Assessment of two immunodepletion methods: Off-target effects and variations in immunodepletion efficiency may confound plasma proteomics

Journal of Proteome Research

Volumn 11, Issue 12, 2012, Pages 5947-5958

  Patel, Bhavinkumar B ^a   Barrero, Carlos A ^b   Braverman, Alan ^b   Kim, Phillip D ^a   Jones, Kelly A ^a   Chen, Dian Er ^d   Bowler, Russell P ^c   Merali, Salim ^b   Kelsen, Steven G ^b   Yeung, Anthony T ^a  

^a FOX CHASE CANCER CENTER   (United States)

^b TEMPLE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c DEPARTMENT OF MEDICINE   (United States)

^d Sigma Aldrich Co   (United States)

Author keywords

EMMOL normalization; IgY; immunodepletion; iTRAQ; off target; Qproteome; Seppro

Indexed keywords

ALBUMIN; IMMUNOGLOBULIN; PLASMA PROTEIN; RESIN;

ABSORPTION; ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; HUMAN; IMMUNODEPLETION; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; PROTEOMICS; QUANTITATIVE ANALYSIS;

ALBUMINS; BLOOD PROTEINS; HUMANS; IMMUNOASSAY; IMMUNOGLOBULIN G; ISOELECTRIC FOCUSING; MALE; MASS SPECTROMETRY; PEPTIDES; PROTEOMICS; PULMONARY DISEASE, CHRONIC OBSTRUCTIVE; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 84870896177     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr300686k     Document Type: Article

References (28)

1. Anderson, N. L.; Polanski, M.; Pieper, R.; Gatlin, T.; Tirumalai, R. S.; Conrads, T. P.; Veenstra, T. D.; Adkins, J. N.; Pounds, J. G.; Fagan, R.; Lobley, A. The human plasma proteome: a nonredundant list developed by combination of four separate sources Mol. Cell Proteomics 2004, 3 (4) 311-326
2. Burgess-Cassler, A.; Johansen, J. J.; Kendrick, N. Immunodepletion of albumin from human serum samples Clin. Chim. Acta 1989, 183 (3) 359-365
3. Beer, L. A.; Tang, H. Y.; Sriswasdi, S.; Barnhart, K. T.; Speicher, D. W. Systematic discovery of ectopic pregnancy serum biomarkers using 3-D protein profiling coupled with label-free quantitation J. Proteome Res. 2011, 10 (3) 1126-1138
4. Maccarrone, G.; Milfay, D.; Birg, I.; Rosenhagen, M.; Holsboer, F.; Grimm, R.; Bailey, J.; Zolotarjova, N.; Turck, C. W. Mining the human cerebrospinal fluid proteome by immunodepletion and shotgun mass spectrometry Electrophoresis 2004, 25 (14) 2402-2412
5. Shen, Z.; Want, E. J.; Chen, W.; Keating, W.; Nussbaumer, W.; Moore, R.; Gentle, T. M.; Siuzdak, G. Sepsis plasma protein profiling with immunodepletion, three-dimensional liquid chromatography tandem mass spectrometry, and spectrum counting J. Proteome Res. 2006, 5 (11) 3154-3160
6. Koutroukides, T. A.; Guest, P. C.; Leweke, F. M.; Bailey, D. M.; Rahmoune, H.; Bahn, S.; Martins-de-Souza, D. Characterization of the human serum depletome by label-free shotgun proteomics J. Sep. Sci. 2011, 34 (13) 1621-1626
7. Smith, M. P.; Wood, S. L.; Zougman, A.; Ho, J. T.; Peng, J.; Jackson, D.; Cairns, D. A.; Lewington, A. J.; Selby, P. J.; Banks, R. E. A systematic analysis of the effects of increasing degrees of serum immunodepletion in terms of depth of coverage and other key aspects in top-down and bottom-up proteomic analyses Proteomics 2011, 11 (11) 2222-2235
8. Scumaci, D.; Gaspari, M.; Saccomanno, M.; Argiro, G.; Quaresima, B.; Faniello, C. M.; Ricci, P.; Costanzo, F.; Cuda, G. Assessment of an ad hoc procedure for isolation and characterization of human albuminome Anal. Biochem. 2011, 418 (1) 161-163
9. Gundry, R. L.; Fu, Q.; Jelinek, C. A.; Van Eyk, J. E.; Cotter, R. J. Investigation of an albumin-enriched fraction of human serum and its albuminome Proteomics Clin. Appl. 2007, 1 (1) 73-88
10. Juhasz, P.; Lynch, M.; Sethuraman, M.; Campbell, J.; Hines, W.; Paniagua, M.; Song, L.; Kulkarni, M.; Adourian, A.; Guo, Y.; Li, X.; Martin, S.; Gordon, N. Semi-targeted plasma proteomics discovery workflow utilizing two-stage protein depletion and off-line LC-MALDI MS/MS J. Proteome Res. 2011, 10 (1) 34-45
11. Foreman, M. G.; Zhang, L.; Murphy, J.; Hansel, N. N.; Make, B.; Hokanson, J. E.; Washko, G.; Regan, E. A.; Crapo, J. D.; Silverman, E. K.; DeMeo, D. L. Early-onset chronic obstructive pulmonary disease is associated with female sex, maternal factors, and African American race in the COPDGene Study Am. J. Respir. Critical Care Med. 2011, 184 (4) 414-420
12. Han, M. K.; Kazerooni, E. A.; Lynch, D. A.; Liu, L. X.; Murray, S.; Curtis, J. L.; Criner, G. J.; Kim, V.; Bowler, R. P.; Hanania, N. A.; Anzueto, A. R.; Make, B. J.; Hokanson, J. E.; Crapo, J. D.; Silverman, E. K.; Martinez, F. J.; Washko, G. R. Chronic obstructive pulmonary disease exacerbations in the COPDGene study: associated radiologic phenotypes Radiology 2011, 261 (1) 274-282
13. Kim, D. K.; Jacobson, F. L.; Washko, G. R.; Casaburi, R.; Make, B. J.; Crapo, J. D.; Silverman, E. K.; Hersh, C. P. Clinical and radiographic correlates of hypoxemia and oxygen therapy in the COPDGene study Respir. Med. 2011, 105 (8) 1211-1221
14. Kim, V.; Han, M. K.; Vance, G. B.; Make, B. J.; Newell, J. D.; Hokanson, J. E.; Hersh, C. P.; Stinson, D.; Silverman, E. K.; Criner, G. J. The chronic bronchitic phenotype of COPD: an analysis of the COPDGene Study Chest 2011, 140 (3) 626-633
15. Rambod, M.; Porszasz, J.; Make, B. J.; Crapo, J. D.; Casaburi, R. Six-minute walk distance predictors, including CT scan measures, in the COPDGene cohort Chest 2012, 141 (4) 867-875
16. Regan, E. A.; Hokanson, J. E.; Murphy, J. R.; Make, B.; Lynch, D. A.; Beaty, T. H.; Curran-Everett, D.; Silverman, E. K.; Crapo, J. D. Genetic epidemiology of COPD (COPDGene) study design COPD 2010, 7 (1) 32-43
17. Wan, E. S.; Hokanson, J. E.; Murphy, J. R.; Regan, E. A.; Make, B. J.; Lynch, D. A.; Crapo, J. D.; Silverman, E. K. Clinical and radiographic predictors of GOLD-unclassified smokers in the COPDGene study Am. J. Respir. Crit. Care Med. 2011, 184 (1) 57-63
18. Washko, G. R.; Lynch, D. A.; Matsuoka, S.; Ross, J. C.; Umeoka, S.; Diaz, A.; Sciurba, F. C.; Hunninghake, G. M.; San Jose Estepar, R.; Silverman, E. K.; Rosas, I. O.; Hatabu, H. Identification of early interstitial lung disease in smokers from the COPDGene Study Acad. Radiol. 2010, 17 (1) 48-53
19. Geoui, T.; Urlaub, H.; Plessmann, U.; Porschewski, P., Extraction of proteins from formalin-fixed, paraffin-embedded tissue using the Qproteome extraction technique and preparation of tryptic peptides for liquid chromatography/mass spectrometry analysis. Current Protocols in Molecular Biology; Ausubel, F. M., et al., Eds.; 2010, Chapter 10, Unit 10 27, 1-12.
20. 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: MCP 2008, 7 (10) 1963-1973
21. Kim, P. D.; Patel, B. B.; Yeung, A. T. Isobaric Labeling and Data Normalization without Requiring Protein Quantitation J. Biomol. Techn.: JBT 2012, 23 (1) 11-23
22. Lengqvist, J.; Uhlen, K.; Lehtio, J. iTRAQ compatibility of peptide immobilized pH gradient isoelectric focusing Proteomics 2007, 7 (11) 1746-1752
23. 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) 3008-3018
24. Ke, E.; Patel, B. B.; Liu, T.; Li, X. M.; Haluszka, O.; Hoffman, J. P.; Ehya, H.; Young, N. A.; Watson, J. C.; Weinberg, D. S.; Nguyen, M. T.; Cohen, S. J.; Meropol, N. J.; Litwin, S.; Tokar, J. L.; Yeung, A. T. Proteomic analyses of pancreatic cyst fluids Pancreas 2009, 38 (2) e33-42
25. Ishihama, Y.; Oda, Y.; Tabata, T.; Sato, T.; Nagasu, T.; Rappsilber, J.; Mann, M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein Mol. Cell Proteomics 2005, 4 (9) 1265-1272
26. Fanali, G.; di Masi, A.; Trezza, V.; Marino, M.; Fasano, M.; Ascenzi, P. Human serum albumin: from bench to bedside Mol. Aspects Med. 2012, 33 (3) 209-290
27. Lin, V. K.; Wang, S. Y.; Boetticher, N. C.; Vazquez, D. V.; Saboorian, H.; McConnell, J. D.; Roehrborn, C. G. Alpha(2) macroglobulin, a PSA binding protein, is expressed in human prostate stroma Prostate 2005, 63 (3) 299-308
28. Zhang, W. M.; Finne, P.; Leinonen, J.; Salo, J.; Stenman, U. H. Determination of prostate-specific antigen complexed to alpha(2)-macroglobulin in serum increases the specificity of free to total PSA for prostate cancer Urology 2000, 56 (2) 267-272