The official Bluesky account of the Picotti lab at the IMSB at ETH Zürich
Picotti Lab
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In mass spectrometry-based proteomics, peptides can fragment after chromatographic separation and before MS analysis. This phenomenon is called in-source fragmentation (ISF), and the resulting fragment peptides can be misinterpreted as biologically meaningful.
In our latest study, we assessed the prevalence and impact of ISF on protein- and peptide-centric proteomics approaches, including immunopeptidomics, phosphoproteomics, and structural proteomics. Our analysis covered 38 datasets, both newly generated and previously published.
We are delighted to announce that Paola Picotti has been awarded the Otto Naegeli prize for biomedical research!
otto-naegeli-preis.ch
The extent of ISF varied substantially between datasets, influenced by factors such as sample complexity, instrumentation, peptide sequence, and method parameters. In some cases, ISF accounted for more than 30% of peptide identifications.
Our findings highlight the importance of detecting in-source fragments as part of standard data analysis workflows to avoid misinterpretation.
With increasingly sensitive mass spectrometers detecting ever more m/z features, ISF is likely to become a growing concern.
Picotti Lab
The good news: @Thorben Schramm, postdoc who led this work, developed an open-source algorithm that allows you to detect and remove in-source fragments from your data, making ISF correction straightforward to implement.
See our preprint here: doi.org/10.64898/202...
Paola is deeply grateful to the Otto Naegeli Foundation, to her former and current lab members whose talent, curiosity, and dedication made this possible, to her collaborators, her current and past colleagues and administrative team @imsb-eth.bsky.social, and to @ethz.ch for the long-term support.
Picotti Lab
Picotti Lab
Picotti Lab
new lab preprint - Protein function prediction is a well established problem but proteins exist in different post-translationally modified forms. Here, @julianvangerwen.bsky.social built a ML model to predict the biological process regulated by individual phosphosites www.biorxiv.org/content/10.6...
