Hi Brendan,

I noticed a bug in MS1 filtering / spectra assignment when multiple spectra match to the same peptide. Here is my workflow:

1. search data using mascot 2.4
2. download .dat file
3. build reference genome in skyline
4. import spectral library
5. add all peptides to the document
6. import .raw file

In case there are more than one spectra, all other spectra are not assigned and an error message is displayed "Failure loading spectrum. Library might be corrupted."

.dat file contains a variable modification on D or E of C6N4H12O as well as variable M (oxidation) and static C (carbamidomethyl)
background proteome was digested with AspN, resulting in N-terminal peptides with D and E.

This error is reproducible on skyline-daily 64 bit 2.5.1.6484 (my PC) and skyline 2 64 bit (Watson).

Best, Alex.

Kaipo, please have a look at this one.

ok, I have a theory regarding this bug: if the proteins in the background (set in skyline) don't match the proteins from the database searched (mascot), then this error occurs. My evidence: I matched now both databases and all spectra work fine (see attachment).

I hope this helps. At least now I have a solution to the posted problem.
Alex.