Matrix Science

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Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years https://www.matrixscience.com

Quality control plot drawn by MSstats.

Photo of branded goods.

WP 449: Mascot DIA Introduces probabilistic scoring.

WP 464: Mascot DIA enables direct comparison of DDA and DIA.

WP 622: Overcoming Peptide-Centric DIA Limitations: Discovering Unsuspected Modifications.

WP 449: Mascot DIA Introduces probabilistic scoring to spectrum-centric analysis of DIA data.

Probabilistic scoring enables direct control of false positive rate, demonstrated in this poster with MS/MS spectra containing very different noise patterns (ion trap, TMT, Orbitrap AIF).

WP 464: Mascot DIA enables direct comparison of DDA and DIA identification and quantitation results.

Mascot uses the same sequence matching and precursor quantitation algorithms for DDA and DIA spectra, allowing results to be directly compared and the same downstream processing to be used between the two techniques.

WP 622: Overcoming Peptide-Centric DIA Limitations: Discovering Unsuspected Modifications in Narrow-Window DIA Using Mascot Error Tolerant Search.

The Mascot Error Tolerant search is a two-pass search: a standard first-pass search identifies proteins, then a comprehensive second pass iterates through the entire Unimod modification list, plus sequence variants.

Example QC report for a DDA data set generated using Claude.

Bar chart comparison of standard acqusition method compared to Thunder-DDA-PASEF.

Pie chart illustration of the top species detected: Mycobacteroides abscessus (61%); Sus scrofa (22%); Homo sapiens (11%); Mycolicibacterium goodii (5.6%).

Screenshot of blib2msp.pl output, displaying conversion results, time spent and a table of peptide modifications in the spectral library.

Screenshot of Mascot Distiller showing the menu item for cleaning up old cache files.

Example MS/MS spectrum of KQLATKAAR using peak area as peak intensity (top) or signal-to-noise as peak intensity (bottom).

Illustration of a DIA MS/MS spectrum with unidentified peaks (top) and labelled peaks for two identified peptides (middle and bottom).

MS/MS spectrum of RPQYSNPPVQGEVMEGADNQGAGEQGR zoomed in to the region 1150-1750Da. Several complementary b and y ion pairs are labelled.

Diagram of Mascot DIA: Mascot Distiller processes DIA runs into peak lists and detects precursor masses in MS1 and MS2 scans; these are sent to Mascot Server for database searching; finally, Distiller downloads the PSMs and performs MS1 quantitation.

Mascot Newsletter

Photo of pens, notebooks and promotional bags.

Matrix Science Breakfast Meeting, Monday 2nd June:

Using MS2Rescore to boost identification rates in complex samples,
Tim Van Den Bossche, Computational Omics and Systems Biology Group (CompOmics), Ghent University/VIB-UGent Center for Medical Biotechnology

Mascot DIA: Universal spectrum-centric approach,
Ville Koskinen, Matrix Science

Mascot DIA: Thermo LFQ example,
Patrick Emery, Matrix Science

Count of protein hits and peptide matches, comparing Percolator node (6785 proteins) to Mascot ML (6899 proteins).

Matrix Science Breakfast Meeting, Monday 2nd June:

Using MS2Rescore to boost identification rates in complex samples,
Tim Van Den Bossche, Computational Omics and Systems Biology Group (CompOmics), Ghent University/VIB-UGent Center for Medical Biotechnology

Mascot DIA: Universal spectrum-centric approach,
Ville Koskinen, Matrix Science

Mascot DIA: Thermo LFQ example,
Patrick Emery, Matrix Science

Mascot Newsletter

Matrix Science Breakfast Meeting, Monday 2nd June:

Using MS2Rescore to boost identification rates in complex samples,
Tim Van Den Bossche, Computational Omics and Systems Biology Group (CompOmics), Ghent University/VIB-UGent Center for Medical Biotechnology

Mascot DIA: Universal spectrum-centric approach,
Ville Koskinen, Matrix Science

Mascot DIA: Thermo LFQ example,
Patrick Emery, Matrix Science

Screenshot of the format controls in Protein Family Summary, showing a dropdown item for example_ML_adapter.py

Screenshot of an LFQ project in Mascot Distiller. Left window: XICs of a peptide match with retention time alignment enabled. Right window: isotopic distribution of the precursor peaks in the survey (MS) scan.

Mascot Newsletter

Table comparing counts of protein hits and proteins quantified by Mascot Distiller between Mascot Server 3.0 (no refining) and Mascot Server 3.1 (with MS2PIP HCD2021).

Number of protein groups and peptide groups in PD 3.1 and PD 2.4, comparing Mascot 3.0 (no ML) with Mascot 3.1 (with ML).

Table illustrating protein and peptide match counts in Proteome Discoverer 3.1 when using Mascot Server 3.0 and 3.1.

Table of example data sets shipped with Mascot. Sections visible in the screenshot are MS/MS Ion Search, Quantitation, Spectral Libraries, Crosslinking and Top-down.

Illustration of site analysis confidence. The top three matches to the spectrum have the same sequence (DIGSESTEDQAMEDIK) with two serines and one threonine, one of which is phosphorylated. Mascot reports site localisation confidence S4 85%, S6 15% and T7 0.7%.

Illustration of the score distribution, estimated FDR, count of significant sequences and two peptide matches with TMTpro ratios visible.