You can now use large language model (LLM) coding assistants to interact with Mascot Server. This includes anything that can be programmed with the LLM, from simple automation tasks to complex mining and merging of results.

https://www.matrixscience.com/blog/automate-data-processing-and-reporting-with-coding-assistants.html

#proteomics #MassSpec

Mascot Newsletter, April 2026:

Mycobacteria spectral libraries.

Orthogonal translation systems for lysine aminoacylation.

Matrix Science at ASMS 2026.

https://www.matrixscience.com/nl/202604/newsletter.html

#proteomics #massspec

Mascot Newsletter, March 2026:

Search BLIB spectral libraries with Mascot.

PET hydrolase expressed in fruit flies.

UK office has moved.

https://www.matrixscience.com/nl/202603/newsletter.html

#proteomics #massspec

Thunder-DDA-PASEF is an acquisition strategy for capturing more human leukocyte antigen (HLA) class I peptide ligands on Bruker timsTOF instruments. This month's blog shows how you can process Thunder-DDA-PASEF data with Mascot Distiller.

https://www.matrixscience.com/blog/processing-thunder-dda-pasef-data-with-mascot-distiller.html

#proteomics #massspec

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

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