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Updated: Jun 26, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
Published on: August 19, 2025
Improving mass measurement accuracy in mass spectrometry based proteomics by combining open source tools for
Magnus Palmblad1, Yuri E M van der Burgt, Hans Dalebout
1Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands. n.m.palmblad@lumc.nl
Abstract:
Accurate mass determination enhances peptide identification in mass spectrometry based proteomics. We here describe the combination of two previously published open source software tools to improve mass measurement accuracy in Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The first program, msalign, aligns one MS/MS dataset with one FTICRMS dataset. The second software, recal2, uses peptides identified from the MS/MS data for automated internal calibration of the FTICR spectra, resulting in sub-ppm mass measurement errors.
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