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We are delighted to announce the release of Mascot Server 2.6. The major new feature is the integration of spectral library searching.

If your Mascot Server licence is covered by warranty or a support contract, you will soon receive an email with download links and a new product key. If your support has expired, please enquire about update options by email, quoting your existing product key (displayed at the top of the Database Status page).

This month's highlighted publication elucidates the network of HSP chaperone complexes and how this can be disrupted, leading to potential cancer therapies. If you have a recent publication that you would like us to consider for an upcoming Newsletter, please send us a PDF or a URL.

Mascot tip of the month concerns submitting very large searches to Mascot Server on Windows.

Please have a read and feel free to contact us if you have any comments or questions.


December 2016

Spectral library searching
Featured publication
Mascot tip of the month

NEW: Spectral library searching in Mascot 2.6

In Mascot Server 2.6, you can search any combination of amino acid Fasta files, nucleic acid Fasta files, and spectral library files. The search engine for spectral libraries is NIST MSPepSearch.

When a search is complete, the results can be viewed and interrogated using the unique features of the protein family summary. This provides the advantages of rigorous protein inference together with grouping of related proteins into families.

In Database Manager, spectral libraries are handled symmetrically with Fasta files. Many public libraries can be enabled for automatic download, configuration and updating with a few mouse clicks. You can also schedule the automatic creation of spectral libraries from Mascot search results according to flexible import filters.

This, and other new features in Mascot Server 2.6 and Mascot Daemon 2.6 are summarised on this page.

spectral library

Featured publication using Mascot

Here we highlight a recent interesting and important publication that employs Mascot for protein identification, quantitation, or characterization. If you would like one of your papers highlighted here please send us a PDF or a URL.


The epichaperome is an integrated chaperome network that facilitates tumour survival

Anna Rodina, Tai Wang, Pengrong Yan, Erica DaGama Gomes, Mark P. S. Dunphy, Nagavarakishore Pillarsetty, John Koren, John F. Gerecitano, Tony Taldone, Hongliang Zong, Eloisi Caldas-Lopes, Mary Alpaugh, Adriana Corben, Matthew Riolo, Brad Beattie, Christina Pressl, Radu I. Peter, Chao Xu, Robert Trondl, Hardik J. Patel, Fumiko Shimizu, Alexander Bolaender, Chenghua Yang, Palak Panchal, Mohammad F. Farooq, Sarah Kishinevsky, Shanu Modi, Oscar Lin, Feixia Chu, Sujata Patil, Hediye Erdjument-Bromage, Pat Zanzonico, Clifford Hudis, Lorenz Studer, Gail J. Roboz, Ethel Cesarman, Leandro Cerchietti, Ross Levine, Ari Melnick, Steven M. Larson, Jason S. Lewis, Monica L. Guzman & Gabriela Chiosis

Nature 538, 397-401 (20 October 2016)

The authors have investigated the multi-protein complexes centered around the chaperones, heat shock proteins 70 and 90, and have determined that they are part of a larger network encompassing numerous cellular processes vital for tumor cell function. They term this larger network the epichaperome.

They also found that this network is active in certain types of cancer cells, giving them a degree of protection. However, disruption of the chaperone complexes causes dismantling of the network and cell death. They investigated a range of cancer cell lines (pancreatic, gastric, lung, and breast cancers, as well as lymphomas and leukaemias) and found that approximately 60-70% presented medium to high levels of epichaperome complexes. Additionally the oncogene MYC was able to rewire the network and to drive the formation of the epichaperone. The vulnerability of the network to disruption may pose opportunities for pharmaceutical interventions.

Thumbnail from featured publication

Mascot tip of the month

In the February edition of this newsletter, we described how to avoid the 4 GB upload limit of IIS, the web server that comes with Microsoft Windows, by submitting a search at the command line.

Now that Mascot Server 2.6 is available, there is an easier solution. When Mascot Daemon 2.6 is running on the Mascot Server, it submits searches directly to Mascot, bypassing the web server. This eliminates file size limits and timeout issues.

Another much requested change in Daemon is more complete status information including percent complete and a button to allow a running search to be cancelled. Details of other new features in Mascot Daemon 2.6 can be found here.

Mascot Daemon

About Matrix Science

Matrix Science is a provider of bioinformatics tools to proteomics researchers and scientists, enabling the rapid, confident identification and quantitation of proteins. Mascot software products fully support data from mass spectrometry instruments made by Agilent, Bruker, Sciex, Shimadzu, Thermo Scientific, and Waters.

Please contact us or one of our marketing partners for more information on how you can power your proteomics with Mascot.


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Matrix Science Ltd, 64 Baker Street, London W1U 7GB, UK
T +44 (0)20 7486 1050  F +44 (0)20 7224 1344  E

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