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Posted by John Cottrell (June 18, 2016)

High FDRs for methylated peptides III

The MCP paper "Large Scale Mass Spectrometry-based Identifications of Enzyme-mediated Protein Methylation Are Subject to High False Discovery Rates" raises some important questions concerning the accuracy and interpretation of database search results. In this third article, we look at the difference between using counts of matches (PSMs) and counts of distinct sequences to calculate the false discovery rate (FDR). filestarget [...]

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Posted by John Cottrell (May 18, 2016)

High FDRs for methylated peptides II

In a previous article, we discussed how the false discovery rate (FDR) for modified peptides would be higher than the global FDR for all PSMs if the proportion of modified peptides in the search space for false matches was higher than for true matches. This is only one factor in the very high FDRs for methylated peptides reported in the [...]

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Posted by John Cottrell (April 21, 2016)

High FDRs for methylated peptides

"Large Scale Mass Spectrometry-based Identifications of Enzyme-mediated Protein Methylation Are Subject to High False Discovery Rates" in the March edition of Molecular & Cellular Proteomics represents a very substantial and systematic piece of work from the University of New South Wales. Three types of sample preparation (coomassie gel, unstained gel, HILIC) were combined with three different ionisation methods (CID, ETD, [...]

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