Handling of shared (non-unique) peptides by dataProcess

[juan.per...@gladstone.ucsf.edu]

Hi all,

Could anyone help me understand how the dataProcess() function handles non-unique peptides in DDA? I know that we are supposed to provide a rather curated list but I have also observed that the function does some sort of filtering.

I went through the code but can't figure out clearly. 

thanks!

Juan

[Meena Choi]

Dear Juan,

If you used 'MQtoMSstatsFormat' function to convert MaxQuant output to MSstats input format, unique peptides will be removed with default option.

If you use other tool, MSstats assumes that 'PeptideSequence' or 'PeptideModifiedSequence' column has unique peptide. So, certain PeptideSequence measured for more than 1 protein, MSstats will generate error message with list of these peptides, as duplicated rows. 

So, If you have non-unique peptides, I recommend to remove before using MSstats.

Hope to help.

- Meena