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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 (October 19, 2016)

Retention time

Although retention time is not part of the Mascot scoring algorithm, it can be used by Percolator to improve the re-scoring of search results and it is important or essential information for many types of quantitation. This article examines how retention time is represented in the peak list, the search results, and various export formats. Mascot Server works off a [...]

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Posted by Ville Koskinen (August 15, 2015)

PSI file formats, part 3: repositories

We’ve talked about mzIdentML validity only in terms of file structure. Proteomics repositories, such as PRIDE or ProteoRed, of course require files to be valid in that sense, but they impose additional requirements. If you need to upload your search results to a repository, it is worth looking at this more extended idea of validity. For simplicity, I’ll only consider [...]

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Posted by John Cottrell (April 30, 2014)

Peak list arcana*

This article addresses some aspects of how the information in a peak list is used by Mascot, what is not used, and how the peak list is processed prior to a search. These things are all in the manual, but can be difficult to find, short of reading it from cover to cover. Fragment charge is not used in the [...]

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