TY - JOUR
T1 - A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas
AU - Farrah, Terry
AU - Deutsch, Eric W.
AU - Omenn, Gilbert S.
AU - Campbell, David S.
AU - Sun, Zhi
AU - Bletz, Julie A.
AU - Mallick, Parag
AU - Katz, Jonathan E.
AU - Malmström, Johan
AU - Ossola, Reto
AU - Watts, Julian D.
AU - Lin, Biaoyang
AU - Zhang, Hui
AU - Moritz, Robert L.
AU - Aebersold, Ruedi
PY - 2011/1/1
Y1 - 2011/1/1
N2 - Human blood plasma can be obtained relatively noninvasively and contains proteins from most, if not all, tissues of the body. Therefore, an extensive, quantitative catalog of plasma proteins is an important starting point for the discovery of disease biomarkers. In 2005, we showed that different proteomics measurements using different sample preparation and analysis techniques identify significantly different sets of proteins, and that a comprehensive plasma proteome can be compiled only by combining data from many different experiments. Applying advanced computational methods developed for the analysis and integration of very large and diverse data sets generated by tandem MS measurements of tryptic peptides, we have now compiled a high-confidence human plasma proteome reference set with well over twice the identified proteins of previous high-confidence sets. It includes a hierarchy of protein identifications at different levels of redundancy following a clearly defined scheme, which we propose as a standard that can be applied to any proteomics data set to facilitate cross-proteome analyses. Further, to aid in development of blood-based diagnostics using techniques such as selected reaction monitoring, we provide a rough estimate of protein concentrations using spectral counting. We identified 20,433 distinct peptides, from which we inferred a highly nonredundant set of 1929 protein sequences at a false discovery rate of 1%. We have made this resource available via PeptideAtlas, a large, multiorganism, publicly accessible compendium of peptides identified in tandem MS experiments conductedby laboratories around the world.
AB - Human blood plasma can be obtained relatively noninvasively and contains proteins from most, if not all, tissues of the body. Therefore, an extensive, quantitative catalog of plasma proteins is an important starting point for the discovery of disease biomarkers. In 2005, we showed that different proteomics measurements using different sample preparation and analysis techniques identify significantly different sets of proteins, and that a comprehensive plasma proteome can be compiled only by combining data from many different experiments. Applying advanced computational methods developed for the analysis and integration of very large and diverse data sets generated by tandem MS measurements of tryptic peptides, we have now compiled a high-confidence human plasma proteome reference set with well over twice the identified proteins of previous high-confidence sets. It includes a hierarchy of protein identifications at different levels of redundancy following a clearly defined scheme, which we propose as a standard that can be applied to any proteomics data set to facilitate cross-proteome analyses. Further, to aid in development of blood-based diagnostics using techniques such as selected reaction monitoring, we provide a rough estimate of protein concentrations using spectral counting. We identified 20,433 distinct peptides, from which we inferred a highly nonredundant set of 1929 protein sequences at a false discovery rate of 1%. We have made this resource available via PeptideAtlas, a large, multiorganism, publicly accessible compendium of peptides identified in tandem MS experiments conductedby laboratories around the world.
UR - http://www.scopus.com/inward/record.url?scp=79959499115&partnerID=8YFLogxK
U2 - 10.1074/mcp.M110.006353
DO - 10.1074/mcp.M110.006353
M3 - Article
C2 - 21632744
AN - SCOPUS:79959499115
SN - 1535-9476
VL - 10
JO - Molecular and Cellular Proteomics
JF - Molecular and Cellular Proteomics
IS - 9
ER -