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Posted by Ville Koskinen (October 14, 2019)

Is your database search reproducible?

A lot has been written about the reproducibility of shotgun proteomics workflows, as well as controlling measurement variability between instruments and laboratories. An equally important factor is data analysis transparency and reproducibility, which is gaining increasing visibility. This boils down to two essentials: recording all software parameters used, and ensuring the software produces the same output given the same input [...]

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Posted by John Cottrell (June 27, 2014)

Spring clean your mascot.dat

Updates to Mascot 2.5 will be going out shortly. When an existing installation is updated, settings in the options section of mascot.dat are only modified by the installer in exceptional cases. The assumption is that any changes have been made with good reason and should be honoured. The down-side of this approach is that values may be persisted that are [...]

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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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Posted by John Cottrell (April 9, 2013)

Non-standard amino acid residues

Mascot only supports the 26 letters of the Latin alphabet as one-letter codes in sequence database entries. And, it is case-insensitive, so you cannot use (say) R and r for different residues. This is quite a limitation if you want to create a custom database that encodes non-standard or modified residues. It isn’t a concern if you search only public [...]

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