Redesign of Mascot Distiller technical support pages

The Mascot Distiller technical support pages have been redesigned. The main page now lists the full version history, including links to related content like blog articles and Youtube videos. Each major version has its own page, like Distiller 2.8, which contains the list of known issues and the full change log for that major version. We hope this makes release information easier to find.

Moving searches older than 2015 to cold storage

When you submit a free search on the public Mascot server, the search results are stored on the server for a certain time, but we don’t guarantee they will be kept indefinitely. The size of the search archive has increased substantially since the limits were increased in March 2020. In order to avoid running out of storage space, we are gradually moving some of the historic archive into cold storage.

In November 2022, we archived search results up to 1 Jan 2010. On 5 September 2023, we have now moved all searches up to 1 Jan 2015 into cold storage. If you submitted a search before 1 Jan 2015 and would like to download a copy after the archival, please send us an e-mail and we can send you the results file.

The archival policy only affects Mascot running on our public website. If you have an in-house licence, the above policy does not apply.

Mascot Server 2.8.3 patch release

Mascot Server 2.8.3 has been released. This patch fixes six small bugs in the search engine (nph-mascot.exe), four in Mascot Perl scripts, one in ms-monitor.exe regarding a spurious log message and one issue with licensing on AMD EPYC processors.

We recommend all users to install the update. The cumulative update from 2.8.0, 2.8.1 and 2.8.2 can be downloaded from the support page.

• 14038: Chimeric spectrum peaklist with some dodgy precursors causes Mascot to crash almost immediately
• 14095: ShowSubSets in export_dat_2.pl is probably broken in 2.8.1
• 14105: Crash from chimeric spectra MGF when decoy selected
• 14142: Scoring of N-terminal and C-terminal crosslinks occasionally too low, caused by fragment mass miscalculation when linking terminus to residue
• 14189: Can’t call method “resetKeepAlive” on an undefined value at ./common_subs.pl line 667.
• 14246: MaxConcurrentSearches not respected evenly on the master and the node
• 14270: “Prepare ../taxonomy/acc_to_taxid.mapping.txt_*.cdb” even though nothing needs to be done
• 14291: Disulfide crosslink search hangs at 67% due to number of open filehandles
• 14340: Executable aborts immediately on AMD EPYC 7763 if creating an ms_processors object
• 14366: xiView column CalcMz calculated using a hydrogen rather than a proton
• 14367: Prevent PMF with Big Mascot
• 14403: Peptide View reports C-terminal modification on wrong residue

Please do not hesitate to contact us with any questions.

New help page for chimeric spectra

We’ve added a new help page for chimeric spectra. Support for identifying peptides from chimeric spectra was added in Mascot Server 2.5 (2014) and Mascot Distiller 2.5 (2013), but it was not properly documented until now.

Mascot Distiller 2.8.4 patch release

Mascot Distiller 2.8.4 is a new patch release.

This release includes a number of important bug fixes, and we advise all users to download and install it. In addition, it adds support for more recent Agilent instruments such as the 6546 LC/QTOF.

Please do not hesitate to contact us with any questions.

New Mascot Server release history page

We’ve added a summary of the Mascot Server release history to the technical support page. The list includes the release date as well as links to the release announcement, overview of new features, any blog or ASMS user meeting content describing the new version and the latest available patch. All the information has always been available in the news, blog and technical support section of this website, but having everything in one place makes it much easier to find.

25th anniversary of Matrix Science

Matrix Science was founded in 1998, which makes this year our 25th anniversary! We have added a brand new About page, which details the company timeline, and there is a bit more history in the blog article 25 years of Matrix Science.

Thank you for your trust, custom, bug reports, ideas and feedback over the past quarter century.

Moving old searches to cold storage

When you submit a free search on the public Mascot server, the search results are stored on the server for a certain time, but we don’t guarantee they will be kept indefinitely. The size of the search archive has increased substantially since the limits were increased in March 2020. In order to avoid running out of storage space, we are implementing a new archival policy.

In upcoming months, we will gradually move some of the historic archive into cold storage. There will be a news announcement for each archival event. The search results will not be deleted permanently, but they will no longer be available online at matrixscience.com.

The archival policy only affects Mascot running on our public website. If you have an in-house licence, the above policy does not apply.

On 1 December 2022, we will start by moving all public Mascot searches up to 1 Jan 2010 to cold storage. If you submitted a search before 1 Jan 2010 and would like to download a copy after the archival, please send us an e-mail and we can send you the results file.

Mascot Distiller 2.8.3 patch release

Mascot Distiller 2.8.3 is a new patch release.

This release includes a number of important bug fixes, and we advise all users to download and install it.

• 14151: Check to see if display changes require requantitation is over-sensitive
• 14200: Protein descriptions in ANOVA plus Clustering report table are wrong
• 14202: Unclustered Table Headers in Hierarchical Clustering Report
• 14205: Table Peptides Report has incorrect protein ratios
• 14220: Time alignment offset calculation incorrect in some cases
• 14228: Creating a new project when connected to Mascot 2.6 or earlier fails
• 14232: Crash if using normalisation to specified proteins

Please do not hesitate to contact us with any questions.