I am looking a Mass spectrum data for human samples, but in the protein list identified by MS, there are many proteins described as from other species or as "xxxx Reverse 000xxxx" (such as 7507 Reverse_0007507), could anybody tell me what these names mean? Thanks.
Hi,
When identifying proteins based on peptides identified by MS/MS, the confidence of a protein ID depends, amongst others, on the size of the interrogated database. In order to increase database size and to get a feeling for so-called 'false discoveries', databases can be expanded by including reversed protein sequences next to the actual forward sequences. This means that all sequences in the database are also included in their reverse order (i.e. protein sequence A: ACDEF and its reverse sequence FEDCA).
The fact that you're identifying a lot of reverse sequences could indicate that your false discovery rate is high, which in turn is a signal to look into your data quality and into the settings that were used to generate the search result you're referring to.
Good luck!
Hi,
When identifying proteins based on peptides identified by MS/MS, the confidence of a protein ID depends, amongst others, on the size of the interrogated database. In order to increase database size and to get a feeling for so-called 'false discoveries', databases can be expanded by including reversed protein sequences next to the actual forward sequences. This means that all sequences in the database are also included in their reverse order (i.e. protein sequence A: ACDEF and its reverse sequence FEDCA).
The fact that you're identifying a lot of reverse sequences could indicate that your false discovery rate is high, which in turn is a signal to look into your data quality and into the settings that were used to generate the search result you're referring to.
Good luck!
Eef, Thank you very much. Make sense. The majority of peptides identified are human peptides, the peptides of other species as well as Reverse sequence are on the bottom of the list, suggesting false positive. I can delete these peptides from my analysis, right? Thanks.
Since the peptides of other species and Reverse one should not be in the human data
Hi De-Liang,
Correct. Anything that has an annotation such as "Decoy" or "Reverse" in the name, should be deleted since they are simply nonsense amino acid sequence matches..
You will also notice that if you start to tighten the identification parameters to eg., show you hits that are only found when false discovery rate or FDR is 1%, then you may find that, depending on your data set, 99/100 hits will be correct and you will eliminate the false hits..
Good luck, Hediye.
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