Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years


Articles tagged: site analysis

Return to blog archive

Posted by Patrick Emery (July 15, 2020)

Variable Modifications in Mascot 2.7

Most protein samples will exhibit some degree of modification which needs to be considered when carrying out a database search In this article we’ll take a look at some important changes we introduced in Mascot 2.7 in how Mascot handles variable modifications. Variable modification permutation in Mascot 2.6 and earlier In Mascot 2.6 or earlier, variable modification permutation is handled [...]

Full article and comments form

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 [...]

Full article and comments form

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 [...]

Full article and comments form

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 [...]

Full article and comments form