25 Percent of Labs Successfully ID 20 Proteins in HUPO Protein Standard Effort
SEOUL — Only six of the 24 laboratories who participated in HUPO’s protein standard mixture initiative were able to identify all 20 equimolar proteins properly without help from the organization, HUPO officials said this week.
In August, John Bergeron, immediate past president of HUPO, told ProteoMonitor that the participating labs had experienced difficulties identifying the proteins [See PM 09/06/07]. This week, officials provided further details of the extent of the problems they encountered.
The 18 laboratories that could not identify the proteins experienced issues ranging from undersampling to inappropriately high stringents to trypsinization. The major bottleneck, Bergerson said, was matching mass spectra with peptides in databases.
Despite the low success rate, Bergeron said that the problems encountered were “trivial” and easily fixed. He and others involved on the initiative are currently drafting a paper on their study.
When that is completed and published, they will move on to another test sample of 20 proteins with three orders of dynamic range and two orders of relative abundance.
Human Protein Atlas 3.0 Released at HUPO
SEOUL — The third version of the Human Protein Atlas was released this week here at the Human Proteome Organization’s 6th Annual World Congress.
HPA 3 contains 2.8 million images corresponding to 2,618 proteins and 3,015 antibodies.
New features for the atlas include validation data for the antibodies based on protein arrays and Western blots, and an advanced search function allowing tissue-specific profiling to facilitate in silico biomarker discovery.
In addition, the atlas contains immunofluorescent images of three human cell lines using confocal microscopy. Currently, 769 antibodies have subcellular localization mapped using the confocal approach, said Matthias Uhlen from AlbaNova University in Stockholm and the head of the HPA project.
Uhlen said that the HPA effort aims to generate data for 8,000 proteins by 2009 and to generate a draft version of the complete proteome by 2015.