Friday, March 15, 2013

'Experiment Control' is a valuable tool

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.

Now I looked at the figures again. It is very clear that there is 12ppm accuracy shift!

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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