Using the blib2msp converter, Mascot Server can now search DDA spectral libraries in BLIB format. Here's an example for identifying mycobacteria.

https://www.matrixscience.com/blog/identifying-mycobacteria-with-custom-spectral-libraries.html

#proteomics #massspec

The UK office of Matrix Science Ltd has moved one block up the road. New address: 83 Baker Street, London W1U 6AG, UK. There is no other change to bank details or email addresses.

https://www.matrixscience.com/whats_new/change-of-address-for-uk-office.html

Mascot Newsletter, February 2026:

Strange software errors? Check your disk space.

Proteomic signatures in human fingertip regeneration.

Customise columns in the search log.

https://www.matrixscience.com/nl/202602/newsletter.html

#proteomics #massspec

Mascot Server can create and search NIST MSP formatted spectral libraries but not BLIB -- until now! We have developed an MSP to BLIB to MSP converter that allows Mascot Server to use BLIB libraries.

https://www.matrixscience.com/blog/converting-blib-spectral-libraries-to-msp-and-back-again-for-use-with-mascot-server.html

#proteomics #massspec

Mascot Newsletter, January 2026:

Ion intensity: peak area vs signal to noise?

Duplexing deuterated water-labeled samples for protein turnover rate estimation.

Role-based access with Mascot Security is useful in a variety of cases.

https://www.matrixscience.com/nl/202601/newsletter.html

#proteomics #massspec

Proteomics software is prone to filling up the disk with data and temp files, which can cause weird issues. This blog article lists the most common errors in Mascot products and how to free up disk space.

https://www.matrixscience.com/blog/strange-software-failures-check-your-disk-space.html

#proteomics #massspec

Mascot Newsletter, December 2025:

NCBI nr FASTA replacement.

Immunoregulation during pregnancy.

Mascot Server as system service on Linux.

https://www.matrixscience.com/nl/202512/newsletter.html

#proteomics #massspec

When raw data is processed into peak lists, there is a choice: how should peak intensity be calculated? Mascot Distiller defaults to peak area. The alternative, signal-to-noise (S/N), can be useful with detecting diagnostic ions.

#proteomics #massspec

https://www.matrixscience.com/blog/peak-list-arcana-area-vs-signal-to-noise.html

Mascot Newsletter, November 2025:

Top-3 quant with DDA-PASEF.

ZooMS peptide markers for South American Xenarthrans.

Migrating from Windows 10 to Linux could extend the lifetime of your hardware.

https://www.matrixscience.com/nl/202511/newsletter.html

#proteomics #massspec

The NCBI nr FASTA file of protein sequences is no longer updated. We've summarised instructions for creating it from the BLAST database -- or you may be better off using TrEMBL.

https://www.matrixscience.com/blog/replacements-for-ncbi-nr.html

#proteomics #massspec