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Articles tagged: site analysis

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Posted by Ville Koskinen (January 18, 2019)

O-fucosylated CID spectra

O-linked fucose is easily lost in CID. A recent paper by Swearingen et al. in the Journal of Proteome Research discusses this in the context of identifying O-fucosylated thrombospondin type 1 repeats (TSRs) in Plasmodium parasites using database searching. The main problem is, the O-glycosidic bond is weaker than the peptide backbone. Collision energies typical for peptide fragmentation cause it [...]

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Posted by John Cottrell (February 15, 2017)

Exporting search results: tips and tricks

The Mascot Server export utility allows search results to be exported in a wide range of formats, together with the native result file and the MGF peak list. Exporting the result file can be useful if you need it for a third party application and don’t have file share access to the Mascot Server. Exporting the MGF might be useful [...]

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Posted by John Cottrell (May 8, 2013)

Site analysis

Site analysis in the Peptide View report is based on the score differences between matches with different arrangements of modifications. This started off as a rule of thumb, but was given a quantitative basis by Bernhard Kuster’s group at TUM, who analysed a collection of synthetic analogs of natural phosphopeptides to determine false localisation rate as a function of score [...]

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