Problem in using MSstats

Problem in using MSstats linda198015  2016-11-03 23:06
Hi Skyline team,

When we analyzed the DIA data by skyline and MSstats softwares, we have some troubles.

We used the MSstats software to normalize the DIA data (QC function); however, we see the following error massage and lots of duplicated peptide sequences showed also in the message window :

“Error in dataProcess(raw, normalization = inputnormalize, nameStandards = standardpepname, : Please remove duplicate rows in the list above.
Error : Can't process the data. ” .

How to solve this problem so that we can process data using MSstats software ?

thank you.

Nick Shulman responded:  2016-11-04 01:20
This error happens when the same transition appears more than once within a given protein.
The most common cause of this is when a Protein contains the same Peptide twice.

I can see in your attached PowerPoint file that you have some duplicated peptides.
MSstats can handle the same Peptide under different proteins, but it has problems if the same peptide appears twice within the same protein.

More precisely, if you export the MSstats Input report:
File > Export > Report
then, within the .csv file, the following columns need to uniquely identify each row:
ProteinName, PeptideModifiedSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, FileName
You can use something such as Microsoft Excel to find those duplicate rows, and delete the appropriate items from you Skyline document.