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.
Thanks for sharing the post in brief. Do share more of this post of it's continuation.
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A client send in a dataset created from Orbitrap instrument. At the point when he utilized PEAKS to break down the information, shockingly, he just got not very many PSMs.Do My Assignment I inspected the figures in the 'Test Control' segment in the 'Rundown View' and saw that the forerunner mass mistake dispersion of the PSMs is odd. So I expanded the parent particle blunder resistance from 10ppm to 20ppm and got awesome outcome. 33% of the range have been recognized under 1% FDR.
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