Recently I tried to use MS-Dial to analyze GC-QQQ data (Standard of Fames), acquired by Thermo QQQ. Here I compare 2 Fames standards with 2 blank. I set the parameter "Minimum peak height" at 1E06. (see parameters_1.png) After the alignment I checked all the peaks. As expected, I note that in the blank, there is no peak C18: 3n6 (Peak Id :-2). (see Picture_2.png). Although the software automatically takes background noise for Blank, the peak heights are less than 1E06. Having set the parameter "Minimum peak height" at 1E06, I wonder why the blank value is not 0?
Sorry for this basic question, but i need our advice about relative lipids quantifiation between two sample. I'm beginner.
Imagine that we started with the same starting quantity of a sample (weight (ie 10 mg DW). We wish to compare samples A versus B. No internal standard during extraction Injection using LC-QTOF ddmS2, data procesing using MS_Dial and Lipid blast for annotation. Is it possible to perform a relative quantification between A and B (normalization to total amount of a lipid class or all measured lipid classes) ? or an internal standard need to be put during extraction process ?
Sorry for this basic question, but i need our advice about relative lipids quantifiation between two sample. I'm beginner.
Imagine that we started with the same starting quantity of a sample (weight (ie 10 mg DW). We wish to compare samples A versus B. No internal standard during extraction Is it possible to perform a relative quantification between A and B (normalization to total amount of a lipid class or all measured lipid classes) ?
I have samples which consist of lipids (TG, PC, PE, CL) which are not present in the database (unusual fatty acids). I would like to create a * txt or * msp file of MSMS spectra of my lipids automatically. Is it possible to do this using the lipidblast template to generate in silico MSMS spectra of my PC, PE, TG, CL having unusual fatty acids? Best regards,
I have two basic questions and I would like your opinion.
1. I have a Qtof from Agilent (6538). In the parameters of the auto MS MS, it is possible to make an acquisition in ddms2 top 20. However in publications I often see people doing the top 3. Is it a standard ? Is it due to the machine's ability to do this? by making the top 20 is it possible to take an M + 1 and to fragment it and to make possible bad identification?
2. I also have questions about solvents. Is it possible that by putting ammonium acetate certain families of lipids are less detectable than by putting ammonium formate? especially MGDG and DGDG ?
Thank you in advance for your time spent answering these basic questions.
When I use the "export GNPS" function, I have: - the peak table - the MGF file I do not understand why I don't find all the IDs of the peak table in the MGF file. I took an example here (Présentation1.pdf) where I have the IDs 9,10,11,15, 26,34 which are present in the peaktable. However in the MGF file, the ID 15 and 26 are not present. If it is because IDs 15 and 26 are not MSMS data, can we create an MGF file corresponding exactly to the peak table?
First of all I wish you a very happy new year 2020. I have been using MS_dial for a few days for lipidomics in LC-MS in DDA mode using the fiehn method. However, I modified the HPLC method. I reduced the flow rate to 250 µl / min. So the method is longer than the original method. - Is it possible to replace the original retention times automatically on the lipidomic database ? If yes, how can I do it?
Overall, how can I predict retention times from your database with my method that are very close to your method?
