within a lab when that lab uses their own routine settings and QC measures. A survey is conducted with each sample submission to catalog changes in operators, acquisition settings, as well as routine and non-routine maintenance procedures. As of date, there were 95 labs in 23 countries requesting sample. Within these labs are 25 different models of mass spectrometers from 6 commercial vendors.

Published
2012

26. In Reply

Author

Bystrom, Cory E, primary, Reitz, Richard, primary, and Clarke, Nigel J, primary

Published
2011
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28. Hair Bundles Are Specialized for ATP Delivery via Creatine Kinase

Author

Shin, Jung-Bum, primary, Streijger, Femke, additional, Beynon, Andy, additional, Peters, Theo, additional, Gadzala, Laura, additional, McMillen, Debra, additional, Bystrom, Cory, additional, Van der Zee, Catharina E.E.M., additional, Wallimann, Theo, additional, and Gillespie, Peter G., additional

Published
2007
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31. Crystal structures of Escherichia coli glycerol kinase variant S58 -> W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion

Author

Bystrom, Cory E., Pettigrew, Donald W., Branchaud, Bruce P., O'Brien, Patrick, and Remington, S. James

Subjects
Glycerol kinase -- Research, Escherichia coli -- Research, Adenosine triphosphate -- Research, Biological sciences, Chemistry
Abstract

A study was conducted to analyze the regulatory dimer-dimer interface of glycerol kinase related to fructose 1,6-bisphosphate inhibition. The Muta-Gene In Vitro Mutagenesis Kit was utilized to carry out site-directed mutagenesis. The amplification products were then digested and ligated. Results indicated that the presence of an asymmetric dimer that arises from domain I-domain II motion within one monomer.

Published
1999

35. Crystal structures of Escherichia coli glycerol kinase variant S58--W in complex with...

Author

Bystrom, Cory E. and Pettigrew, Donald W.

Subjects
*ESCHERICHIA coli, *PROTEIN kinases, *ADENOSINE triphosphate, *ALLOSTERIC regulation, *FRUCTOSE
Abstract

Probes the role of the dimer-tetramer assembly found in Escherichia coli glycerol kinase (GK). Reactivity of GK to adenosine triphosphate and allosteric regulation by fructose 1,6-biphosphate (FBP); Designing of a mutation to sterically block formation of dimer-dimer interface near the FBP binding site.

Published
1999
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38. The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses.

Author

Bennett KL, Wang X, Bystrom CE, Chambers MC, Andacht TM, Dangott LJ, Elortza F, Leszyk J, Molina H, Moritz RL, Phinney BS, Thompson JW, Bunger MK, and Tabb DL

Subjects
Animals, Cattle, Humans, Laboratories, Longitudinal Studies, Proteins analysis, Quality Control, Reproducibility of Results, Surveys and Questionnaires, Chromatography, Liquid methods, Peptides isolation & purification, Proteins metabolism, Proteomics methods, Tandem Mass Spectrometry methods
Abstract

Questions concerning longitudinal data quality and reproducibility of proteomic laboratories spurred the Protein Research Group of the Association of Biomolecular Resource Facilities (ABRF-PRG) to design a study to systematically assess the reproducibility of proteomic laboratories over an extended period of time. Developed as an open study, initially 64 participants were recruited from the broader mass spectrometry community to analyze provided aliquots of a six bovine protein tryptic digest mixture every month for a period of nine months. Data were uploaded to a central repository, and the operators answered an accompanying survey. Ultimately, 45 laboratories submitted a minimum of eight LC-MSMS raw data files collected in data-dependent acquisition (DDA) mode. No standard operating procedures were enforced; rather the participants were encouraged to analyze the samples according to usual practices in the laboratory. Unlike previous studies, this investigation was not designed to compare laboratories or instrument configuration, but rather to assess the temporal intralaboratory reproducibility. The outcome of the study was reassuring with 80% of the participating laboratories performing analyses at a medium to high level of reproducibility and quality over the 9-month period. For the groups that had one or more outlying experiments, the major contributing factor that correlated to the survey data was the performance of preventative maintenance prior to the LC-MSMS analyses. Thus, the Protein Research Group of the Association of Biomolecular Resource Facilities recommends that laboratories closely scrutinize the quality control data following such events. Additionally, improved quality control recording is imperative. This longitudinal study provides evidence that mass spectrometry-based proteomics is reproducible. When quality control measures are strictly adhered to, such reproducibility is comparable among many disparate groups. Data from the study are available via ProteomeXchange under the accession code PXD002114., (© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.)

Published
2015
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