Not able to see "library peak area" in peak areas-replicate comparison Monica E  2019-09-15


I am trying to compare the peak areas of my different proteins among 16 different samples. I can now see the different peptides for each protein as well as the spectra corresponding to every replicate. However, I cannot see the "library" peak area, only the peak area for each replicate. I had a read through the forum and found a suggestion that said to "right click" on the replicate comparison panel and select to see the library peak area, however, this option does not come up when I "right click". Would you be able to help me? The library I am using in peptide settings is a reference pool sample of all the 16 replicates. I attach a screen shot as well in case it is any help.

Thanks in advance,
Monica Espinosa

Brendan MacLean responded:  2019-11-30
Title: Not able to see

Hi Monica,
This appears to be quite old. Sorry that it went unanswered. From your screenshot, it looks like your Peak Areas - Replicate Comparison plot is only showing precursors. You can fix that by using right-click > Transitions > Products, or you could choose All and then use "Split Graph" to split the chromatograms into two panes showing both Precursors and Products separately.

It is unclear to me why your screenshot does not show the "Expected" isotope distribution for your precursor ions ("precursor", "precursor [M+1]", "precursor [M+2]"), but maybe you turned that off in your search for a bar labeled "Library". Usually, when you are viewing precursors, you would get "Expected" and when you are viewing products you would see "Library" if there is a corresponding library spectrum.

Hopefully, you have already worked this out long ago, but I thought I should at least respond. Sorry again this one got by us initially.