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Welcome
Mascot Distiller supports Thunder-DDA-PASEF acquisition on Bruker timsTOF instruments.
This month's highlighted publication identifies L- and D-lactylation on histones in mouse testis.
Come meet us at IMSC 2026 in Lyon, France this August.
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Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years
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Processing Thunder-DDA-PASEF data
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Thunder-DDA-PASEF is a recently introduced acquisition strategy for LC-IMS-MS on Bruker timsTOF instruments.
The method takes its name from the lightning shape of the fragment isolation filter applied in the 1/K0 ion mobility and m/z channels.
It is better at capturing the characteristics of HLAlps (human leukocyte antigen (HLA) class I peptide ligands), including the frequent presence of singly charged precursors and their narrow length distribution.
Mascot Distiller supports DDA-PASEF natively, and this includes Thunder-DDA-PASEF.
We reprocessed raw files from the JPOST project PXD040385 comparing a plasma sample between standard and Thunder-DDA-PASEF methods.
The default processing options include a 1/K0 tolerance on the precursor grouping defined by the "precursorIonMobilityGroupTol" setting.
For these data, we used 0.01, which is tighter than the default tolerance 0.026.
Database search settings were derived from the original publication.
The sequence database was the mixed species database referred to in the paper, searched using no enzyme specificity.
Finally, results were refined with machine learning (MS2PIP, Percolator)
The standard DDA-PASEF method produced 4937 significant sequence matches at 1% FDR, while Thunder-DDA-PASEF yielded 8814, almost 80% increase.
The count of identified peptides length 8-13 that NetMHCpan predicts to be HLAIps increased from 2919 (DDA-PASEF) to 4860 (Thunder-DDA-PASEF).
The full results are on our website.
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Featured publication using Mascot
Here we highlight a recent interesting and important publication that employs Mascot for protein identification, quantitation, or characterization. If you would like one of your papers highlighted here, please send us a PDF or a URL.
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Both L-Lactyl and D-Lactyl Enantiomers Modify Histones in Mouse Testis
Julie Manessier, Hassan Hijazi, Lisa Vizzini, Sabine Brugière, Marie Courçon, Christophe Masselon, Alberto de la Iglesia, Julie Cocquet, Delphine Pflieger
Molecular & Cellular Proteomics 25(7):101601, July 2026, doi:10.1016/j.mcpro.2026.101601
Dynamic histone post-translational modifications have a crucial role in gene expression.
Lysine lactylation is a recently discovered histone PTM which exists as two enantiomers, L- and D-lactylation.
The authors developed a targeted LC-MS/MS workflow for identifying these on lysines of histones in healthy mouse tissue.
Histones were extract from adult mouse testis and mixed with heavy isotope-labelled synthetic peptides carrying either L- or D-lactyl groups.
After LC-MS/MS analysis, raw data were converted to peaklists using the in-house MGFBoost software.
Data-dependent acquisition (DDA) data were searched using Mascot Server 2.8, then
processed in Proline to estimate acetylation stoichiometry, enabling comparison with lactylation levels.
Quantitative analysis of parallel reaction monitoring (PRM) data was performed in Skyline, using the synthetic peptides as internal standards.
The authors identified both forms of lactylation on multiple lysine residues of histones H3 and H4.
Despite the higher abundance of L-lactate in the cell, several sites contained almost equal amounts of L- and D-lactylation.
Although histone lactylation was found to occur at low stoichiometry across the whole of histones H3 and H4, approximately 0.01–0.44%, it exceeded acetylation at the C-termini of histones H3 and H4 and became more abundant in the histone fold domain.
The authors suggest a mechanism is producing a mixture of the two enantiomers of lactate, or that there is a more direct substrate for lactylation that leads to histone modification by L- and D-lactylation.
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IMSC 2026
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In August, meet us in Lyon, France at IMSC 2026.
We'll be at booth #40 for the duration of the conference, 22nd-28th August.
Join us there and see a demo of the latest version of Mascot.
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About Matrix Science
Matrix Science is a provider of bioinformatics tools to proteomics researchers and scientists, enabling the rapid, confident identification and quantitation of proteins. Mascot continues to be cited by over 2000 publications every year. Our software products fully support data from mass spectrometry instruments made by Agilent, Bruker, SCIEX, Shimadzu, Thermo Scientific, and Waters.
Get a quote
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You can also contact us or one of our marketing partners for more information on how you can power your proteomics with Mascot.
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