|Title||»||Ambiguous peptide spectrum matches are removed during library building without any notification|
|Assigned To||»||Brendan MacLean|
Over the years people have been confused and sought support when ambiguous peptide spectrum matches get removed during spectral library building. It usually starts with a request for why certain peptides are missing in the library.
It would be a big improvement, if Skyline could notify the user that ambiguous peptides were removed and give them information on how many and which ones. I just typed up the following report for one such case:
DNKDGTITVR++ -> EKTGYRVVSGNEQGR+++ (scan 6440)
LNELVEYVSTNR++ -> LLLLLPPAIRGPGLGVAGVAGAAG+++ (scan 5150)
DFSALESQLQDTQELLQEENR++ -> MLDGSRKDKALPNSGDETLMRRTSTIGKKSVQTI+++ (scan 9036)
VQLNFLKLLSATAR++ -> LDLFYKCVCFLPVKLIFVAM+++ (scan 7175)
YIYFHKAPSPEKAEEESERLLR+++ -> SCGSCGGSKGGCGSCGGSKGGC++ (scan 8847)
It would be nice if something like this were automatically accessible any time PSMs were removed due to ambiguity.