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Welcome to issue #107

Happy birthday, Mascot Distiller! Distiller launched in June 2003, and we're grateful for all the valuable feedback from the user community over the past twenty years.

This month's highlighted publication shows a new rapid method for the detection of tuberculosis in cattle. 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.

Export Distiller quantitation reports automatically with Mascot Daemon Export Extender.

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


October 2023, #107

Distiller's 20th anniversary
Featured publication using Mascot
Automated Distiller reports
About Matrix Science

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

Mascot Distiller 20th anniversary

Mascot Distiller 1.0 was launched 20 years ago to provide a single user interface for processing and cross-platform browsing of raw data. Then, as now, many labs have instruments from multiple vendors. Having a unified interface to process data from any instrument is very helpful for maintaining consistency as well as minimizing the learning effort.

Constant development – 11 major releases and 24 patch releases – has made for an ever more valuable set of features and workflows. We are grateful to have a tremendous community of users that provides us with ideas and suggestions for improvements.

Here are the toolboxes that have been added to the original Distiller:

  • Mascot Daemon to automate Distiller processing
  • Developer Toolbox to call the Distiller peak picking module from your own Windows applications
  • Search Toolbox provides de novo sequencing and database search integration with Mascot Server
  • Quantitation Toolbox supports isobaric, isotopic and label free quantitation methods

Additionally, the reporting functionality, convenience, speed and scaling of Distiller quantitation have been vastly improved over the years. Go to our blog to read about the evolution of Mascot Distiller and how it can facilitate your workflows and analyses.

And if you would like to evaluate Mascot Distiller, send us an email for a free 30-day trial.

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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.


LAP-MALDI MS Profiling and Identification of Potential Biomarkers for the Detection of Bovine Tuberculosis

Sophie E. Lellman, Christopher K. Reynolds, A.K. Barney Jones, Nick Taylor, and Rainer Cramer

J. Agric. Food Chem. 2023, 71, 13899−13905

Bovine tuberculosis (bTB) is a worldwide disease that is devastating for the cattle population and has serious economic and social impacts for dairy farming, with significant risks to the human population through zoonotic transmission. In 2021 bTB cost the UK approximately £100 million with over 27,000 cattle being slaughtered for disease control.

The authors explored the use of liquid atmospheric pressure (LAP)-MALDI MS for the detection of bTB. They collected 95 nasal swabs from healthy cattle, cattle with bTB and cattle with mastitis. The samples were prepared in <4 hr (vs 72 hr for the standard test method) by protein precipitation followed by reduction, alkylation, digestion with trypsin and purification using C18 ZipTips. The purified samples were then analyzed using LAP-MALDI MS profiling and LAP-MALDI MS/MS analysis.

The MS profile data were analyzed using supervised linear discriminant analysis (LDA) and principal component analysis (PCA) for dimensionality reduction. They developed a three-class prediction model for the identification of bTB, having overall classification accuracy of 85.7% with a bTB detection sensitivity of 75.0% and specificity of 90.1%. Detailed MS/MS analysis identified a bovine protein, S100-A12, as a key protein responsible for the discrimination between healthy and the diseased cattle.

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Automated Distiller quantitation reports

Mascot Daemon has a powerful feature called the External Processes Dialog, which allows running scripts and programs at different time points: start of task, before search, after search and after task completion. The only real limitation is that you can only call one external task per time point.

We have written a helper script, Mascot Daemon eXport Extender (MDXE), to bypass the limitation. MDXE runs not only several scripts in one step, it also runs these for a batch of Distiller projects. This is very useful when you process several raw files as a single Daemon task.

The initial use case is to export Distiller quantitation reports automatically after the search and quantitation is completed. Our blog gives the instructions how to download and install MDXE. Getting started is simple: copy the factory default configuration, enable or disable the Distiller reports you need and set up MDXE as an "After completing task" step in Daemon.

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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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