DDA analysis from Bruker Amazon SL data

DDA analysis from Bruker Amazon SL data rliyana  2019-12-07

I am try to load data from Bruker Amazon SL using mzML (raw) and .dat (MASCOT). Having issues. Appreciate someone can help me with this. I am attaching files of interest with this. Thanks !!

Nick Shulman responded:  2019-12-07

It appears that you did not attach any files here.

If your files are less than 50MB, you can attach them to this support request.

If your files are larger than that you can upload them here:

Also let us know whether you are seeing any sort of error message.
-- Nick
rliyana responded:  2019-12-07
Hi Nick,
I just uploaded two files
Nick Shulman responded:  2019-12-07

You should take a look at the MS1 Full Scan filtering tutorial.

That tutorial will show you how to get Skyline to read peptide search results and extract MS1 chromatograms.

One tricky thing that you might run into with your data is that in your search results file "74697_E1_2_01_625.dat", Skyline thinks that the raw file that was searched was called "281474976714603.mgf".
It might be necessary to rename your file "74697_E1_2_01_625.mzML" to "281474976714603.mzML" in order for Skyline to actually associate the peptide spectrum matches with that particular file.

Please do take a look at the MS1 full scan filtering tutorial and let us know if you have any questions.
-- Nick
rliyana responded:  2019-12-07
I used to do this all the time, atleast for five to six years. It never looked for .mgf file. I use skyline all the time. I ran in to this problem after recent skyline upgrade. I am very confident that it is due to changes made to skyline in the recent version.
Brendan MacLean responded:  2019-12-07
Maybe not, though. Often people miss something new about their current situation and blame it on a new version.

Nick likes to just get files, but I would prefer to hear a bit more about the issues reported as just "Having issues."

Can you describe the steps you have taken and what you are seeing that is different from what you expected?

Please provide some screenshots.

Thanks for reporting this and providing files.

rliyana responded:  2019-12-08
Hi Brendan,
Here is the screen captures of steps when I load my data, including names of the two files .dat and .mzML (same name as you can see in the same directory, anyways files I uploaded in to the forum has the same file names as it is, I am using..). I truly appreciate both you and Nick's help on this.
Brendan MacLean responded:  2019-12-08
Hi Rohana,
Nick is right. You should just need to rename your mzML file to "281474976714603.mzML" in the same folder with your .dat file and Skyline should find it and work just fine. Skyline doesn't actually need the .mgf file. It is just telling you what it finds in the .dat file as the name of the source file used in the search. Skyline will accept any mass spec data file with the same base name, i.e.:


This has to do with the fact that the source data file for the search (embedded in the .dat file) being "281474976714603.mgf". This has been this way for a very long time and is unlikely to have anything to do with recent changes. As I said, much more likely, you just never ended up with this kind of naming mismatch in the past. You probably did use .mgf files as input before, but their base names (without extension) matched you mzML or other raw data file names, and Skyline was able to proceed without asking for your help.

Even once you reach that screen where it is asking for the .mgf, if you just rename your mzML file as we have suggested, you should be able to click the Find or Find in Folder buttons and point Skyline to where to find any mass spec data file with the same base name, as described above.

We probably need to make this clearer that we are just looking for a mass spec file with the same base name. Skyline probably would not even accept a .mgf file at this location. It is just telling you the spectrum source file it has to match with a mass spec data file from which it can get MS1 spectra.

Hope this helps to clarify. Sorry for the confusion, but this is the original design and has worked this way since we created this wizard.

rliyana responded:  2019-12-08
Thanks Brendan !!