A Systematic Analysis of Eluted Fraction of Plasma Post Immunoaffinity Depletion: Implications in Biomarker Discovery
作者： Amit Kumar Yadav , Gourav Bhardwaj , Trayambak Basak , Dhirendra Kumar , Shadab Ahmad
DOI: 10.1371/JOURNAL.PONE.0024442
关键词:
摘要: Plasma is the most easily accessible source for biomarker discovery in clinical proteomics. However, identifying potential biomarkers from plasma a challenge given large dynamic range of proteins. The are generally present at very low abundance levels and hence identification these proteins necessitates depletion highly abundant Sample pre-fractionation using immuno-depletion high multi-affinity removal system (MARS) has been popular method to deplete multiple can result concomitant Although there some reports suggesting non-targeted proteins, predominant view that number such small. In this study, we identified removed along with targeted Three samples were depleted each three MARS (Hu-6, Hu-14 Proteoprep 20) cartridges. affinity bound fractions subjected gelC-MS an LTQ-Orbitrap instrument. Using four database search algorithms including MassWiz (developed house), selected peptides <1% FDR. Peptides by least two protein identification. After rigorous bioinformatics analysis, 101 confidence. Thus, believe proper quantitation it might be better study both any sample.
harvard.edu
paperity.org
core.ac.uk 参考文章(49)
T. S. Keshava Prasad, Kumaran Kandasamy, Akhilesh Pandey, Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods of Molecular Biology. ,vol. 577, pp. 67- 79 ,(2009) , 10.1007/978-1-60761-232-2_6
Babylakshmi Muthusamy, G Hanumanthu, Shubha Suresh, B Rekha, D Srinivas, L Karthick, BM Vrushabendra, Salil Sharma, Goparani Mishra, Pritam Chatterjee, KS Mangala, HN Shivashankar, KN Chandrika, Nandan Deshpande, M Suresh, N Kannabiran, Vidya Niranjan, Anuradha Nalli, TS Keshava Prasad, KS Arun, Raghunath Reddy, Sreenath Chandran, Trafina Jadhav, D Julie, M Mahesh, S Lynate John, Kshitish Palvankar, D Sudhir, P Bala, NS Rashmi, G Vishnupriya, Kaushik Dhar, S Reshma, Raghothama Chaerkady, TKB Gandhi, HC Harsha, S Sujatha Mohan, Krishna S Deshpande, Malabika Sarker, Akhilesh Pandey, None, Plasma Proteome Database as a resource for proteomics research Proteomics. ,vol. 5, pp. 3531- 3536 ,(2005) , 10.1002/PMIC.200401335
Peter Juhasz, Moira Lynch, Mahadevan Sethuraman, Jennifer Campbell, Wade Hines, Manuel Paniagua, Leijun Song, Mahesh Kulkarni, Aram Adourian, Yu Guo, Xiaohong Li, Stephen Martin, Neal Gordon, Semi-targeted plasma proteomics discovery workflow utilizing two-stage protein depletion and off-line LC-MALDI MS/MS. Journal of Proteome Research. ,vol. 10, pp. 34- 45 ,(2011) , 10.1021/PR100659E
Gilbert S Omenn, David J States, Marcin Adamski, Thomas W Blackwell, Rajasree Menon, Henning Hermjakob, Rolf Apweiler, Brian B Haab, Richard J Simpson, James S Eddes, Eugene A Kapp, Robert L Moritz, Daniel W Chan, Alex J Rai, Arie Admon, Ruedi Aebersold, Jimmy Eng, William S Hancock, Stanley A Hefta, Helmut Meyer, Young‐Ki Paik, Jong‐Shin Yoo, Peipei Ping, Joel Pounds, Joshua Adkins, Xiaohong Qian, Rong Wang, Valerie Wasinger, Chi Yue Wu, Xiaohang Zhao, Rong Zeng, Alexander Archakov, Akira Tsugita, Ilan Beer, Akhilesh Pandey, Michael Pisano, Philip Andrews, Harald Tammen, David W Speicher, Samir M Hanash, None, Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. ,vol. 5, pp. 3226- 3245 ,(2005) , 10.1002/PMIC.200500358
Karin Björhall, Tasso Miliotis, Pia Davidsson, Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics. ,vol. 5, pp. 307- 317 ,(2005) , 10.1002/PMIC.200400900
Wan-Yu Lo, Chien-Chen Lai, Chun-Hung Hua, Ming-Hsui Tsai, Shiuan-Yi Huang, Chang-Hai Tsai, Fuu-Jen Tsai, S100A8 Is Identified as a Biomarker of HPV18-Infected Oral Squamous Cell Carcinomas by Suppression Subtraction Hybridization, Clinical Proteomics Analysis, and Immunohistochemistry Staining Journal of Proteome Research. ,vol. 6, pp. 2143- 2151 ,(2007) , 10.1021/PR060551+
Matthew P. Welberry Smith, Steven L. Wood, Alexandre Zougman, Jenny T. C. Ho, Jianhe Peng, David Jackson, David A. Cairns, Andrew J. P. Lewington, Peter J. Selby, Rosamonde E. Banks, 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. ,vol. 11, pp. 2222- 2235 ,(2011) , 10.1002/PMIC.201100005
Lei Huang, Gulia Harvie, Jerald S. Feitelson, Kosi Gramatikoff, David A. Herold, David L. Allen, Ravi Amunngama, Rachel A. Hagler, Michael R. Pisano, Wei-Wei Zhang, Xiangming Fang, Immunoaffinity separation of plasma proteins by IgY microbeads: meeting the needs of proteomic sample preparation and analysis. Proteomics. ,vol. 5, pp. 3314- 3328 ,(2005) , 10.1002/PMIC.200401277
Ruben K. Dagda, Tamanna Sultana, James Lyons-Weiler, Evaluation of the Consensus of Four Peptide Identification Algorithms for Tandem Mass Spectrometry Based Proteomics. Journal of Proteomics & Bioinformatics. ,vol. 3, pp. 39- 47 ,(2010) , 10.4172/JPB.1000119
Ming Zhou, David A. Lucas, King C. Chan, Haleem J. Issaq, Emanuel F. Petricoin, Lance A. Liotta, Timothy D. Veenstra, Thomas P. Conrads, An investigation into the human serum "interactome". Electrophoresis. ,vol. 25, pp. 1289- 1298 ,(2004) , 10.1002/ELPS.200405866