Analyses of human plasma and serum proteomes using HUPO filter criteria

All the data described above were analyzed using the XCorr DCn Sf criteria. From experience, we know that a substantial number ofthe proteins identified by a single peptide using these criteria are incorrect and the probability of a protein being correctly identified increases with the number of unique peptides identified. However, for biomarker discovery it is better to have a less stringent filter so that potentially interesting low-abundance proteins will not be excluded from the analysis....

Reference materials

Reference materials (RMs) are applied in a variety of analytical procedures to perform harmonized quantifications of analytes. Methods can be standardized by the use of common RMs 30 . The use of international RMs ensures world wide uniformity in most analytical measurements and provides users with reliable and comparable quantitative information based on operationally defined conventional true values in the sense of a gold standard of the certified analytes. The agreement of a measured average...

Systematic protein array pixelation of the human serum proteome

Protein array pixelation of the HUPO serum sample, BDCA02-Serum, was performed using a method similar to that used for the plasma sample, except this method incorporated several refinements to further improve coverage of the pro-teome (Fig. 5A). The major protein depletion was performed on 415 mL (35.3 mg) of serum using a dual MARS column. A total of 4.3 mg of unbound proteins were recovered, indicating that approximately 88 of the total serum protein content was removed in this sample...

HUPO reference sample collection protocol

HUPO reference samples were collected at, and using materials from BD Diagnostics. For each ethnic group (Caucasian, Asian American, African American), blood was acquired by venipuncture from one male donor and one female donor. Donors were tested and determined negative for HIV-1 and HIV-2 antibody, HIV-1 antigen (HIV-1), Hepatitis B surface antigen (HBsAg), Hepatitis B core antigen (anti-HBc), Hepatitis C virus (anti-HCV), HTLV-I II antibody (anti-HTLV-I II), and syphilis. Blood intended for...

Systematic protein array pixelation ofthe human plasma proteome

The profiling of human plasma proteome began with major protein depletion from a total of 193 mL (14.5 mg) plasma (BDCA02-Heparin) using the MARS antibody column (Fig. 3A). Following depletion, 2.4 mg of unbound proteins were recovered, indicating that the six targeted proteins constituted approximately 83 of plasma proteins in this sample. Analysis ofthe bound fraction by 2-DE showed that the bound proteins were the six targeted proteins with no apparent evidence of other proteins 9 . The...

Dr Eric W Deutsch

Institute for Systems Biology, 1441 N 34th Street, Seattle, Overview of the HUPO Plasma Proteome Project Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of3020 proteins and a publicly-available database 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,...