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We've built a small tool for planning proteolytic digests. You enter a UniProt accession or paste a sequence, choose one or two enzymes, and the page shows the cleavage sites, peptide masses and m/z values, along with how much of the sequence falls inside your measurement range.
- We've included 13 enzyme presets, each with a reference to the primary literature, or you can define your own specificity across P4–P4′, including positions defined by exclusion ("not Pro")
- Two enzymes at a time, with cut sites coloured per enzyme
- Monoisotopic and average masses, and m/z for the selected charge states
- Fixed cysteine modification: carbamidomethyl (IAA, +57), methylthio (MMTS, +46) or none
- Sequence coverage for the chosen measurement range, updated as you type
- Hovering a peptide shows its position in the protein, its sequence and its m/z at each charge
- Settings are kept in the URL, so a permalink reopens the same digest
- It runs in the browser; the only request it makes is for an accession you fetch from UniProt
Needs no installation or account. → https://mslab-ibb.pl/digest
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MASSTRIM is a state-of-the-art mass spectrometry platform set to transform how molecular discoveries reach clinical practice. It is being built at the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, on the foundation of more than 25 years of experience of the IBB PAS Mass Spectrometry Laboratory — the largest facility of its kind in Poland and one of the largest in Central and Eastern Europe.
On 4 August 2026, MASSTRIM was entered on the Polish Roadmap for Research Infrastructures (PMIB) as a national research infrastructure of strategic importance for the development of Polish science. IBB PAS is the applicant institution.
The platform combines advanced proteomic and metabolomic technologies with bioinformatics, enabling comprehensive analysis of thousands of proteins and metabolites in a single biological or clinical sample. This delivers a complete molecular picture where, until recently, only individual parameters were within reach.
MASSTRIM is not a plan for the future — we are building it today. Over the past two years, the platform has been enhanced with two Orbitrap Astral mass spectrometers, instruments at the absolute forefront of global technology. This new equipment makes possible highly sensitive analyses of samples with very limited material, rapid profiling of large clinical cohorts, and work on a scale that was previously out of reach.
The platform will support biomarker discovery and validation, the development of diagnostic and prognostic panels, and the monitoring of therapeutic efficacy. It will also provide technological backing for biobanks and for projects carried out in collaboration with research institutions, clinical centres and the biomedical sector.
We want to shorten the path from molecular discovery to a real tool in the clinician's hands. MASSTRIM will accelerate the development and implementation of new diagnostic solutions and of methods supporting therapy selection and monitoring — to the benefit of translational and personalised medicine, and above all, of patients.
We welcome collaboration. If your research requires advanced proteomic or metabolomic analysis, get in touch with us.
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Say hello to our newest team member: the Thermo Orbitrap Astral mass spectrometer!
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Session 1 | Advancing Proteomics: New Methods with the Astral Mass Spectrometer, Best Practices, and Challenges in Experimental Design and Data Analysis
Time: 18.02.2025, 9:30 AM (GMT+1)
Speakers:
Bianka Świderska – Lead Proteomics Mass Spectrometry Specialist, IBB PAS
Dr Agata Malinowska – Senior Specialist in Proteomic Data Analysis, IBB PAS
Session 2 | Revolutionize Your Biomarker Discovery – Unravelling the Proteome by Untargeted Mass Spectrometry Proteomics at Scale
Time: 18.02.2025, 11:30 AM (GMT+1)
Speaker:
Dr Maik M. Pruess – Senior Field Application Scientist, Seer