remove peptides that are not present in all replicates contet  2019-09-27
 
Hi,
I am working with Skyline files from a DIA experiment in which samples were processed in 2 batches, which each contain replicates from all experimental conditions and have their own reference for normalization. I want to merge the Skyline files from the 2 batches to analyze the data in MSstats. What I have done so far is open the Skyline file of batch 1 then File>Import>Document to import the file of batch 2. I selected Add new replicates and Merge matching peptides, such that peptides that have been detected in both batches show up under the same protein ID. My problem is that some peptides were detected in only 1 of the 2 batches, which causes problems with MSstats (the error message says that "the input dataset has incomplete rows"). I only want to keep peptides that have been detected in both batches. How can I remove peptides that are not present in all replicates (e.g., in the attached screenshot, keep the aqua peptide but exclude the green one)?
Thanks for your help!
Candice
 
 
Nick Shulman responded:  2019-09-29
You can use the Pivot Editor in the Document Grid to do this.

I would start with a report that had the two columns "Precursor" and "Total Area".
Then, use the Pivot Editor and make it so the row header is "Precursor", and the add "Count of Total Area" as a Value column.
Then, you can sort that Count of Total Area column and select all of the rows where that number is fewer than the number of replicates you want your precursors to have.
After you have selected the rows you want to have removed, you can use the "Actions" dropdown at the top of the Document Grid to delete those precursors.

If you want to learn more about the Document Grid, you can take a look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

If you want to learn more about the Pivot Editor in the Document Grid, you can take a look at this page:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PivotEditor

-- Nick
 
contet responded:  2019-09-29
thank you very much for your suggestion Nick! I ended up having to do it at the transitions, rather than the precursors, level, but it solved my issue in an efficient manner :-)