Cardiovascular‐related proteins identified in human plasma by the HUPO Plasma Proteome Project Pilot Phase

Berhane, Beniam T.; Zong, Chenggong; Liem, David A.; Huang, Aaron; Le, Steven Q.; Edmondson, Ricky D.; Jones, Richard C.; Qiao, Xin; Whitelegge, Julian P.; Ping, Peipei; Vondriska, Thomas M.

doi:10.1002/pmic.200401308

Cited by 79 publications

(30 citation statements)

References 24 publications

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“…Berhane et al [57] focused on 345 proteins of particular interest for cardiovascular research. They classified the proteins into eight categories, most of which have relevance to other organ systems, as well: markers of inflammation in cardiovascular disease, vasoactive and coagulation proteins, signal transduction pathways, growth and differentiationassociated, cytoskeletal, transcription, channels and receptors, and heart failure and remodeling-related proteins.…”

Section: Annotation Of the Hupo Ppp Core Dataset(s)mentioning

confidence: 99%

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

et al. 2005

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HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics.med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multi- We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches.This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.

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Section: Annotation Of the Hupo Ppp Core Dataset(s)mentioning

confidence: 99%

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

et al. 2005

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“…Out of 3020 proteins identified, 345 proteins were found to have cardiovascular-related functions through manual literature searches [56]. Using a rigorous statistical approach for taking into account the length of coding regions in genes, and multiple hypothesis-testing techniques, a reduced set of 889 proteins was reported with a confidence level of at least 95% [57].…”

Section: Solution Ief/1-de/rp-lc-ms/ms [38] 2-de/maldi-tof-ms/ Msmentioning

confidence: 99%

Human body fluid proteome analysis

2006

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The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, and amniotic fluid, as well as its applications to human disease biomarker discovery. We aim to summarize the proteomics technologies currently used for global identification and quantification of body fluid proteins, and elaborate the putative biomarkers discovered for a variety of human diseases through human body fluid proteome (HBFP) analysis. Some critical concerns and perspectives in this emerging field are also discussed. With the advances made in proteomics technologies, the impact of HBFP analysis in the search for clinically relevant disease biomarkers would be realized in the future.

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“…The proteins present in the albumin-enriched fraction were compared to (i) the comprehensive lists of cardiovascular biomarkers compiled by Anderson [31] and Berhane et al [62] and (ii) to a literature search for other types of biomarkers [31,[62][63][64][65][66][67][68][69][70][71]. The results from these searches are provided in Table 2sup.…”

Section: Biomarker Potentialmentioning

confidence: 99%

Investigation of an albumin‐enriched fraction of human serum and its albuminome

Gundry

Jelinek

et al. 2007

Proteomics Clinical Apps

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The removal of albumin and other high abundance proteins is a routine first step in the analysis of serum and plasma proteomes. However, as albumin can bind proteins and peptides, there is a universal concern as to how the serum proteome is changed by the removal of albumin. To address this concern, the current study was designed to identify proteins and peptides removed from the serum during albumin depletion; to determine which of these are bound to albumin (rather than copurified) and whether the bound proteins are intact proteins or peptide fragments. Sequential, independent analyses including both anti-albumin antibody (anti-HSA) affinity chromatography and SEC were used to isolate albumin-bound proteins. RP-HPLC and 1-D SDS-PAGE were then used to further separate the proteins prior to identification by MS/MS. Finally, whole protein molecular weight (MW) MS measurements coupled with protein coverage obtained by MS were combined to assess whether the bound proteins were intact or peptide fragments. Combining the results from multiple approaches, 35 proteins, of which 24 are intact, were found to be associated with albumin, and they include both known high and low abundance proteins.

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Cardiovascular‐related proteins identified in human plasma by the HUPO Plasma Proteome Project Pilot Phase

Cited by 79 publications

References 24 publications

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

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

Human body fluid proteome analysis

Investigation of an albumin‐enriched fraction of human serum and its albuminome

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