Immunodepletion plasma proteomics by TripleTOF 5600 and Orbitrap Elite/LTQ-Orbitrap Velos/Q Exactive mass spectrometers

Journal of Proteome Research

Volumn 12, Issue 10, 2013, Pages 4351-4365

  Jones, Kelly A ^a   Kim, Phillip D ^a   Patel, Bhavinkumar B ^a   Kelsen, Steven G ^b   Braverman, Alan ^b   Swinton, Derrick J ^c   Gafken, Philip R ^d   Jones, Lisa A ^d   Lane, William S ^e   Neveu, John M ^e   Leung, Hon Chiu E ^f   Shaffer, Scott A ^g   Leszyk, John D ^g   Stanley, Bruce A ^h   Fox, Todd E ^h   Stanley, Anne ^h   Hall, Michael J ^a   Hampel, Heather ⁱ   South, Christopher D ⁱ   De La Chapelle, Albert ⁱ   Burt, Randall W ^j   Jones, David A ^j   Kopelovich, Levy ^k   Yeung, Anthony T ^a   more..

^a FOX CHASE CANCER CENTER   (United States)

^b TEMPLE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c LINCOLN UNIVERSITY   (United States)

^d Fred Hutchinson Cancer Research Center   (United States)

^e HARVARD UNIVERSITY   (United States)

^f BAYLOR COLLEGE OF MEDICINE   (United States)

^g UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^h PENN STATE COLLEGE OF MEDICINE   (United States)

ⁱ OHIO STATE UNIVERSITY   (United States)

^j UNIVERSITY OF UTAH   (United States)

^k NATIONAL CANCER INSTITUTE   (United States)

more..

Author keywords

EMMOL normalization; IgY14; immunodepletion; iTRAQ; Orbitrap; Q Exactive; Seppro; TripleTOF

Indexed keywords

PEPTIDE; PROTEOME;

ALGORITHM; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; DATA BASE; ELECTROSPRAY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HUMAN TISSUE; ISOELECTRIC FOCUSING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETER; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEOMICS; TANDEM MASS SPECTROMETRY;

BLOOD PROTEINS; HUMANS; IMMUNOPRECIPITATION; PEPTIDE MAPPING; PROTEOMICS; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; TANDEM MASS SPECTROMETRY;

EID: 84885205763     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400307u     Document Type: Article

References (36)

1. DeSouza, L.; Diehl, G.; Rodrigues, M. J.; Guo, J.; Romaschin, A. D.; Colgan, T. J.; Siu, K. W. Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry J. Proteome Res. 2005, 4 (2) 377-86
2. Chong, P. K.; Gan, C. S.; Pham, T. K.; Wright, P. C. Isobaric tags for relative and absolute quantitation (iTRAQ) reproducibility: Implication of multiple injections J. Proteome Res. 2006, 5 (5) 1232-40
3. Boehm, A. M.; Putz, S.; Altenhofer, D.; Sickmann, A.; Falk, M. Precise protein quantification based on peptide quantification using iTRAQ BMC Bioinf. 2007, 8, 214
4. Raman, S. P.; Kawamoto, S.; Blackford, A.; Hruban, R. H.; O'Brien-Lennon, A. M.; Wolfgang, C. L.; Rezaee, N.; Edil, B.; Fishman, E. K. Histopathologic findings of multifocal pancreatic intraductal papillary mucinous neoplasms on CT AJR, Am. J. Roentgenol. 2013, 200 (3) 563-9
5. Talar-Wojnarowska, R.; Pazurek, M.; Durko, L.; Degowska, M.; Rydzewska, G.; Smigielski, J.; Janiak, A.; Olakowski, M.; Lampe, P.; Grzelak, P.; Stefanczyk, L.; Malecka-Panas, E. Pancreatic cyst fluid analysis for differential diagnosis between benign and malignant lesions Oncol. Lett. 2013, 5 (2) 613-6
6. Shimizu, Y.; Yamaue, H.; Maguchi, H.; Yamao, K.; Hirono, S.; Osanai, M.; Hijioka, S.; Hosoda, W.; Nakamura, Y.; Shinohara, T.; Yanagisawa, A. Predictors of Malignancy in Intraductal Papillary Mucinous Neoplasm of the Pancreas: Analysis of 310 Pancreatic Resection Patients at Multiple High-Volume Centers Pancreas 2013, 42, 883-8
7. Atef, E.; El Nakeeb, A.; El Hanafy, E.; El Hemaly, M.; Hamdy, E.; El-Geidie, A. Pancreatic cystic neoplasms: predictors of malignant behavior and management Saudi J. Gastroenterol. 2013, 19 (1) 45-53
8. Schmidt, C. M. Pancreatic cyst cytology: optimization of cancer risk profiling Cancer Cytopathol. 2013, 121 (1) 2-3
9. Thornton, G. D.; McPhail, M. J.; Nayagam, S.; Hewitt, M. J.; Vlavianos, P.; Monahan, K. J. Endoscopic ultrasound guided fine needle aspiration for the diagnosis of pancreatic cystic neoplasms: a meta-analysis Pancreatology 2013, 13 (1) 48-57
10. Lim, L. G.; Lakhtakia, S.; Ang, T. L.; Vu, C. K.; Dy, F.; Chong, V. H.; Khor, C. J.; Lim, W. C.; Doshi, B. K.; Varadarajulu, S.; Yasuda, K.; Wong, J. Y.; Chan, Y. H.; Nga, M. E.; Ho, K. Y.; Asian EUS Consortium. Factors determining diagnostic yield of endoscopic ultrasound guided fine-needle aspiration for pancreatic cystic lesions: A multicentre Asian study Dig. Dis. Sci. 2013, 58, 1751-7
11. Zhan, X. B.; Wang, B.; Liu, F.; Ye, X. F.; Jin, Z. D.; Li, Z. S. Cyst fluid carcinoembryonic antigen concentration and cytology by endosonography-guided fine needle aspiration in predicting malignant pancreatic mucinous cystic neoplasms J Dig Dis 2013, 14 (4) 191-5
12. Rockacy, M. J.; Zahid, M.; McGrath, K. M.; Fasanella, K. E.; Khalid, A. Association between KRAS mutation, detected in pancreatic cyst fluid, and long-term outcomes of patients Clin. Gastroenterol. Hepatol. 2013, 11 (4) 425-9
13. Shilov, I. V.; Seymour, S. L.; Patel, A. A.; Loboda, A.; Tang, W. H.; Keating, S. P.; Hunter, C. L.; Nuwaysir, L. M.; Schaeffer, D. A. The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra Mol. Cell. Proteomics 2007, 6 (9) 1638-55
14. Lengqvist, J.; Uhlen, K.; Lehtio, J. iTRAQ compatibility of peptide immobilized pH gradient isoelectric focusing Proteomics 2007, 7 (11) 1746-52
15. Kim, P. D.; Patel, B. B.; Yeung, A. T. Isobaric labeling and data normalization without requiring protein quantitation J. Biomol. Tech. 2012, 23 (1) 11-23
16. Rai, A. J.; Gelfand, C. A.; Haywood, B. C.; Warunek, D. J.; Yi, J.; Schuchard, M. D.; Mehigh, R. J.; Cockrill, S. L.; Scott, G. B.; Tammen, H.; Schulz-Knappe, P.; Speicher, D. W.; Vitzthum, F.; Haab, B. B.; Siest, G.; Chan, D. W. HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples Proteomics 2005, 5 (13) 3262-77
17. Yi, J.; Kim, C.; Gelfand, C. A. Inhibition of intrinsic proteolytic activities moderates preanalytical variability and instability of human plasma J. Proteome Res. 2007, 6 (5) 1768-81
18. Yeung, A. T.; Patel, B. B.; Li, X. M.; Seeholzer, S. H.; Coudry, R. A.; Cooper, H. S.; Bellacosa, A.; Boman, B. M.; Zhang, T.; Litwin, S.; Ross, E. A.; Conrad, P.; Crowell, J. A.; Kopelovich, L.; Knudson, A. One-hit effects in cancer: altered proteome of morphologically normal colon crypts in familial adenomatous polyposis Cancer Res. 2008, 68 (18) 7579-86
19. Half, E.; Bercovich, D.; Rozen, P. Familial adenomatous polyposis Orphanet J. Rare Dis. 2009, 4, 22
20. Knudson, A. G. Two genetic hits (more or less) to cancer Nat. Rev. Cancer 2001, 1 (2) 157-62
21. Lynch, H. T.; Smyrk, T.; Lynch, J. An update of HNPCC (Lynch syndrome) Cancer Genet. Cytogenet. 1997, 93 (1) 84-99
22. Qian, W. J.; Kaleta, D. T.; Petritis, B. O.; Jiang, H.; Liu, T.; Zhang, X.; Mottaz, H. M.; Varnum, S. M.; Camp, D. G., 2nd; Huang, L.; Fang, X.; Zhang, W. W.; Smith, R. D. Enhanced detection of low abundance human plasma proteins using a tandem IgY12-SuperMix immunoaffinity separation strategy Mol. Cell. Proteomics 2008, 7 (10) 1963-73
23. Patel, B. B.; Barrero, C. A.; Braverman, A.; Kim, P. D.; Jones, K. A.; Chen, D. E.; Bowler, R. P.; Merali, S.; Kelsen, S. G.; Yeung, A. T. Assessment of two immunodepletion methods: Off-target effects and variations in immunodepletion efficiency may confound plasma proteomics J. Proteome Res. 2012, 11, 5947-58
24. Eriksson, H.; Lengqvist, J.; Hedlund, J.; Uhlen, K.; Orre, L. M.; Bjellqvist, B.; Persson, B.; Lehtio, J.; Jakobsson, P. J. Quantitative membrane proteomics applying narrow range peptide isoelectric focusing for studies of small cell lung cancer resistance mechanisms Proteomics 2008, 8 (15) 3008-18
25. Farrah, T.; Deutsch, E. W.; Aebersold, R. Using the Human Plasma PeptideAtlas to study human plasma proteins Methods Mol. Biol. 2011, 728, 349-74
26. Evans, C.; Noirel, J.; Ow, S. Y.; Salim, M.; Pereira-Medrano, A. G.; Couto, N.; Pandhal, J.; Smith, D.; Pham, T. K.; Karunakaran, E.; Zou, X.; Biggs, C. A.; Wright, P. C. An insight into iTRAQ: where do we stand now? Anal. Bioanal. Chem. 2012, 404 (4) 1011-27
27. Pichler, P.; Kocher, T.; Holzmann, J.; Mohring, T.; Ammerer, G.; Mechtler, K. Improved precision of iTRAQ and TMT quantification by an axial extraction field in an Orbitrap HCD cell Anal. Chem. 2011, 83 (4) 1469-74
28. Chambers, M. C.; Maclean, B.; Burke, R.; Amodei, D.; Ruderman, D. L.; Neumann, S.; Gatto, L.; Fischer, B.; Pratt, B.; Egertson, J.; Hoff, K.; Kessner, D.; Tasman, N.; Shulman, N.; Frewen, B.; Baker, T. A.; Brusniak, M. Y.; Paulse, C.; Creasy, D.; Flashner, L.; Kani, K.; Moulding, C.; Seymour, S. L.; Nuwaysir, L. M.; Lefebvre, B.; Kuhlmann, F.; Roark, J.; Rainer, P.; Detlev, S.; Hemenway, T.; Huhmer, A.; Langridge, J.; Connolly, B.; Chadick, T.; Holly, K.; Eckels, J.; Deutsch, E. W.; Moritz, R. L.; Katz, J. E.; Agus, D. B.; MacCoss, M.; Tabb, D. L.; Mallick, P. A cross-platform toolkit for mass spectrometry and proteomics Nat. Biotechnol. 2012, 30 (10) 918-20
29. Zhang, J.; Xin, L.; Shan, B.; Chen, W.; Xie, M.; Yuen, D.; Zhang, W.; Zhang, Z.; Lajoie, G. A.; Ma, B. PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification Mol. Cell. Proteomics 2012, 11 (4) M111 010587
30. Lacerda, C. M.; Xin, L.; Rogers, I.; Reardon, K. F. Analysis of iTRAQ data using Mascot and Peaks quantification algorithms Briefings Funct. Genomics Proteomics 2008, 7 (2) 119-26
31. Agusti, A.; MacNee, W.; Donaldson, K.; Cosio, M. Hypothesis: does COPD have an autoimmune component? Thorax 2003, 58 (10) 832-4
32. Chung, K. H.; Ryu, J. K.; Oh, H. S.; Seo, J. Y.; Jin, E.; Lee, D. H.; Kim, Y. T.; Yoon, Y. B. Pancreatic pseudocyst after endoscopic ultrasound-guided fine needle aspiration of pancreatic mass Clin. Endosc. 2012, 45 (4) 431-4
33. Seymour, S.; Hunter, C. L. ProteinPilot Descriptive Statistics Template; ABSCIEX, Framingham, MA, 2013; available from http://www.absciex.com/PDST.
34. Ow, S. Y.; Salim, M.; Noirel, J.; Evans, C.; Rehman, I.; Wright, P. C. iTRAQ underestimation in simple and complex mixtures: ″the good, the bad and the ugly″ J. Proteome Res. 2009, 8 (11) 5347-55
35. Karp, N. A.; Huber, W.; Sadowski, P. G.; Charles, P. D.; Hester, S. V.; Lilley, K. S. Addressing accuracy and precision issues in iTRAQ quantitation Mol. Cell. Proteomics 2010, 9 (9) 1885-97
36. Yang, Y.; Qiang, X.; Owsiany, K.; Zhang, S.; Thannhauser, T. W.; Li, L. Evaluation of different multidimensional LC-MS/MS pipelines for isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis of potato tubers in response to cold storage J. Proteome Res. 2011, 10 (10) 4647-60