Welcome to issue #103

We enjoyed seeing many of you at the ASMS breakfast meeting in Houston. If you couldn't make it to our annual user meeting, the slides and speaker notes can be found below.

We feature a selection of posters presented at ASMS that highlight the range of applications for Mascot. If you presented work at ASMS using Mascot that you would like us to consider for an upcoming Newsletter, please send us a PDF or a URL.

Mascot tip of the month is to enjoy our updated training materials.

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

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

Mascot user meeting at ASMS 2023

The slides and speaker notes are now available for two of the presentations from the user meeting. The first talk describes strategies for single-cell proteomics and recommends suitable settings for Mascot Server and Mascot Distiller. The second talk gives a condensed history of the 25 years since the founding of Matrix Science.

Single cell proteomics with Mascot (PDF)
Patrick Emery, Matrix Science

• SCoPE-MS spectra are similar to bulk sample spectra, and standard settings work fine
• Single-cell spectra are quite different to bulk spectra, with lower signal to noise
• Mascot gets good results with the right peak picking; we also recommend enabling Percolator rescoring

25 years of Matrix Science (PDF)
Ville Koskinen, Matrix Science

• 1998: Matrix Science Ltd founded by John Cottrell and David Creasy
• Mascot Server 1.0 released 1999, and free service launched
• 2019: 25 millionth free online Mascot search

Links to the slides are also available on our website.

Mascot posters at ASMS

Here are five selected posters presented at ASMS 2023 that showcase the utility of Mascot to a wide array of problems. If you presented work at ASMS using Mascot that you would like us to consider for an upcoming Newsletter, please send us a PDF or a URL.

TP 370: The Challenge of Plant Identification in Complex Mixtures: Closely Related Families, Large Proteomes, and Unsequenced Genomes (PDF abstract)

Melinda A. McFarland¹; Sara M. Handy¹; Elizabeth Hunter¹; Christine H. Parker¹; Ann M. Knolhoff¹

¹FDA-CFSAN, College Park, MD

MP 009: Collagen Remains in Palaeotherium Bone from the Isle of Wight (UK) (PDF abstract)

Joseph Hubbard¹; Steven Robinson²; Ardern Hulme-Beaman³; Martin Munt⁴; Krzysztof Pawlak²; Steve Taylor¹

¹Department of Electrical Engineering & Electronics, University of Liverpool; ²Materials Innovation Factory, University of Liverpool; ³University of Liverpool, Liverpool, United Kingdom; ⁴Dinosaur Isle Museum, Sandown, United Kingdom

MP 600: Inside into the proteome of Chelidonium majus latex (PDF abstract)

Joanna Gracz-Bernaciak¹; Oliwia Mazur¹; Natalia Kielich¹; Michalina Krakowiak¹; Sophia Bałdysz¹; Martyna Węglewska¹; Oskar Musidlak¹; Agata Malinowska²; Robert Nawrot¹

¹Adam Mickiewicz University in Poznan, Faculty of Biology, Department of Molecular Virology, Poznan, Poland; ²Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Mass Spectrometry Laboratory, Warsaw, Poland

MP 734: Quantitative spatial proteomics combined with lipidomic analysis of human hippocampus using laser capture microdissected cells from MALDI-imaged tissue sections (PDF abstract)

Lauren R. DeVine¹; Caitlin M. Tressler¹; Rahul A. Bharadwaj²; Kristine Glunde¹; Daniel Weinberger²; Robert N. Cole¹

¹Johns Hopkins School of Medicine, Baltimore, MD; ²Lieber Institute for Brain Development, Baltimore, MD

TP 575: Automated Data Analysis Workflow Leveraging PASEF Data Accelerates Confident Detection of Low-Abundance HCPs (PDF abstract)

Amy Claydon¹; Guillaume Tremintin²; Juergen Kastler³; Stuart Pengelley⁴; Jonathan Krieger²; Arnd Brandenburg³

¹Genedata Ltd., Cambridge, United Kingdom; ²Bruker, San Jose, CA; ³Genedata AG, Basel, Switzerland; ⁴Bruker Daltonics, Bremen, Germany

Mascot training materials

We have recently updated the Mascot training materials. Two new modules have been added for spectral library searching and crosslinking, and we have updated all screenshots and reviewed every slide. The content now describes versions up to Mascot Server 2.7 and Distiller 2.7. We're currently working on updated content for the current version, 2.8. The training course materials are available free of charge and suitable for self study or as basis for an in-house training course.

Each module now also links to related content. This is, for example, recent blog articles that add more depth, relevant sections in the online help and Youtube videos. We'll continue adding more links as relevant content is published. The aim is to provide comprehensive tutorials on all aspects of Mascot functionality.

This summer, from May to July, we are also uploading the classic training course videos to Youtube! The videos are based on an intensive 2-day course and describe Mascot Server 2.5, although much of the content is 'timeless' and still relevant with the current version. The video links are on our website, or have a look at our Youtube channel @matrixscience1998.

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. Read more about the company on our about page.

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