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Articles tagged: Mascot Distiller
Mascot Distiller quantitates more proteins with machine learning
Mascot Distiller can now use machine learning with LFQ, TMT and other quantitation methods, thanks to API changes made in the recent Mascot Server 3.1 release. Machine learning typically increases the number of identified peptides at a fixed false discovery rate, which often leads to a substantial boost in the number of proteins quantified. We demonstrate this with an LFQ [...]
Matrix Science at ASMS 2024
The ASMS 2024 conference was held in Anaheim, California, on 2-6 June 2024. It was great to see many of you at our booth as well as the annual Breakfast Meeting! We presented three talks at the meeting. If you were unable to attend, or want to review any of the material that was presented, the talks are summarised below [...]
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, [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]