There are so many factors that can make database search engines fail to produce a decent result. Today I saw such an interesting case.
A user send in a dataset generated from Orbitrap instrument. When he used PEAKS to analyze the data, surprisingly, he only got very few PSMs. I examined the figures in the 'Experiment Control' section in the 'Summary View' and noticed that the precursor mass error distribution of the PSMs is strange. So I increased the parent ion error tolerance from 10ppm to 20ppm and got very good result. One third of the spectrum have been identified under 1% FDR.
The figures in the 'Summary View' sometimes can help identify the problem when the search result is not ideal. In this case, the instrument is not well calibrated.
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