Blog

Posted by Patrick Emery (March 15, 2023)

Generating high quality spectral libraries for DIA-MS

Using Mascot Daemon, Mascot Distiller and Mascot Server A recent paper from Manda et al.[1] describes a pipeline to generate high quality spectral libraries from Data-Dependent Acquisition (DDA) experiments for use in searching Data-Independent Acquisition (DIA) data, starting from the raw data, through to generating the library from the search results. The pipeline uses a collection of different tools in [...]

Full article and comments form

Posted by Ville Koskinen (February 24, 2023)

25 years of Matrix Science

Happy 25th birthday, Matrix Science! A lot has happened since John Cottrell and David Creasy founded the company in 1998, and proteomics today certainly looks very different to the bleeding edge of science back then. The success of any company could be attributed to various causes, but the simple fact is that we would not be here without our loyal [...]

Full article and comments form

Posted by Ville Koskinen (January 17, 2023)

Mascot in the Cloud

Cloud computing is the IT paradigm of our times. More and more business services and applications are delivered as a subscription service, where the software runs in a data centre somewhere, operated by a third-party cloud platform. We are often asked whether you can run Mascot Server “in the cloud” and if so, whether it’s the right solution. The answers [...]

Full article and comments form

Posted by Patrick Emery (December 16, 2022)

Peak picking intact crosslink spectra with Mascot Distiller

There are several important factors to take into account when carrying out peakpicking for an intact crosslinked dataset. You’ll typically be dealing with higher charge state precursors to handle the larger masses of the linked peptides, and the MS/MS spectra are inherently complex, chimeric spectra with fragments from the alpha and beta peptides. To look at the effects of adjusting [...]

Full article and comments form

Posted by Ville Koskinen (November 16, 2022)

Paleoproteomics

Paleoproteomics is a growing application area for mass spectrometry. Its cross-disciplinary remit includes analysis of ancient proteins (bone, skin, silk), ancient proteomes (enamel, egg shells, plant seeds) and most ambitiously ancient metaproteomes (dental calculus, food remains). The recent review by Warinner et al. in Chemical Reviews has excellent coverage not just of the varied applications but also the sample processing [...]

Full article and comments form

Posted by Richard Jacob (October 14, 2022)

Complementary reporter ion clusters in TMT/TMTpro labeling

We recently received a support request about complementary ions in TMTpro labeling. Complementary ions are formed during fragmentation, where the precursor loses the reporter ion and carbon monoxide, leaving behind the peptide and the balance region of the label. Complementary ion spacing is similar to reporter ions but the mass varies depending on peptide mass. The customer was concerned that [...]

Full article and comments form

Posted by Patrick Emery (September 23, 2022)

Reporting quantitation datasets with Mascot Distiller 2.8

In previous versions of Distiller, reporting of quantitation results was handled using XSLT transformation of the XML export of the quantitation results. XSLT is a powerful language, but it’s not commonly used, so writing custom reports could be an uphill stuggle. In Mascot Distiller 2.8, reports are written in Python and use Mascot Parser to access the search and quantitation [...]

Full article and comments form

Posted by Ville Koskinen (August 31, 2022)

Downloading UniProt proteomes via new API

The UniProt website received a snazzy facelift in June 2022. Both the browser interface and the REST API were updated. The previous version, now termed legacy website, remains available until the 2022_04 release under a new URL (https://legacy.uniprot.org/) – so there is limited time to compare and admire the improvements! The new API is an almost seamless transition for Mascot [...]

Full article and comments form

Posted by Ville Koskinen (July 20, 2022)

Does your search engine show the evidence?

You’ve submitted a protein sequence database search and start looking at the results. Why did the search engine identify that protein? What is the peptide evidence? Which alternatives did the software consider? Is the software’s decision correct? These are basic yet important questions with any software-driven approach – which is the bulk of today’s MS/MS data analysis. A lot of [...]

Full article and comments form

Posted by Patrick Emery (June 20, 2022)

Divide and conquer: Fractionated Label Free Quantitation in Mascot Distiller 2.8.2

We have recently released Mascot Distiller 2.8.2. The headline new feature is support for Label-Free Quantitation of fractionated samples. With Mascot Distiller 2.8, individual raw files in a project are aligned against a consensus generated by roughly aligning and combining the total ion chromatograms (TICs) of each raw file. If a peptide match is found in one sample file and [...]

Full article and comments form

Posted by Ville Koskinen (May 20, 2022)

mzIdentML 1.2

Mascot Server supports several formats for exporting database search results. One of them is the Proteomics Standards Initiative’s mzIdentML. The Mascot 2.8.1 patch release upgrades the file format version to mzIdentML 1.2. You can now export crosslinked search results in XML, CSV, xiVIEW CSV and mzIdentML format. When you export standard database searches, error tolerant searches and spectral library searches, [...]

Full article and comments form

Posted by Ville Koskinen (April 19, 2022)

NCBI nr in Mascot Server 2.8.1

Mascot Server 2.8.01 patch was released in March 2022. One of the big improvements is optimising the compression speed of the NCBI nr database, available as the NCBIprot predefined definition. We’ve greatly decreased the time it takes to bring the database online, as well as removed an inadvertent limitation on database size. The patch is available to download on the [...]

Full article and comments form