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Welcome to issue #102

We are looking forward to seeing many of you at the upcoming ASMS meeting in Houston, Texas, where we will host our Annual User Meeting. Please also stop by at exhibit booth #726.

If you are presenting a poster or talk at ASMS using Mascot, send us the title or poster/talk number and we will feature it in the newsletter and social media.

Mascot Server is compatible with cloud computing, and we have tips how to get started.

This month’s highlighted publication shows an automated workflow for the rapid characterization of snake venoms. 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.

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


May 2023, #102

ASMS 2023
Featured publication using Mascot
Mascot in the Cloud
About Matrix Science

Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Matrix Science at ASMS

We are pleased to invite you to our Annual ASMS User Meeting in Houston, Texas on Monday, 5 June at 7:00am – 8:00am, which will feature the following presentations.

  • Connecting the Prots: Analyzing crosslinked data in a core lab using Mascot – Professor Susan Weintraub, University of Texas Health Science Center at San Antonio
  • Single cell proteomics with Mascot – Patrick Emery, Matrix Science
  • 25 years of Matrix Science – Ville Koskinen, Matrix Science

There is no charge for attending these meetings, but advance registration is required. Breakfast will be provided. Register now.

Illustration for ASMS

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.


High-Throughput Venomics

Julien Slagboom, Rico J. E. Derks, Raya Sadighi, Govert W. Somsen, Chris Ulens, Nicholas R. Casewell, and Jeroen Kool

J. Proteome Res. 2023, published online: April 3, 2023

Though snakebites are rare events for many of us, they result in 138,000 deaths per year due to lack of availability of affordable and effective antivenoms. To assist in the development of next-generation antivenoms, the authors have optimized and validated an automated profiling procedure for determining the composition of toxins from medically relevant snake venoms.

The initial LC separation of the venom is semi-quantified with UV. Then, tentative toxin classes are proposed from intact MS analysis. The LC is flow split, fractionating the eluting venom proteins, which are then dried and robotically digested with trypsin. LC-MS/MS of the digestions with a fast gradient yielded 100 measurements per day, enabling the full proteomic analysis of a single snake venom in less than two days.

Mascot Daemon automates the database search and protein identification. This is followed by a series of in-house R scripts which compile and sort the data. The scripts create so-called Protein Score Chromatograms (PSCs), where protein score is plotted on the y-axis versus retention time. The peaks in the PSCs are integrated to yield semi-quantitation of the toxins and correlated with the intact MS data.

The authors showed data from 11 species and concluded that the new workflow is orders of magnitude faster than any other venomics approach described in literature to date.

Thumbnail from featured publication

Mascot in the Cloud

Mascot Server is a server application, which is easy and natural to install in a cloud environment. Should you run Mascot in the cloud? The short answer is... it depends. To begin with, it's useful to separate cloud services into two broad categories: Software as a Service (SaaS) and Infrastructure as a Service (IaaS).

Software as a service is a good delivery model for a variety of web-based services that have relatively low resource requirements per user, little need for user-specific customization, can benefit from economies of scale and have a large number of potential users. However, we don't offer Mascot under a SaaS model, because it is not a good fit for typical proteomics use. The raw file and MGF files can be small or several gigabytes in size. A single experiment can have one or dozens of MS/MS runs. The database could be small or very large. The search duration is very hard to predict from the search parameters. These factors make resource use and provisioning unpredictable and actively hinder scaling.

Infrastructure as a service, on the other hand, is a good fit for Mascot Server. It is an alternative to buying and maintaining physical hardware, and you simply click a button to provision a 32-vCPU virtual machine in the cloud when you need it. The virtual CPU, RAM and disk requirements are basically the same as in general hardware virtualization, and performance and security are typically excellent.

If you want to try Mascot in the cloud, we can give you a free 1-CPU 30-day license, provided you have a current Server license under warranty or support. Read more about Mascot and cloud computing in our blog.

Illustration of a cloud

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.

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

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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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