The Global Proteome Machine Organization
   News Archive

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

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 (2006/10/25)

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 and 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:

  6.; and

Updates for X! Series search engines (2006/9/17)

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.

  1. 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.
  2. 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.
  3. 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.
  4. 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 (2006/9/11)

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. (Full Text).

System outage (2006/9/11)

Because of a hacker breakin, the servers,, and will be out of service for most of today as we reinstall software and make the necessary security adjustments.

PepSeeker links added (2006/7/19)

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 (see Abstract). 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 (2006/7/18)

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 proteomics technique.

Addition of Neurospora crassa (2006/7/18)

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 are available from the GPM ftp site.

Change in honey bee sequences (2006/7/10)

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 ( and bee_e.fasta.gz) 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 (2006/7/5)

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 (Abstract).

Mannose-6-phosphate modification in lysosomal proteins (2006/6/27)

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 (2006/6/27)

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 (2006/6/22)

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 (Abstract).

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 (2006/5/26)

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 Biology.

GPM used to understand plant resistance to insects (2006/5/15)

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 PNAS.

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 projects;
  • 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 repository.
  • 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

    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,

    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

    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

    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 features.

    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