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Posted by John Cottrell (December 13, 2016)

Protein inference for spectral library searches

The major new feature of Mascot Server 2.6, now running on this web site, is that searches of spectral libraries have been fully integrated with ‘conventional’ Mascot searches of Fasta files. The search engine for spectral library searches is MSPepSearch from Steve Stein and colleagues at NIST. We didn’t have any revolutionary ideas for improving spectral library scoring so, rather [...]

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Posted by John Cottrell (January 19, 2015)

Creating a list of confidently identified proteins

This can be done very easily using Report Builder: Select the Decoy checkbox when submitting the search Open the result report as a Protein Family Summary Switch to the Report Builder tab Expand the decoy search section and set the peptide FDR to 1% Expand the filters section and set ‘Num of significant unique sequences’ > 1 Optionally, expand the [...]

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Posted by John Cottrell (November 22, 2013)

Does protein FDR have any meaning?

Its easy to grasp the concept of using a target/decoy search to estimate peptide false discovery rate. You search against a decoy database where there are no true matches available, so the number of observed matches provides a good estimate of the number of false matches in the results from the target. People debate implementation details, such as whether the [...]

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