The Global Proteome Machine
Organization Proteomics Database and Open Source
Software www.thegpm.org
Welcome!
The Global Proteome Machine Organization was set up so that
scientists involved in proteomics using tandem mass
spectrometry could use that data to analyze proteomes. The
projects supported by the GPMO have been selected to improve
the quality of analysis, make the results portable and to
provide a common platform for testing and validating proteomics
results.
Latest
GPM News
Data set of the week: (2010/07/25) Proteomic analysis of the secretome of human umbilical vein endothelial cells using a combination of free-flow electrophoresis and nanoflow LC-MS/MS.
This data set contains a single
LC/MS/MS data set, using a combination of free-flow electrophoresis and nanoflow HPLC separations.
The original raw data was made available as a Scaffold file from a web site maintained by the authors (www.vascular-proteomics.com).
It was published by Tunica DG, Yin X, Sidibe A, Stegemann C, Nissum M, Zeng L, Brunet M, and Mayr M in
Proteomics. 2009, 9:4991-6 (PubMed).
This study attempts to discover a difficult thing: the secretome of human umbilical vein endothelial cells in the face
of the background proteins in a complex growth medium. The
results provide a good basis for the examination of this important cell type, with a very good set of
identifications that provides a broad survey of the proteins that can be readily obtained
from these cells.
Additions to the S. cerevisiae proteome (2010/07/21).
As has been mentioned several times in the Data Set of Week announcements, proteins from the two viruses
Saccharomyces cerevisiae virus L-A (L1) and Saccharomyces cerevisiae virus L-BC (La) have
been very commonly observed in proteomics data sets obtained from S. cerevisiae. The
signals associated with peptides from these viruses can be quite strong, so it is our belief that
not including the proteome of these viruses when searching S. cerevisiae data may lead to missed (or misinterpreted)
identifications. Therefore, the proteome of S. cerevisiae has been altered on all of the GPM public
search sites to include the proteomes of these viruses
(NC_003745 and
NC_001641) by default.
These two viruses contain a total of five (5)
proteins, so there will be little impact on the overall search speed caused by this proteome-level change.
New X! Hunter Annotated Spectrum Libraries for model species available (2010/07/20).
The most recent versions the the Annotated Spectrum Libraries for H. sapiens, M. musculus,
R. norvegicus, S. cerevisiea, D. melanogaster and C. elegans are now available
at the X! Hunter project ftp site. These
libraries use the ENSEMBL v. 58 protein sequences. Specifics of the build are available at the ASL
statistics page. The libraries are available for searches at the X! Hunter
server.
Data set of the week: (2010/07/18) Proteomics Analysis of the Causative Agent of Typhoid Fever.
This data set contains 313
LC/MS/MS runs using Thermo LTQ mass spectrometers.
The original raw files originally from the Resource Center for Biodefense Proteomics Research, which
has been superceded by the Pathogen Portal (raw data).
It was published by Ansong C, Yoon H, Norbeck AD, Gustin JK, McDermott JE, Mottaz HM, Rue J, Adkins JN, Heffron F, and Smith RD in
J Proteome Res. 2008, 7:546-57 (PubMed).
This very thorough data set is the primary large collection of information that has allowed for the
creation of the rather comprehensive annotated spectrum libraries that are now available for
S. enterica related species, including S. typhi and S. typhimurium. The Pacific Northwestern
National Laboratory group was an early proponent of making publicly-funded proteomics raw data widely available and
their efforts legitimized the idea for many other groups.
Data set of the week: (2010/07/11) Discovery of Anthrax Biomarkers Using Label-Free Quantitative Phosphoproteomics via Mass Spectrometry.
This data set contains 66 individual phosphopeptide enriched
LC/MS/MS runs made using a Thermo Orbitrap hybrid mass spectrometer.
The original raw files were transferred from TRANCHE.
The data was credited to Nathan P. Manes, Li Dong, Weidong Zhou, Xiuxia Du, Nikitha Reghu, Arjan C. Kool,
Dahan Choi, Charles L. Bailey, Emanuel F. Petricoin III, Lance A. Liotta, and Serguei G. Popov.
It was made available prior to publications, although some part of the data was presented at the 2010 ASMS conference.
The analyzed results are simply the best, most consistent set of phosphopeptide results that we have ever seen.
The combination of sample preparation, HPLC and mass spectrometry used by the authors has generated
what can only be considered a milestone in the application of phospho-proteomics technique to
real tissue samples.
X! Hunter Annotated Spectrum Libraries for 115 prokaryote and 4 virus proteomes are now available
The X! Hunter ASL collection of bacterial proteome libraries has been expanded from the original 16 species to now include 115 prokaryote species and strains.
The new species include important pathogenic organisms, such as Shigella dysenteriae, Yersinia pestis and Brucella abortus. The new release
also includes 30 individual strains of Escherichia coli. This update of the ASL collection has, for the first time, libraries for four viruses:
Data set of the week: (2010/07/04) Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions.
This data set contains 61 individual experiments using
both SILAC and label-free quantitation. The experimental protocols used either trypsin or endo-LysC to digest
the proteins, depending on the type of protocol being used.
The original raw files were transferred from TRANCHE via ProteomExchange.
The data was published by Hubner NC, Bird AW, Cox J, Splettstoesser B, Bandilla P, Poser I, Hyman A, Mann M in
J Cell Biol. 2010 189:739-54 (PubMed).
The data was generated to demonstrate the utility of a new technique for protein quantitation
developed by the authors: "quantitative BAC-green fluorescent protein interactomics" (QUBIC). The
technique is meant to be applied to the quantitative study of protein-protein interactions, several of
which are demonstrated here. The technical quality of the MS/MS data is excellent, with many ids for individual proteins
in the top 10% of all GPMDB observations.
Video tutorial (2010/07/03): Finding phosphorylation sites using GPMDB
We have started to make a set of tutorial videos to explain how to use GPMDB for common
biomedical research tasks. The first video in this set describes the steps necessary to
find the observed phosphorylation sites for a particular protein. The description is in
the form of a casual conversation between a biomedical researcher (as played by HRM Queen Elizabeth II) and
a GPMDB power user (Beavo the clown), during a chance meeting at the dépanneur. We will be releasing these videos as they
are produced. Please see our new tutorials page to
check for new videos.
