Blog

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 [...]

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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 [...]

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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 [...]

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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 [...]

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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 [...]

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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 [...]

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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, [...]

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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 [...]

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Posted by Richard Jacob (March 23, 2022)

Analyzing the disulfide bond structure of the SARS-Cov-2 Spike protein

The SARS-Cov-2 virus has been under intense investigation since its discovery two years ago. Almost every feasible analytical method has been used and according to PubMed, that includes over 3000 proteomics papers. The most important protein immunologically speaking is the spike protein that is involved in the initial binding to the target cells. An example of the more encompassing spike [...]

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Posted by Ville Koskinen (February 16, 2022)

Single-cell peptide fragmentation spectra

More single-cell proteomics studies are published each year as instruments become more sensitive and sample preparation is optimised. A recent publication in the Journal of Proteome Research, Features of Peptide Fragmentation Spectra in Single-Cell Proteomics, highlights potential challenges to protein and peptide identification by database searching. Boekweg et al. computationally examined the fragmentation spectra of peptides from bulk samples, 2ng [...]

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Posted by Patrick Emery (January 24, 2022)

Default or prof_prof? Peak picking Thermo .RAW data with Mascot Distiller

We supply a number of processing options files for each of the main vendor raw file types with Mascot Distiller. These .opt files are designed as a reasonable starting point for peak picking your own data – but to get the very best you’ll need to tweak the parameters on a typical raw file from your instruments and then use [...]

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Posted by Ville Koskinen (December 16, 2021)

Mascot cluster installation security on Linux

Mascot Server has a built-in cluster mode, where the database search can be executed in parallel on a networked cluster of PCs. This requires no special hardware or operating software. The cluster can consist of ‘commodity’ PCs running Windows or Linux. Cluster mode is usually the most practical option for licences of 5 CPU or more, as discussed in Mascot [...]

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