Welcome

Join us at the upcoming Matrix Science User Meeting on 2 June at ASMS 2025, Baltimore, Maryland.

Are you presenting a poster or talk at ASMS that uses Mascot? Send us the poster/talk number, presenter name and abstract to newsletter@matrixscience.com and we will feature it in a future newsletter.

This month's highlighted publication reveals an opal stop codon that accelerates equid oxygen metabolism.

Mascot Server can easily search tens of millions of protein sequences and large peak list files.

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

Get a quote

Matrix Science ASMS User Meeting

Please join us at the upcoming ASMS User Meeting held on 2 June in Baltimore, Maryland.

There is no charge for attending the meeting, but advance registration is required. Numbers will be limited, so early registration is advisable. Breakfast will be provided.

Monday 2 June, 7:00 am – 8:00 am
Room 338, Baltimore Convention Center, Baltimore, MD

• Using MS²Rescore to boost identification rates in complex samples,
  Tim Van Den Bossche, Computational Omics and Systems Biology Group (CompOmics), Ghent University/VIB-UGent Center for Medical Biotechnology

• Mascot DIA: Universal spectrum-centric approach,
  Ville Koskinen, Matrix Science

• Mascot DIA: Thermo LFQ example,
  Patrick Emery, Matrix Science

Register now

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.

Running a genetic stop sign accelerates oxygen metabolism and energy production in horses

Gianni M. Castiglione, Xin Chen, Zhenhua Xu, Nadir H. Dbouk, Anamika A. Bose, David Carmona-Berrio, Emiliana E. Chi, Lingli Zhou, Tatiana N. Boronina, Robert N. Cole, Shirley Wu, Abby D. Liu, Thalia D. Liu, Haining Lu, Ted Kalbfleisch, David Rinker, Antonis Rokas, Kyla Ortved, Elia J. Duh

Science 387, 1375 (2025)

Horses have unusually high mass-adjusted oxygen consumption and other metabolic adaptations that support high energy production. The authors study the molecular mechanisms behind these, particularly the NRF2/KEAP1 pathway: NRF2 governs cellular and tissue redox homeostasis during exercise, while KEAP1 is the major negative regulator of NRF2. They have identified a premature stop codon in KEAP1 (R15X) in horses and other equids, where a de novo opal stop codon (UGA) is recoded into a cysteine (C15). The R15C KEAPI mutation enhances NRF2 activity, which accelerates oxygen metabolism and ATP production.

To demonstrate this, the authors first analysed horse tissue and cells using LC-MS/MS. Samples were enriched for KEAP1 and run using discovery DDA and a targeted method. The MS/MS spectra were searched against an Equus caballus protein sequence database using Mascot Server, including horse KEAP1 constructs created in this study. Because the UGA stop codon can be recoded into selenocysteine or cysteine in humans and mice, they included selenocysteine and carbamidomethyl as cysteine variable mods. The authors show that horse KEAP1 position 15 is predominantly cysteine. Downstream consequences of the mutation are elucidated using structural biology, cellular assays and comparative metabolomics.

Big databases and large peak lists

When it comes to sequence database searches, how large is too large to handle? This is actually two questions in one: a search can be large because the database has millions of protein sequences; or it can be large because of the number of peak lists.

Mascot Server has no limits because of its design. With sequence databases, Mascot streams linearly through the entries without having to keep much in RAM, so the only real limitation is disk space. For example, Mascot can easily handle the NCBI nr database, which has around 707 million entries.

With large peak list files, Mascot Server has no limits either, because it splits the input into independent chunks, and a search can have an unlimited number of chunks. You may, however, encounter other limits in the web server. Briefly, the main issue (in Microsoft IIS and Apache httpd) is the file upload size limit, typically 2GB or 4GB. You should be able to fit 1 million MS/MS spectra in a 2GB MGF file, so file size is mainly an issue with very long gradients or very fast instruments. This is discussed in more detail in our blog.

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 continues to be cited by over 2000 publications every year. Our software products fully support data from mass spectrometry instruments made by Agilent, Bruker, Sciex, Shimadzu, Thermo Scientific, and Waters.

Get a quote

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

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