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1. Characterization of an expanded set of assays for immunomodulatory proteins using targeted mass spectrometry

Author

Whiteaker, Jeffrey R., Zhao, Lei, Schoenherr, Regine M., Huang, Dongqing, Kennedy, Jacob J., Ivey, Richard G., Lin, Chenwei, Lorentzen, Travis D., Colantonio, Simona, Caceres, Tessa W., Roberts, Rhonda R., Knotts, Joseph G., Reading, Joshua J., Perry, Candice D., Garcia-Buntley, Sandra S., Bocik, William, Hewitt, Stephen M., and Paulovich, Amanda G.

Published
2024
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2. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer

Author

Chowdhury, Shrabanti, Kennedy, Jacob J., Ivey, Richard G., Murillo, Oscar D., Hosseini, Noshad, Song, Xiaoyu, Petralia, Francesca, Calinawan, Anna, Savage, Sara R., Berry, Anna B., Reva, Boris, Ozbek, Umut, Krek, Azra, Ma, Weiping, da Veiga Leprevost, Felipe, Ji, Jiayi, Yoo, Seungyeul, Lin, Chenwei, Voytovich, Uliana J., Huang, Yajue, Lee, Sun-Hee, Bergan, Lindsay, Lorentzen, Travis D., Mesri, Mehdi, Rodriguez, Henry, Hoofnagle, Andrew N., Herbert, Zachary T., Nesvizhskii, Alexey I., Zhang, Bing, Whiteaker, Jeffrey R., Fenyo, David, McKerrow, Wilson, Wang, Joshua, Schürer, Stephan C., Stathias, Vasileios, Chen, X. Steven, Barcellos-Hoff, Mary Helen, Starr, Timothy K., Winterhoff, Boris J., Nelson, Andrew C., Mok, Samuel C., Kaufmann, Scott H., Drescher, Charles, Cieslik, Marcin, Wang, Pei, Birrer, Michael J., and Paulovich, Amanda G.

Published
2023
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3. Multiomic analysis identifies CPT1A as a potential therapeutic target in platinum-refractory, high-grade serous ovarian cancer

Author

Huang, Dongqing, Chowdhury, Shrabanti, Wang, Hong, Savage, Sara R., Ivey, Richard G., Kennedy, Jacob J., Whiteaker, Jeffrey R., Lin, Chenwei, Hou, Xiaonan, Oberg, Ann L., Larson, Melissa C., Eskandari, Najmeh, Delisi, Davide A., Gentile, Saverio, Huntoon, Catherine J., Voytovich, Uliana J., Shire, Zahra J., Yu, Qing, Gygi, Steven P., Hoofnagle, Andrew N., Herbert, Zachary T., Lorentzen, Travis D., Calinawan, Anna, Karnitz, Larry M., Weroha, S. John, Kaufmann, Scott H., Zhang, Bing, Wang, Pei, Birrer, Michael J., and Paulovich, Amanda G.

Published
2021
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4. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer

Author

Chowdhury, Shrabanti, primary, Kennedy, Jacob J., additional, Ivey, Richard G., additional, Murillo, Oscar D., additional, Hosseini, Noshad, additional, Song, Xiaoyu, additional, Petralia, Francesca, additional, Calinawan, Anna, additional, Savage, Sara R., additional, Berry, Anna B., additional, Reva, Boris, additional, Ozbek, Umut, additional, Krek, Azra, additional, Ma, Weiping, additional, da Veiga Leprevost, Felipe, additional, Ji, Jiayi, additional, Yoo, Seungyeul, additional, Lin, Chenwei, additional, Voytovich, Uliana J., additional, Huang, Yajue, additional, Lee, Sun-Hee, additional, Bergan, Lindsay, additional, Lorentzen, Travis D., additional, Mesri, Mehdi, additional, Rodriguez, Henry, additional, Hoofnagle, Andrew N., additional, Herbert, Zachary T., additional, Nesvizhskii, Alexey I., additional, Zhang, Bing, additional, Whiteaker, Jeffrey R., additional, Fenyo, David, additional, McKerrow, Wilson, additional, Wang, Joshua, additional, Schürer, Stephan C., additional, Stathias, Vasileios, additional, Chen, X. Steven, additional, Barcellos-Hoff, Mary Helen, additional, Starr, Timothy K., additional, Winterhoff, Boris J., additional, Nelson, Andrew C., additional, Mok, Samuel C., additional, Kaufmann, Scott H., additional, Drescher, Charles, additional, Cieslik, Marcin, additional, Wang, Pei, additional, Birrer, Michael J., additional, and Paulovich, Amanda G., additional

Published
2024
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5. Genetic Structure of the Purebred Domestic Dog

Author

Parker, Heidi G., Kim, Lisa V., Sutter, Nathan B., Carlson, Scott, Lorentzen, Travis D., Malek, Tiffany B., Johnson, Gary S., DeFrance, Hawkins B., Ostrander, Elaine A., and Kruglyak, Leonid

Published
2004

7. A 1-Mb Resolution Radiation Hybrid Map of the Canine Genome

Author

Guyon, Richard, Lorentzen, Travis D., Hitte, Christophe, Kim, Lisa, Cadieu, Edouard, Parker, Heidi G., Quignon, Pascale, Lowe, Jennifer K., Renier, Corinne, Gelfenbeyn, Boris, Vignaux, Françoise, DeFrance, Hawkins B., Gloux, Stephanie, Mahairas, Gregory G., André, Catherine, Galibert, Francis, and Ostrander, Elaine A.

Published
2003

9. A multiplexed assay for quantifying immunomodulatory proteins supports correlative studies in immunotherapy clinical trials

Author

Whiteaker, Jeffrey R., primary, Zhao, Lei, additional, Schoenherr, Regine M., additional, Huang, Dongqing, additional, Lundeen, Rachel A., additional, Voytovich, Ulianna, additional, Kennedy, Jacob J., additional, Ivey, Richard G., additional, Lin, Chenwei, additional, Murillo, Oscar D., additional, Lorentzen, Travis D., additional, Colantonio, Simona, additional, Caceres, Tessa W., additional, Roberts, Rhonda R., additional, Knotts, Joseph G., additional, Reading, Joshua J., additional, Perry, Candice D., additional, Richardson, Christopher W., additional, Garcia-Buntley, Sandra S., additional, Bocik, William, additional, Hewitt, Stephen M., additional, Chowdhury, Shrabanti, additional, Vandermeer, Jackie, additional, Smith, Stephen D., additional, Gopal, Ajay K., additional, Ramchurren, Nirasha, additional, Fling, Steven P., additional, Wang, Pei, additional, and Paulovich, Amanda G., additional

Published
2023
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10. Preserving the Phosphoproteome of Clinical Biopsies Using a Quick-Freeze Collection Device

Author

Kennedy, Jacob J., primary, Woodcock, Amanda, additional, Ivey, Richard G., additional, Lin, ChenWei, additional, Corral, Guy, additional, Hooper, Eli, additional, Martin, Gregory, additional, Longman, Gina, additional, Stancik, Blake, additional, Cromwell, Elizabeth A., additional, Whiteaker, Jeffrey R., additional, Zhao, Lei, additional, Lorentzen, Travis D., additional, Thielman, Scott, additional, and Paulovich, Amanda G., additional

Published
2022
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13. Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens

Author

Whiteaker, Jeffrey R., primary, Lundeen, Rachel A., additional, Zhao, Lei, additional, Schoenherr, Regine M., additional, Burian, Aura, additional, Huang, Dongqing, additional, Voytovich, Ulianna, additional, Wang, Tao, additional, Kennedy, Jacob J., additional, Ivey, Richard G., additional, Lin, Chenwei, additional, Murillo, Oscar D., additional, Lorentzen, Travis D., additional, Thiagarajan, Mathangi, additional, Colantonio, Simona, additional, Caceres, Tessa W., additional, Roberts, Rhonda R., additional, Knotts, Joseph G., additional, Reading, Joshua J., additional, Kaczmarczyk, Jan A., additional, Richardson, Christopher W., additional, Garcia-Buntley, Sandra S., additional, Bocik, William, additional, Hewitt, Stephen M., additional, Murray, Karen E., additional, Do, Nhan, additional, Brophy, Mary, additional, Wilz, Stephen W., additional, Yu, Hongbo, additional, Ajjarapu, Samuel, additional, Boja, Emily, additional, Hiltke, Tara, additional, Rodriguez, Henry, additional, and Paulovich, Amanda G., additional

Published
2021
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14. Proteogenomic Characterization of Highly Enriched Viable Leukemic Blasts in Acute Myeloid Leukemia: A SWOG Report

Author

Naru, Jasmine, primary, Othus, Megan, additional, Lin, ChenWei, additional, Moseley, Anna, additional, Willman, Cheryl L, additional, Pogosova-Agadjanyan, Era L, additional, Wu, Feinan, additional, Appelbaum, Frederick R., additional, Erba, Harry P., additional, Jenkins, Isaac C., additional, Kennedy, Jacob J, additional, Delrow, Jeffrey, additional, Whiteaker, Jeffrey, additional, Radich, Jerald P., additional, Godwin, John E., additional, Beppu, Lan, additional, Fitzgibbon, Matthew, additional, Fang, Min, additional, Wang, Pei, additional, Gafken, Phillip R, additional, Ivey, Richard G, additional, Meshinchi, Soheil, additional, Chauncey, Thomas R., additional, Lorentzen, Travis D, additional, Voytovich, Uliana J, additional, Paulovich, Amanda G, additional, and Stirewalt, Derek, additional

Published
2021
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15. Global Proteomic Profiling Identifies Novel Prognostic Factors in Undifferentiated Leukemia Blasts from Patients with NPM1 Mutations: A Previously Unreported Approach to Biomarker Discovery from the Fred Hutch and SWOG

Author

Stirewalt, Derek, primary, Othus, Megan, additional, Naru, Jasmine, additional, Kennedy, Jacob J, additional, Pogosova-Agadjanyan, Era L, additional, Appelbaum, Frederick R., additional, Beppu, Lan, additional, Chauncey, Thomas R., additional, Delrow, Jeffrey, additional, Erba, Harry P., additional, Gafken, Phillip R, additional, Godwin, John E., additional, Fitzgibbon, Matthew, additional, Hua, Xing, additional, Jenkins, Isaac C., additional, Fang, Min, additional, Ivey, Richard G, additional, Lin, ChenWei, additional, Lorentzen, Travis D, additional, Moseley, Anna, additional, Radich, Jerald P., additional, Voytovich, Uliana J, additional, Wang, Pei, additional, Whiteaker, Jeffrey, additional, Willman, Cheryl L, additional, Wu, Feinan, additional, Meshinchi, Soheil, additional, and Paulovich, Amanda G, additional

Published
2021
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16. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

Author

Petralia, Francesca, primary, Tignor, Nicole, additional, Reva, Boris, additional, Koptyra, Mateusz, additional, Chowdhury, Shrabanti, additional, Rykunov, Dmitry, additional, Krek, Azra, additional, Ma, Weiping, additional, Zhu, Yuankun, additional, Ji, Jiayi, additional, Calinawan, Anna, additional, Whiteaker, Jeffrey R., additional, Colaprico, Antonio, additional, Stathias, Vasileios, additional, Omelchenko, Tatiana, additional, Song, Xiaoyu, additional, Raman, Pichai, additional, Guo, Yiran, additional, Brown, Miguel A., additional, Ivey, Richard G., additional, Szpyt, John, additional, Guha Thakurta, Sanjukta, additional, Gritsenko, Marina A., additional, Weitz, Karl K., additional, Lopez, Gonzalo, additional, Kalayci, Selim, additional, Gümüş, Zeynep H., additional, Yoo, Seungyeul, additional, da Veiga Leprevost, Felipe, additional, Chang, Hui-Yin, additional, Krug, Karsten, additional, Katsnelson, Lizabeth, additional, Wang, Ying, additional, Kennedy, Jacob J., additional, Voytovich, Uliana J., additional, Zhao, Lei, additional, Gaonkar, Krutika S., additional, Ennis, Brian M., additional, Zhang, Bo, additional, Baubet, Valerie, additional, Tauhid, Lamiya, additional, Lilly, Jena V., additional, Mason, Jennifer L., additional, Farrow, Bailey, additional, Young, Nathan, additional, Leary, Sarah, additional, Moon, Jamie, additional, Petyuk, Vladislav A., additional, Nazarian, Javad, additional, Adappa, Nithin D., additional, Palmer, James N., additional, Lober, Robert M., additional, Rivero-Hinojosa, Samuel, additional, Wang, Liang-Bo, additional, Wang, Joshua M., additional, Broberg, Matilda, additional, Chu, Rosalie K., additional, Moore, Ronald J., additional, Monroe, Matthew E., additional, Zhao, Rui, additional, Smith, Richard D., additional, Zhu, Jun, additional, Robles, Ana I., additional, Mesri, Mehdi, additional, Boja, Emily, additional, Hiltke, Tara, additional, Rodriguez, Henry, additional, Zhang, Bing, additional, Schadt, Eric E., additional, Mani, D.R., additional, Ding, Li, additional, Iavarone, Antonio, additional, Wiznerowicz, Maciej, additional, Schürer, Stephan, additional, Chen, Xi S., additional, Heath, Allison P., additional, Rokita, Jo Lynne, additional, Nesvizhskii, Alexey I., additional, Fenyö, David, additional, Rodland, Karin D., additional, Liu, Tao, additional, Gygi, Steven P., additional, Paulovich, Amanda G., additional, Resnick, Adam C., additional, Storm, Phillip B., additional, Rood, Brian R., additional, Wang, Pei, additional, Francis, Alicia, additional, Morgan, Allison M., additional, Waanders, Angela J., additional, Viaene, Angela N., additional, Buccoliero, Anna Maria, additional, Chinnaiyan, Arul M., additional, Leonard, Carina A., additional, Kline, Cassie N., additional, Caporalini, Chiara, additional, Kinsinger, Christopher R., additional, Li, Chunde, additional, Kram, David E., additional, Hanson, Derek, additional, Appert, Elizabeth, additional, Kawaler, Emily A., additional, Raabe, Eric H., additional, Jackson, Eric M., additional, Greenfield, Jeffrey P., additional, Stone, Gabrielle S., additional, Getz, Gad, additional, Grant, Gerald, additional, Teo, Guo Ci, additional, Pollack, Ian F., additional, Cain, Jason E., additional, Foster, Jessica B., additional, Phillips, Joanna J., additional, Palma, July E., additional, Ketchum, Karen A., additional, Ruggles, Kelly V., additional, Blumenberg, Lili, additional, Cornwell, Macintosh, additional, Sarmady, Mahdi, additional, Domagalski, Marcin J., additional, Cieślik, Marcin P., additional, Santi, Mariarita, additional, Li, Marilyn M., additional, Ellis, Matthew J., additional, Wyczalkowski, Matthew A., additional, Connors, Meghan, additional, Scagnet, Mirko, additional, Gupta, Nalin, additional, Edwards, Nathan J., additional, Vitanza, Nicholas A., additional, Vaske, Olena M., additional, Becher, Oren, additional, McGarvey, Peter B., additional, Firestein, Ron, additional, Mueller, Sabine, additional, Winebrake, Samuel G., additional, Dhanasekaran, Saravana Mohan, additional, Cai, Shuang, additional, Partap, Sonia, additional, Patton, Tatiana, additional, Le, Toan, additional, Lorentzen, Travis D., additional, Liu, Wenke, additional, and Bocik, William E., additional

Published
2020
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17. Construction of a 2- Mb resolution BAC microarray for CGH analysis of canine tumors

Author

Thomas, Rachel, Scott, Allyson, Langford, Cordelia F., Fosmire, Susan P., Jubala, Cristan M., Lorentzen, Travis D., Hitte, Christophe, Karlsson, Elinor K., Kirkness, Ewen, Ostrander, Elaine, Gailbert, Francis, Lindblad-Toh, Kerstin, Modiano, Jaime F., and Breen, Matthew

Subjects
Genomes -- Research, Nucleic acid hybridization -- Research, Cytogenetics -- Research, Dogs -- Genetic aspects, Dogs -- Diseases, Health
Abstract

A study is conducted on the similarities shared between many human and dog diseases using a wide range of molecular cytogenetic techniques. A comprehensive canine comparative genome hybridization (CGH) array that has 1158 canine BAC clones ordered throughout the genome with an average interval of 2-Mb is studied.

Published
2005

18. An integrated 4249 marker FISH/RH map of the canine genome

Author

Mahairas Gregory G, Guyon Richard, Hudson Ruth, Kirkness Ewen F, Parker Heidi G, Evanno Gwenaelle, Scott Allyson, Sabacan Leah, Cadieu Edouard, Thomas Rachael, Lorentzen Travis D, Hitte Christophe, Breen Matthew, Gelfenbeyn Boris, Fraser Claire M, André Catherine, Galibert Francis, and Ostrander Elaine A

Subjects
canine, dog, radiation hybrid, microsatellites, ESTs, BAC-ends, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The 156 breeds of dog recognized by the American Kennel Club offer a unique opportunity to map genes important in genetic variation. Each breed features a defining constellation of morphological and behavioral traits, often generated by deliberate crossing of closely related individuals, leading to a high rate of genetic disease in many breeds. Understanding the genetic basis of both phenotypic variation and disease susceptibility in the dog provides new ways in which to dissect the genetics of human health and biology. Results To facilitate both genetic mapping and cloning efforts, we have constructed an integrated canine genome map that is both dense and accurate. The resulting resource encompasses 4249 markers, and was constructed using the RHDF5000-2 whole genome radiation hybrid panel. The radiation hybrid (RH) map features a density of one marker every 900 Kb and contains 1760 bacterial artificial chromosome clones (BACs) localized to 1423 unique positions, 851 of which have also been mapped by fluorescence in situ hybridization (FISH). The two data sets show excellent concordance. Excluding the Y chromosome, the map features an RH/FISH mapped BAC every 3.5 Mb and an RH mapped BAC-end, on average, every 2 Mb. For 2233 markers, the orthologous human genes have been established, allowing the identification of 79 conserved segments (CS) between the dog and human genomes, dramatically extending the length of most previously described CS. Conclusions These results provide a necessary resource for the canine genome mapping community to undertake positional cloning experiments and provide new insights into the comparative canine-human genome maps.

Published
2004
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19. Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors

Author

Thomas, Rachael, Scott, Allyson, Langford, Cordelia F., Fosmire, Susan P., Jubala, Cristan M., Lorentzen, Travis D., Hitte, Christophe, Karlsson, Elinor K., Kirkness, Ewen, Ostrander, Elaine A., Galibert, Francis, Lindblad-Toh, Kerstin, Modiano, Jaime F., Breen, Matthew, Thomas, Rachael, Scott, Allyson, Langford, Cordelia F., Fosmire, Susan P., Jubala, Cristan M., Lorentzen, Travis D., Hitte, Christophe, Karlsson, Elinor K., Kirkness, Ewen, Ostrander, Elaine A., Galibert, Francis, Lindblad-Toh, Kerstin, Modiano, Jaime F., and Breen, Matthew

Published
2005
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20. Proteome and transcriptome profiles of a Her2/Neu-driven mouse model of breast cancer

Author

Schoenherr, Regine M., primary, Kelly-Spratt, Karen S., additional, Lin, ChenWei, additional, Whiteaker, Jeffrey R., additional, Liu, Tao, additional, Holzman, Ted, additional, Coleman, Ilsa, additional, Feng, Li-Chia, additional, Lorentzen, Travis D., additional, Krasnoselsky, Alexei L., additional, Wang, Pei, additional, Liu, Yan, additional, Gurley, Kay E., additional, Amon, Lynn M., additional, Schepmoes, Athena A., additional, Moore, Ronald J., additional, Camp II, David G., additional, Chodosh, Lewis A., additional, Smith, Richard D., additional, Nelson, Peter S., additional, McIntosh, Martin W., additional, Kemp, Christopher J., additional, and Paulovich, Amanda G., additional

Published
2011
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21. Blood-Based Detection of Radiation Exposure in Humans Based on Novel Phospho-Smc1 ELISA

Author

Ivey, Richard G., primary, Moore, Heather D., additional, Voytovich, Uliana J., additional, Thienes, Cortlandt P., additional, Lorentzen, Travis D., additional, Pogosova-Agadjanyan, Era L., additional, Frayo, Shani, additional, Izaguirre, Venissa K., additional, Lundberg, Sally J., additional, Hedin, Lacey, additional, Badiozamani, Kas Ray, additional, Hoofnagle, Andrew N., additional, Stirewalt, Derek L., additional, Wang, Pei, additional, Georges, George E., additional, Gopal, Ajay K., additional, and Paulovich, Amanda G., additional

Published
2010
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22. Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping

Author

Hitte, Christophe, primary, Madeoy, Jennifer, additional, Kirkness, Ewen F., additional, Priat, Catherine, additional, Lorentzen, Travis D., additional, Senger, Fabrice, additional, Thomas, Dan, additional, Derrien, Thomas, additional, Ramirez, Christina, additional, Scott, Carol, additional, Evanno, Gwenaelle, additional, Pullar, Barbara, additional, Cadieu, Edouard, additional, Oza, Vinay, additional, Lourgant, Kristelle, additional, Jaffe, David B., additional, Tacher, Sandrine, additional, Dréano, Stéphane, additional, Berkova, Nadia, additional, André, Catherine, additional, Deloukas, Panagiotis, additional, Fraser, Claire, additional, Lindblad-Toh, Kerstin, additional, Ostrander, Elaine A., additional, and Galibert, Francis, additional

Published
2005
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23. An integrated 4249 marker FISH/RH map of the canine genome

Author

Breen, Matthew, primary, Hitte, Christophe, additional, Lorentzen, Travis D, additional, Thomas, Rachael, additional, Cadieu, Edouard, additional, Sabacan, Leah, additional, Scott, Allyson, additional, Evanno, Gwenaelle, additional, Parker, Heidi G, additional, Kirkness, Ewen F, additional, Hudson, Ruth, additional, Guyon, Richard, additional, Mahairas, Gregory G, additional, Gelfenbeyn, Boris, additional, Fraser, Claire M, additional, André, Catherine, additional, Galibert, Francis, additional, and Ostrander, Elaine A, additional

Published
2004
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24. Proteome and transcriptome profiles of a Her2/Neu-driven mouse model of breast cancer.

Author

Schoenherr RM, Kelly-Spratt KS, Lin C, Whiteaker JR, Liu T, Holzman T, Coleman I, Feng LC, Lorentzen TD, Krasnoselsky AL, Wang P, Liu Y, Gurley KE, Amon LM, Schepmoes AA, Moore RJ, Camp DG 2nd, Chodosh LA, Smith RD, Nelson PS, McIntosh MW, Kemp CJ, and Paulovich AG

Subjects
Animals, Databases, Protein, Mice, Mice, Transgenic, Proteomics, Receptor, ErbB-2 analysis, Tandem Mass Spectrometry, Breast Neoplasms genetics, Disease Models, Animal, Gene Expression Profiling, Proteome analysis, Proteome genetics, Receptor, ErbB-2 genetics, Transcription, Genetic genetics
Abstract

Purpose: We generated extensive transcriptional and proteomic profiles from a Her2-driven mouse model of breast cancer that closely recapitulates human breast cancer. This report makes these data publicly available in raw and processed forms, as a resource to the community. Importantly, we previously made biospecimens from this same mouse model freely available through a sample repository, so researchers can obtain samples to test biological hypotheses without the need of breeding animals and collecting biospecimens., Experimental Design: Twelve datasets are available, encompassing 841 LC-MS/MS experiments (plasma and tissues) and 255 microarray analyses of multiple tissues (thymus, spleen, liver, blood cells, and breast). Cases and controls were rigorously paired to avoid bias., Results: In total, 18,880 unique peptides were identified (PeptideProphet peptide error rate ≤1%), with 3884 and 1659 non-redundant protein groups identified in plasma and tissue datasets, respectively. Sixty-one of these protein groups overlapped between cancer plasma and cancer tissue., Conclusions and Clinical Relevance: These data are of use for advancing our understanding of cancer biology, for software and quality control tool development, investigations of analytical variation in MS/MS data, and selection of proteotypic peptides for multiple reaction monitoring-MS. The availability of these datasets will contribute positively to clinical proteomics., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Published
2011
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25. Head-to-head comparison of serum fractionation techniques.

Author

Whiteaker JR, Zhang H, Eng JK, Fang R, Piening BD, Feng LC, Lorentzen TD, Schoenherr RM, Keane JF, Holzman T, Fitzgibbon M, Lin C, Zhang H, Cooke K, Liu T, Camp DG 2nd, Anderson L, Watts J, Smith RD, McIntosh MW, and Paulovich AG

Subjects
Blood Proteins isolation & purification, Chromatography, Liquid, Glycopeptides blood, Glycopeptides chemistry, Glycopeptides isolation & purification, Humans, Male, Mass Spectrometry, Peptide Fragments blood, Peptide Fragments chemistry, Peptide Fragments isolation & purification, Proteomics methods, Spectrometry, Mass, Electrospray Ionization, Trypsin, Blood Proteins chemistry
Abstract

Multiple approaches for simplifying the serum proteome have been described. These techniques are generally developed across different laboratories, samples, mass spectrometry platforms, and analysis tools. Hence, comparing the available schemes is impossible from the existing literature because of confounding variables. We describe a head-to-head comparison of several serum fractionation schemes, including N-linked glycopeptide enrichment, cysteinyl-peptide enrichment, magnetic bead separation (C3, C8, and WCX), size fractionation, protein A/G depletion, and immunoaffinity column depletion of abundant serum proteins. Each technique was compared to results obtained from unfractionated human serum. The results show immunoaffinity subtraction is the most effective means for simplifying the serum proteome while maintaining reasonable sample throughput. The reported dataset is publicly available and provides a standard against which emergent technologies can be compared and evaluated for their contribution to serum-based biomarker discovery.

Published
2007
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