Exploring the human plasma proteome.

The Human Proteome Organization (HUPO) has launched several major initiatives to explore the proteomes of liver, brain, and plasma and to generate informatics standards and large-scale antibody production. This issue of PROTEOMICS presents 28 papers from the pilot phase of the Human Plasma Proteome Project. The papers represent a combination of collaborative analyses of HUPO PPP reference specimens and many lab-specific special projects, both experimental and analytical. Plasma (or serum) will be the preferred specimen for non-invasive sampling of normal individuals and patients for biomarkers discovered and validated to reflect physiological, pathological, and pharmacological phenotypes. As is well-recognized, however, plasma presents enormous challenges due to the extreme complexity reflecting potentially all proteins in the body and their isoforms, at least ten orders of magnitude range in concentration, intra-individual and inter-individual variation, and non-standardized methods of sample processing. Furthermore, the inherent limitations of incomplete sampling of peptides by mass spectrometry and potentially high error rates of peptide identifications and protein assignments with various search algorithms and databases lead to low concordance of protein identifications even with repeat analyses of the same sample. Together these papers examine many features of specimen handling, depletion of abundant proteins, fractionation of intact proteins, fractionation of tryptic digest peptides, and analysis of those peptides with various MS/MS instruments. The subsequent steps of matching spectra to peptide sequences with a variety of search algorithms that have numerous and often unspecified parameters, followed by alignment of peptide sequences with proteins in a variety of protein or gene databases, laden with uncertainties and redundancies, are explored in considerable depth. Especially for longitudinal and collaborative studies, the periodic issuance of remarkably modified versions of the databases creates a moving target for protein identification and annotation. These reports provide a revealing snapshot of the variety of proteomics technologies as of 2004 and the variable depth of analysis across laboratories. Subproteomes based on molecular weight or glycoprotein enrichment yielded additional findings. The extensive annotations show that even our present methods are capable of detecting large numbers of low-abundance proteins of great biological interest from essentially all cellular compartments. As more powerful technologies are applied, we can expect ever more extensive identifications. The high proportion of genes which appear to generate detectable splice isoforms complicates the protein identifications, yet helps to clarify, together with myriad post-translational modifications of proteins, the basis on which humans can have such complex phenotypes with a surprisingly small complement of genes (latest Human Genome Project estimate about 22,000 protein-encoding genes). The PPP datasets offer a rich resource for many follow-on analyses, as illustrated here, and an anchor for new studies. We provide a Core Dataset of 3020 proteins identified with two or more peptides and remaining after integration of protein matches which cannot be distinguished with the available peptides. Numerous other “cuts” of the data can be made. Extensive primary data and analytical results are EDITORIAL