Prokaryote sequences updated (2006/12/08)
The prokaryote search site has
been updated from the NCBI site, including updated sequences for many common
prokaryotes, as well as some new species, such as Mycobacterium smegmatus.
These sequences have been added to those available at the GPM prokaryote sequence ftp site.
New site for ABRF PRG search (2006/11/30)
At the request of Brett Phinney, we have set up a site specifically for
use with ABRF Proteomics Research Group (PRG).
This site uses the protein sequences involved in the PRG 2007 study (prg.fasta.gz).
You can find the site at http://prg.thegpm.org.
Weather problems (2006/11/27)
Because of a severe winter storm, the GPM servers located in Vancouver BC were unavailable for most of
the day, November 27, 2006. This was caused by a general power failure at the University of British Columbia
that shut down the University's computer network.
Addition of the Universal Protein Standard to cRAP (2006/11/19)
The common Respository of Adventious Proteins (cRAP) has been updated to include the UniProt
sequences corresponding to the Sigma-Aldrich Universal Protein Standard UPS1 set of proteins.
The accession numbers and identity of the proteins are listed on the cRAP
project page. All of the GPM public identification servers have been updated to reflect these changes. The
main cRAP FASTA file as well as a separate file containing only the UPS1 sequences can be
obtained from the GPM FTP site.
Updates for X! Series search engines
Minor updates to the 2006.09.15 release of the X! Series search engines are now
available. These changes improve X! Tandem and P3 compatibility with ECD/ETD spectra. We'd
like to thank Brett Phinney for supplying the necessary experimental data that has
allowed us to improve the results for these spectra. New versions of peptide.pl and
peptide_studio.pl are available that properly markup the c and z ions generated by
these ion sources.
System maintenance service interuptions (2006/10/16)
Because of planned maintenance in one of our data centres, some servers may be difficult
to reach on the afternoon of Oct. 16 and the morning of Oct. 17. The affected servers are:
- xhunter.thegpm.org; and
Updates for X! Series search engines
New versions of the X! Series search engines have been released, all with
the version number 2006.09.15. These changes have been consolidated into a
new release of the GPM-XE system.
- X! Tandem and X! P3. No changes have been made to the functionality
of the search engines. The changes made to these projects are to improve the
cross-platform compatibility of the projects and to conform to the latest
security updates from Microsoft for the Windows versions.
- X! Hunter. Changes have been made to the scoring model, incorporating
information about the original assignment confidence of a particular library
spectrum to its associated peptide. Several other changes have been
made to improve memory usage and overall execution speed.
- X! Hunter ASL creation/curation system. We have released the full system
that we use internally to create the Annotated Spectrum Libraries used by
X! Hunter. This system can be used to generate a custom ASL library from
any GPMDB installation. Please refer to the installation documentation
for any site-specific requirements for this release.
- X! Hunter ASL file format. The format for the ASL
library files has been updated to add the information necessary for the change
in the scoring model. The new format is defined here.
A new role for AP2-gamma
Harry and Mary Lynn Duckworth and their collaborators at the University of Manitoba
used the GPM to provide the first direct evidence for the involvement of a placental-specific
transcription factor in the regulation of a member of this gene family.
They reported the work in Endocrinology 2006, 147, 4319.
Because of a hacker breakin, the servers h451.thegpm.org, mouse.thegpm.org,
rat.thegpm.org and xhunter.thegpm.org will be out of service for most of today as
we reinstall software and make the necessary security adjustments.
PepSeeker links added
A multidisciplinary group at the University of Manchester, lead by
Simon J. Gaskell and Simon J. Hubbard, have developed a new proteomics database
called PepSeeker. This database was designed mainly to aid in the
development of new theoretical understanding of gas phase peptide chemistry
GPM spectrum display pages now have links that allow the user to see the evidence
in Pepseeker for the peptide being displayed.
X! Hunter annotated spectrum library paper published
A manuscript describing X! Hunter Annotated Spectrum Library (ASL) searches has been published
on the ASAP section of the Journal of Proteome Research (Abstract).
This paper describes the details of how the ASLs are compiled from the data in the GPMDB and
explains the architecture of the underlying informatics. An example contrasting ASL and
conventional protein identification demonstrates some of the unique features of this new type of
Addition of Neurospora crassa
The model organism GPM search sites have
been updated to include the bread mould Neurospora crassa OR74A.
The sequences correspond to the Entrez May 2006 version of the genome. The sequence files
(n_crassa.fasta and n_crassa.fasta.pro) are available from the GPM
Change in honey bee sequences
ENSEMBL has dropped honey bee from its list of supported species. Since
the GPM search sites use honey bee ENSEMBL accessions, we had switched to
the NCBI version of the honey bee genome. The new honey bee sequence files
are available from our FTP site. All of our search sites have
been updated to use the new sequence set.
Peroxisomes role in yeast lipid metabolism
Joel M. Goodman and his collaborators at the University of Texas Southwestern Medical School
and University of North Texas used X! Tandem to demonstrate the previously unappreciated
coupling of yeast peroxisomes and lipid bodies. They were able to demonstrate that yeast utilizes
both the lipolysis capabilities of the lipid bodies and the oxidative apparatus of the peroxisomes
in its normal metabolism of lipids. They have reported this work in J. Cell Biol. 2006, 173, 719
Mannose-6-phosphate modification in lysosomal proteins
David E Sleat, Haiyan Zheng, Meiqian Qian, and Peter Lobel at the
Center for Advanced Biotechnology (UMDNJ) have used the GPM
to analyze the distribution of mannose-6-phosphate modifications
on lysosomal proteins. This unusual modification is used to
target proteins made in the cytosol to be transported into
lysosomes. They reported this work in Molecular & Cellular Proteomics 2006, 5, 686 (Abstract).
HUPO announces the end of mzData
In a recent press release, HUPO-PSI announced its intention to
discontinue its mzData format for representing mass spectrometry data. In its place, a new format will be developed to merge mzXML and mzData into
a common representation. Therefore, all GPM development on mzData will be frozen at its current implementation.
Chemotaxis receptor concensus methylation sites
Eduardo Perez, Haiyan Zheng, and Ann M. Stock from the UMDNJ-Robert Wood Johnson
Medical School have used the GPM to study post-translational modifications of
the chemotaxis receptors in Thermotoga maritima. They discovered that
methylation of these important proteins occurs at different sites in T. maritima
than in enterobacteria. They have reported their results in the Journal of
Bacteriology, 2006, 188, 4093 (Abstract).
GPM used to analyze wheat organelle (2006/6/21)
In a collaboration between groups at UC Berkeley and the USDA's Western Regional
Research Center, the GPM was used to characterize the proteins present in wheat
amyloplasts. These organelles are used to synthesize starch in most plants. The
results were published in the Journal of Experimental Biology, 2006, 57, 1591
Mouse and zebrafish sequence updates (2006/6/20)
The files for mouse and zebrafish ENSEMBL protein sequences have been updated to
the most recent version of NCBI m36 (mouse) and Zv6 (zebrafish) available from
ENSEMBL build 39.
Service interuption (2006/6/15)
Maintenance work in one of our data centres will result in some servers being
unavailable during the hours of 16:00 to 20:00 CDT on June 15.
OSA1, release 4 now available (2006/6/13)
All of the GPM servers that provide access to the O. sativa have been
updated to the TIGR release 4.0 of the proteome. For more information on this
release, please check the TIGR rice
genome web site.
TAIR 6 now available (2006/6/9)
All of the GPM servers that provide access to the A. thaliana have been
updated to the TAIR version 6.0 of the proteome. This replaces the TIGR version
5.0, which has been available since the inception of the GPM. For more
information on this release, please check the
TAIR web site.
New versions of X! series search engines available
The 2006.06.01 versions of the X! series protein identification search engines
are now available at our ftp site.
All three search engines (X! Tandem, X! P3 and X! Hunter) have been updated to
fix a problem with data obtained from a variant of mzXML spectrum files that do
not contain information about a spectrum's parent ion charge. In previous
versions, the search was performed correctly, but there were circumstances in
which some spectra would not be displayed properly using the GPM interface
software. Thanks to Paul Taylor for pointing out this problem.
X! Tandem used for novel gene detection (2006/5/15)
David States and his colleagues at the University of Michigan have developed a
method using X! Tandem to discover novel genes using proteomics data. They have
published their results in a study entitled "Novel gene and gene model
detection using a whole genome open reading frame analysis in proteomics"
in the open access journal Genome
GPM used to understand plant resistance to insects
Brett Phinney and collaborators recently used some of the unique features of the
GPM to discover a previously unknown mechanism by which plants defend
themselves against insect herbivores. The resulting paper
"Jasmonate-inducible plant enzymes degrade essential amino acids in the
herbivore midgut" was published as a featured article
Launch of new FTP site (2006/5/1)
In response to a number of suggestions made by users and contributors, we have
updated and rationalized our FTP site and software distribution system. The new
FTP site is organized into the following main folders:
data - contains mass spectra and collections of identifications;
fasta - contains the current versions of FASTA and .pro sequence files
used by the public version of the GPM;
projects - contains source code release distributions for GPM-related
proteotypic_peptide_profiles - contains FASTA files with lists of the
peptides normally observed in proteomics; and
repos - contains the current contents of the GPM Subversion Source code
We have also updated our Subversion source code repository to a new version and
a new server. If you already have the Subversion client installed, you will
have to "check out" the code again: simply updating the existing copy
will not work properly. Simply change directories into where you wish to
install the new repository and type the following line:
svn co http://source.thegpm.org/repos
This should create a new copy of the repository on your computer.
Source code repository maintenance (2006/4/29)
In an effort to improve service, we will be doing some maintenance work on the
GPM Subversion code repository, April 29 - May 1, 2006. The repository will be
unavailable during this period. The contents of the repository have been made
available on our ftp site, ftp://ftp.thegpm.org/repos.
X! Hunter now available (2006/4/18)
A version of the X! Hunter spectrum matching algorithm is now available, written
in the same style and using the same interface as X! Tandem. The source code
for Windows, Linux and OS X are available, as well as the annotated spectrum
libraries, from ftp://ftp.thegpm.org/projects/xhunter.
This version of X! Hunter compares experimentally observed spectra to annotated
libraries of averaged peptide spectra, obtained from GPMDB. Libraries are
available for human, brewer's yeast, mouse and thale cress.
If you would like to try this updated version, an experimental server has been
set up at h201.thegpm.org.
New version of X! Tandem available (2006/4/18)
A new version of X! Tandem (2006.04.01.2) is now completely tested and
available. Most of the changes are
associated with extending options available through the applications' user
interface. This version also brings together the code to create X! Tandem and
the proteotypic peptide profiling accelerated engine X! P3.
Denial of Service Attack (2006/2/27)
GPMDB experienced a malicious Denial of Service attack (DOS
explained) over the weekend, which made contacting the server
difficult. We are in the process of ensuring that it doesn't happen again, but
there may be some short periods of service interuption for the next day or two.
No damage was caused by the attack: it only affects the availability of a web
server for external requests.
New version of X! Tandem available (2006/2/13)
The latest version of X! Tandem (2006.2.01) is now available for download from
the GPM FTP site. The new
version is a maintenance release: the changes from the previous release are
minor and meant to improve performance and consistency, rather than to add new
Final recommendations of the Paris Committee (2006/2/12)
Last year, a committee composed of members of the editorial boards of the major
proteomics journals met in Paris to discuss what types of information should be
required for the publication of proteomics results. The meeting and its goals
were described in a recent
JPR editorial. The final version of these recommendations is available
here. This report is part of an ongoing process of collaboration
between the journals, with the intent of keeping these recommendations
up-to-date as the techology and practice of proteomics evolves.
Copyright © 2006, The Global Proteome Machine Organization