I am having the same issue. If I include a post-identification text library, is it possible to get RT, m/z and MS2 matches factored into the total score?
I am using MONAs LCMS spectral library (msp) which does contain MS2 for the entries in my text library. I have included the text library because of the RT info which I would like to leverage for identifications.
Thanks for checking. My issue is that when I select the Lipidomics mode, after I click 'Finish', the program crashes. It works on metabolomics mode but I get no identifications because these are lipid samples. I am using a PC with 16GB RAM so I am not sure what the problem might be. I can try again with the new release of MSDIAL if you think that might help.
Sorry about that, not sure what might have happened. Just resent the file. Also forwarded you the email link you should receive to retrieve the file. Let me know if you dont get it.
Appreciate you being so responsive! I just sent you an ibf file which I created using the ibf converter directly from an Agilent .d file. Let me know if this is a problem and you want me to do .d-->mzml-->ibf conversion instead.
Whats the best way to send you my raw data file? It would be great if you can take a look. The files are large, the Agilent .d file is ~2.8 Gb.
I was able to convert the Agilent .d file to ibf directly using the ibf converter but when I tried to process the file using the MSDIAL, the application closes abruptly. So then I tried converting the .d file to an mzml file using msconvert. But I continue to have the same issue. After entering all the settings , i click finish and see the 'Loading libraries' window briefly and the application closes/crashes.
thanks for the tip. The tutorial uses data dependent MS/MS dataset. Do I have to do anything different from the tutorial since my data is not DDA? It would need some sort of deconvolution. Can I simply choose 'Data independent MS/MS' in the 'MS method type' field here: https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial#section-10-2
I think I would need to do something similar to what is shown here https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial#chapter-8 But my question is, instead of 3 fixed collision energies (as described in the tutorial link above), I have a ramped collision energy....so collision energy is different for different molecules based on their drift time.
I am working with LC-IMS-MS/MS lipidomics data collected on an Agilent (drift tube) instrument using ramped collision energy. The collision energy was a function of the drift time. The tutorial works with data that was collected using 3 discrete collision energies. Is there a way I can use MS-DIAL4 for my data?
