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What's New
 (Press Release Archive)
 
12 Jun 2008 Our eighth workshop and user meeting was held in Denver on Sunday June 1st 2008, immediately before the 56th ASMS Conference on Mass Spectrometry and Allied Topics. If you were unable to attend, or want to review any of the material that was presented, you can find the slides here.
 
28 Jan 2008 The EST_others database has become so large as to be unmanageable, (24 GB). We have split it into three parts, so there are now five EST databases, in total. If you are not sure which one contains your organism of interest, look it up using the NCBI Taxonomy browser
  • EST_human - TaxID 9606
  • EST_mouse - TaxID 10090
  • EST_chordata (vertebrates other than human and mouse) - TaxID 7711
  • EST_viridiplantae (green plants) - TaxID 33090
  • EST_others (anything not covered above, such as worms, insects, fungi, single-cell organisms, etc.)
 
23 Jan 2008 Press Release announcing the integration of Mascot with Thermo Fisher Scientific's BioWorks software.
 
10 Jan 2008 Happy New Year! We decided to mark the New Year by making Mascot Parser free of charge. If you write applications that use Mascot results, you definitely want to use Mascot Parser. It will make application development much faster and your code will be simpler and easier to debug. Best of all, you don't have to worry about updating your code every time a new version of Mascot is released. For more details, go to the Mascot Parser Product page
 
10 Dec 2007 New help page describing how to configure MSIPI, a database derived from IPI that contains additional information about cSNPs, N-terminus peptides, and known variants, produced by the Max-Planck Institute for Biochemistry at Martinsried and the University of Southern Denmark.
 
14 Nov 2007 Three new training course dates for 2008.
 
17 Oct 2007 Stay up-to-date! A new patch release of Mascot Server is now available.
 
9 Oct 2007 A new version of Mascot Wizard is available for download.
 
23 Aug 2007 Press Release announcing a technical and marketing collaboration between Proxeon and Matrix Science. Proxeon's ProteinCenter and Matrix Science's Mascot software applications will be integrated to facilitate data evaluation by proteomics researchers and, in particular, to enable biologists to make better use of proteomics data.
 
14 Jun 2007 Our seventh workshop and user meeting was held in Indianapolis on Sunday June 3rd 2007, immediately before the 55th ASMS Conference on Mass Spectrometry and Allied Topics. If you were unable to attend, or want to review any of the material that was presented, you can find the slides here.
 
28 May 2007 A maintenance release of Mascot Distiller is now available, (version 2.1.1). New providers add support for Agilent MassHunter (Q-TOF) and make Distiller data system independent for Thermo Xcalibur and Applied Biosystems T2D. If you are using an earlier version of Distiller, you should download and install this free update.
 
28 Feb 2007 Mascot version 2.2 is now running on this server. Details of the new features can be found here. These include:
  • Quantitation
  • Browser based configuration editor
  • Automatic Error Tolerant Searches
  • Automatic Decoy Database Searches
  • 64 bit versions of Microsoft Windows are now supported
  • Mascot Daemon has a reduced memory footprint and can now handle raw files and peak lists larger than 2 GB
  • ... and lots more
 
17 Aug 2006 Mascot Distiller 2.1 is released. This update adds new providers for Agilent LC/MSD TOF Wiff files, Kratos Axima 2.7 data, and Bruker baf files, (Apex, MicrOTOF). It is no longer necessary to install Applied Biosystems | Sciex Analyst in order to process Analyst Wiff files, (QStar, QTrap). Other important new features include support for Lockspray calibration of Waters Masslynx data and peak lists can now be saved in mzData format. Read more and download.
 
19 Jun 2006 New page of instrument specific tips for Applied Biosystems Data Explorer
 
13 Jun 2006 Our sixth workshop and user meeting was held in Seattle WA, on Sunday May 28th 2006, immediately before the 54th ASMS Conference on Mass Spectrometry and Allied Topics. If you were unable to attend, or want to review any of the material that was presented, you can find the slides here.
 
23 Mar 2006 Stay up-to-date! New patches for Mascot Server and Mascot Daemon are now available.
 
8 Mar 2006 New help page describing how to use Decoy Databases to validate false postive rates. Includes a link to download a free Perl script to reverse or randomise a Fasta database.
 
8 Feb 2006 New, very detailed page about choosing PC hardware for Mascot Server.
 
29 Nov 2005 Mascot Distiller 2.0 is officially released. Many new features, including the Search Toolbox, which enables Mascot Search results to be imported, and implements sequence tag calling and de novo sequencing. Also, support for mzXML and the facility to save and open project files. Full details here.
 
3 Nov 2005 New patches available with important updates for the Windows version of Mascot Server 2.1 and Mascot Daemon 2.1
 
12 Jul 2005 A set of Flash movies are now available, which illustrate the look and feel of Mascot Integra.
 
15 Jun 2005 Our fifth workshop and user meeting was held in San Antonio TX, on Sunday June 5th 2005, immediately before the 53rd ASMS Conference on Mass Spectrometry and Allied Topics. If you were unable to attend, or want to review any of the material that was presented, you can find the slides here.
 
7 May 2005 Mascot version 2.1 is now released and running on this server. Mascot customers who are under warranty or have support contracts will receive update disks automatically. Details of the new features can be found here. These include:
  • Flexible, role-based security model.
  • Easy export of Mascot search results in a variety of CSV and XML formats.
  • mzData 1.05 is fully supported as an input file format.
  • Many enhancements to Mascot Daemon.
  • Negative ions supported for both PMF and MS/MS.
  • Reports now show flanking residues for each peptide.
  • ... and lots more
 
26 Apr 2005 Press Release announcing a technical collaboration between Waters and Matrix Science. Water's ProteinLynx Global Server (PLGS) can now submit searches to a Mascot server and display the results within the PLGS user interface. Matrix Science gains access to the MassLynx raw file API, improving the support for MassLynx files within Mascot Distiller.
 
25 Feb 2005 Mascot Integra, our complete solution for managing and automating proteomics research, was officially launched at the 2005 ABRF meeting in Savannah, GA.
 
25 Jan 2005 The Mascot product brochure has been revised and updated. A link to download the Acrobat file can be found under Products, on the Mascot Server page.
 
16 Dec 2004 New versions of Mascot Distiller and Mascot Wizard are available for download. Bug fixes plus support for Shimadzu LCMSSolution LCMS-IT-TOF, MassLynx 4.0 SP3 and higher, and Analyst QS 1.1
 
31 Aug 2004 New patches available to update the Windows version of Mascot Server and Mascot Daemon to version 2.0.5
 
12 Aug 2004 New help page describing how to share Mascot results with colleagues who do not have on-line access to the Mascot Server.
 
9 Aug 2004 Press Release announcing that Nonlinear Dynamics protein informatics system will be enhanced to provide seamless integration with Mascot.
 
10 Jul 2004 We have upgraded the public Mascot server to an IBM eServerTM BladeCenterTM, as described on the Mascot Cluster product page. There are 14 blades, each containing dual 3.06 GHz Xeon processors and 1.5 Gb memory. The operating system is Debian Linux. The new system will provide the increased capacity needed to cope with the very large numbers of searches submitted during peak hours.
 
14 Jun 2004 Applied Biosystems have released details of their new iTRAQ™ multiplexed quantitation chemistry. This chemistry is ideal for database searching because the tag is isobaric, meaning that the peptide precursor masses and the MS/MS fragment ion masses are the same for all four channels. The channel dependent reporter mass, used for quantitation, is ignored by Mascot, so the same modifications work for all four channels: iTRAQ (K) and iTRAQ (N-term). Modification details are on Unimod. The tag targets primary amine groups, but a low-level reaction with tyrosine may also be observed. iTRAQ (Y) has been defined as a separate modification so that it can be specified as a variable modification, while iTRAQ (K) and iTRAQ (N-term) are specified as fixed.
 
10 Jun 2004 At this year's ASMS in Nashville, there was much interest in Electron Transfer Dissociation (ETD) for phosphopeptide analysis, (abstract). ETD, which generates c and z fragmentation, is very similar to Electron Capture Dissociation (ECD). Although the authors were interpreting their spectra manually, you can readily search them using Mascot. Choose FTMS-ECD as the INSTRUMENT, which selects c, z, and z+H ion series. If you are looking for phosphorylated peptides, choose modifications without neutral loss: Phospho-NL (S), Phospho-NL (T), and Phospho (Y). The first two are "hidden" modifications. You may need to change your search form defaults to enable their display in the search form. (Follow the hyperlink on the Search form selection page.)
 
7 Jun 2004 New versions of Mascot Distiller and Mascot Wizard are available for download
 
3 Jun 2004 Our fourth workshop and user meeting was held at the Gaylord Opryland Hotel, Nashville TN, immediately before the 52nd ASMS Conference on Mass Spectrometry and Allied Topics. If you were unable to attend, or want to review any of the material that was presented, you can find the slides here.
 
17 May 2004 A cumulative patch to update Mascot 2.0 for Windows to the latest version is now available for download from the Mascot Server Support page.
 
3 Feb 2004 Matrix Science is proud to be awarded the Frost & Sullivan 2003 Technology Leadership Award in the Proteome Informatics Market for the Mascot search engine. The award citation describes Mascot as "the gold standard for the searching of databases with mass spectrometric data". (Press Release)
 
30 Jan 2004 Mascot version 2.0 is now released and running on this server. Mascot customers who are under warranty or have support contracts will receive update disks over the next few weeks. Details of the new features can be found here. These include:
  • Memory efficient mode for very large, MudPIT-type searches.
  • Sequence tags, including error tolerant tags, are fully implemented.
  • Result reports are faster because they use Mascot Parser.
  • Mascot Daemon can use Mascot Distiller to process raw files.
  • Support for high-energy, side-chain cleavage ions (d, v, w).
  • Ambiguous residues X, B and Z are explicitly iterated to find best match.
  • Etc., etc.
 
19 Jan 2004 Press Release announcing the establishment of our new subsidiary in Japan, Matrix Science KK. Management team is Naoki Tanaka and Itaru Usami.
 
17 Dec 2003 New releases of Mascot Distiller and Mascot Wizard are now available for download.
 
21 Sep 2003 Hope you like the new look for the web site. We've eliminated the frames and tried to improve navigation, while keeping the layout simple and low bandwidth.
 
20 Jun 2003 Read all about Mascot Distiller, our new package for browsing and processing native (binary) mass spectrometry data files. Also, enhancements to Mascot Cluster, which now uses IBM eServer™ BladeCenter™ hardware
 
17 Jun 2003 Our third workshop and user meeting was held at the Montréal Marriott Château Champlain Hotel, immediately before the 51st ASMS Conference on Mass Spectrometry and Allied Topics. If you were unable to attend, or want to review any of the material that was presented, you can find the slides here.
 
26 May 2003 The web server has been upgraded to increase the storage capacity for search results. We now have a disk array with a capacity of approximately 1.6 Tb (1600 Gb). You will also notice a faster response when loading result reports. The operating system is Debian Linux and the web server is Apache.
 
24 Mar 2003 Press Release announcing the installation of a central Mascot server at NIH
 
26 Jan 2003 Mascot version 1.9 contains several important new features, details of which can be found here. Very briefly:
  • Mixture mode for peptide mass fingerprint search
  • Semi-specific and mixed enzymes
  • Extensions to error tolerant searching of nucleic acid sequences
  • New import filter for Voyager data in Mascot Daemon
  • Integrated database update script
 
17 Nov 2002 We are pleased to announce the release of Mascot Parser, a toolkit providing an object oriented interface to Mascot result files. Mascot Parser makes it easy for programs written in C++ or Perl to access Mascot results. Further details can be found here
 
12 Nov 2002 New pages of instrument specific tips for Analyst, MassLynx, and Xcalibur
 
5 Aug 2002 Press Release announcing a marketing agreement between LabVantage Solutions and Matrix Science to integrate Sapphire™ Informatics with Mascot®
 
5 Aug 2002 New and expanded help pages for sequence database setup.
 
21 Jun 2002 Our second workshop and user meeting was held at the Marriott Orlando World Center, immediately before the 50th ASMS Conference on Mass Spectrometry and Allied Topics. If you were unable to attend, or want to review any of the material that was presented, you can find the slides here.
 
25 Mar 2002 A new brochure describing Mascot is now available. A link to download the Acrobat file can be found on the Products page.
 
25 Feb 2002 Some of the many new features in Mascot version 1.8:
  • Error tolerant searching of MS/MS data can be used to find unsuspected chemical and post translational modifications plus point substitutions in the primary sequence.
  • A new search parameter: INSTRUMENT, customises the selection of ion series used for matching MS/MS data. This new parameter has been introduced because several new ion series have been added to Mascot, including internal fragments, neutral loss of water as well as ammonia, and high energy ion series c, x, z. These new series are particularly important when searching data from the new generation of MALDI-TOF/TOF instruments.
  • The default report format for peptide mass fingerprint searches is now more concise, and groups together matches to homologous proteins.
  • You can now save your preferred search form defaults as a local browser cookie.
 
24 Jan 2002 Press Release announcing the availability of Mascot for IBM's AIX 5L Unix operating system.
 
19 Oct 2001 In collaboration with the Swiss Institute of Bioinformatics, we are able make Swiss-Prot available for searching with Mascot. The FASTA file has been expanded using the Swissknife VARSPLIC utility. This parses the annotation text and creates new entries representing any splice variants, sequence variants, or sequence conflicts.
 
13 Sep 2001 Server hardware upgraded to a Mascot Cluster system. This provides 10 x 933MHz Pentium III processors, 10 Gb of RAM, and 350 Gb of disk storage for Mascot searches. Apache web server runs on a separate, dual processor PC under freeBSD.

The OWL database has been replaced by MSDB, and Mascot Server has been upgraded to version 1.7, which includes a number of new features.
 
10 Aug 2001 The new support page provides information and updates for anyone running a local (intranet) copy of Mascot Server
 
27 Jun 2001 Proteomics contains a paper describing the use of Mascot to search the draft assembly of the human genome:
Choudhary, JS, Blackstock, WP, Creasy, DM and Cottrell, JS, Interrogating the human genome using uninterpreted mass spectrometry data. Proteomics, 1(5) 651-67 (2001). The abstract can be found here.
 
12 Jun 2001 Our first protein identification workshop was held at the Hyatt Regency Chicago, immediately before the 49th ASMS Conference on Mass Spectrometry and Allied Topics. If you were unable to attend, or want to review any of the material which was presented, you can find the slides here.
 
4 Jun 2001 Press Release announcing OEM agreement with Applied Biosystems | MDS Sciex, who will be distributing Mascot with their products.
 
13 Dec 2000 Press Release announcing that Geneva Proteomics, Inc. (GeneProt) have selected Mascot as the search engine for their first industrial scale proteomics factory.
 
29 Nov 2000 Press Release from BioVisioN and Matrix Science announcing their collaboration to develop new bioinformatic tools.
 
12 Sep 2000 New background article on Quadrupole Ion Trap mass spectrometry.
 
26 May 2000 Mascot Cluster is a complete software and hardware solution for high throughput protein identification. The system is rugged, expandable, and highly cost effective. Both Linux and Microsoft Windows NT4 operating systems are supported. Redundant power supplies and hot-swappable processor nodes ensure excellent reliability.
 
14 Feb 2000 Mascot version 1.5 contains some important new features, full details of which can be found here. Very briefly:
  • In an MS/MS Ions Search, it is no longer necessary to specify which ion series should be used for matching
  • There is a new report format, Peptide Summary, for reporting the results of an MS/MS Ions Search
  • In an MS/MS Ions Search, if more than one arrangement of variable modifications is possible in a peptide, the arrangements are scored independently so that the closest match can be reported
  • The limitation on specifying multiple variable modifications which target the same residue has been lifted
 
15 Dec 1999 Issue 18 of the journal Electrophoresis contains a paper describing Mascot:
Perkins, DN, Pappin, DJ, Creasy, DM and Cottrell, JS, Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20(18) 3551-67 (1999).
The abstract can be found here.
 
20 Sep 1999 It is now possible to specify taxonomy in a search. This can speed up a search, and ensures that the hit list will only contain entries from the selected taxon or species. Please contact us if you wish to suggest additions to the list of species.
 
26 Aug 1999 A new Technical Brief is available discussing specification issues associated with running Mascot on a PC
 
25 Aug 1999 Added support for MS/MS peak list formats from PerSeptive and PE Sciex. Other minor tweaks and fixes include suppression of entries in overview table for peptide mass matches with zero ions score.
 
5 Jul 1999 Web server hardware upgraded to a cluster of four, dual processor Pentium II PC's. One PC running Apache web server under freeBSD, the other three running Mascot searches under Microsoft Windows NT 4 Workstation.
 
25 May 1999 Matching of MS/MS data now uses a more exhaustive iteration procedure which should give better scores for weak or noisy spectra. Main results table now reports actual ions scores, rather than the ratio of the number of peaks matched over the number tested.
 
28 Apr 1999 New random database provides a tool for investigating and verifying the significance of search results. Improvements to several report formats including a new sort option in Protein View.
 
26 Apr 1999 Probability Based Mowse scoring extended to all search types, including those with variable modifications and sequence or composition qualifiers.
 
8 Mar 1999 Mascot now supports variable modifications. Unlike fixed modifications, which apply to all modifiable sites, variable modifications may be present at all, some, or none of the modifiable sites in a protein.
 
12 Feb 1999 ICRF / Matrix Science Press Release announcing launch of Mascot
 
11 Feb 1999 Two new Technical Briefs: Mascot Overview and High Throughput Protein Identification
 
2 Feb 1999 Probability Based Mowse scoring introduced.
 
14 Jan 1999 dbEST now available for searching
 
21 Dec 1998 Web site hardware upgraded to a Silicon Graphics Origin 200 with 4 R10K processors and 3Gb of RAM.
 
30 Nov 1998 Mascot now available on the Matrix Science web site. System hardware is a Silicon Graphics Origin 200 with 2 R10K processors and 500Mb of RAM.
 
 
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