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

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Posted by Richard Jacob (May 20, 2024)

30 years of Sequence Tags

This year we are celebrating 30 years of sequence tags. The technique was developed by Matthias Mann and Matthias Wilm while in the Protein and Peptide group at the European Molecular Biology Laboratory (EMBL). EMBL is itself celebrating its 50th Anniversary and has been an important center for science over that period. The sequence tag paper was published in 1994, [...]

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Posted by Ville Koskinen (April 18, 2024)

Mascot workflow for LC-MS/MS data

Data analysis in mass spectrometry proteomics is complex and, nowadays, almost entirely software driven. Processing a raw file, peptide identification by database searching, protein inference and protein quantitation all have many steps and built-in assumptions, not to mention a huge number of parameters. Software continues to evolve as does best practice. Whether you are new to mass spectrometry proteomics or [...]

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Posted by Patrick Emery (March 18, 2024)

Tutorial: Creating custom reports in Mascot Distiller

Mascot Distiller 2.8 reports are written in Python, a commonly used programming language, and use Mascot Parser to access the search and quantitation results. We supply a range of standard reports, including reports for quality, clustering and statistical analysis, which we took a look at in an earlier blog article. In addition to these, you can develop your own reports [...]

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Posted by Patrick Emery (October 13, 2023)

Spectrum-centric searching of narrow window DIA data with Mascot Server

Data-independent acquisition (DIA) can be broadly separated into narrow window and wide window strategies depending on the size of the isolation window. There are also two data analysis strategies – peptide-centric and spectrum-centric. Wide window DIA typically requires a peptide-centric approach, but narrow window DIA data can be analysed either way. Mascot Server is spectrum-centric, and it’s possible to run [...]

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Posted by Ville Koskinen (September 18, 2023)

Mascot Distiller 20th anniversary

This year is the 25th anniversary of Matrix Science and 25 years of Mascot Server, but it’s also the 20th birthday of Mascot Distiller! Mascot Distiller 1.0 was released in June 2003 and it’s still under active development today. Distiller started as a GUI application for browsing and peak picking native (raw, binary) mass spectrometry data files. Let’s have a [...]

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Posted by Richard Jacob (June 16, 2023)

Mascot Daemon Export Extender

Mascot Daemon has two features to help with automation and creating pipelines. The first is the AutoExport feature that allows you to configure and export a report into a CSV file, mzIdentML file or other format that Mascot Server supports with the options you choose. This happens once the search is complete. The lesser known but more powerful feature is [...]

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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 [...]

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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 [...]

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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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