skyline not recognizing full .mgf name from .dat file

skyline not recognizing full .mgf name from .dat file erik.soderblom  2018-12-10

Hi Skyline Team!

I have a situation where I have a .mgf file (created through PD) searched in Mascot with the search results saved as .dat. Sometimes those .dat files don't match (verbatim) the .raw file. Therefore, when if I manually build a spectral library and select those .dat files and then input my raw data... it doesnt associate the actual search results with the actual raw data (and features such as align retention time, etc. is not available).

Since the .mgf file name (which always will be the same as the .raw name) is in the .dat file structure... would it be possible to go into the .dat file and make sure its assocaited with hte correct .raw file... even if the .dat file and the .raw file are not named the exact same thing?

I've attached uploaded a file called ID19225_03.dat to the skyline FTP for an example. Thanks!


Brian Pratt responded:  2018-12-10
We've seen several different ways that Mascot users embed raw file information into .dat files, it's a bit of a moving target. What version of our software are you on?

In the case of ID19225_03.dat, what is the path and filename of the raw file it's intended to match?


Brian Prat
erik.soderblom responded:  2018-12-12
Hi Brian. Thanks for the response. I was on public release 4.2.0. The full file name is ID19225_03_E749_3961_080415.raw which was listed twice in our .dat file (at least with the .mgf creation/mascot search workflow we use). quick back story... I'm teaching the full MS portion of the Skyline@Duke course and used this .dat file w/ the corresponding .raw file as part of my lecture. Once it was loaded, I couldnt get any of the functionality of the .dat file actually being assocaited with the .raw file (like alignment). Brendan then suggested I submit this request!
Thx! Erik
Brian Pratt responded:  2018-12-13
Hi Erik,

It's a pretty simple change to make, so I made it - can you please update your BiblioSpec files from (look for "Pre-compiled binaries" at the bottom of the page) and let me know if that works better for you?

And thanks for teaching!