You can download the library file containing the Fiehn lab's RT values at: http://prime.psc.riken.jp/compms/msdial/main.html#MSP Download this: MS-DIAL lipidomics (adjusted Oliver Fiehn lab LC-MS method) Then, replace the original "***.lbm2" file in ms-dial folder with the above lib. Thanks,
Not sure your data detail. Could you please send me one of your data with the PPT slides to explain the detail of your situation. The PPT slides containing ms-dial start up setting and parameter conditions' screenshots are very helpful for me.
could you please send me one of your wiff2 file?Actually, I validated the function by using wiff2 that I have. But I have little experience personally for using the wiff2 format file. Therefore, your help is very welcomed to improve my program's robustness. Thanks,
In GC-MS, first, you should choose the msp library that contains retention index (RI) by the same column as you use. The RI value should be reliable. (but hopefully, if you do TMS-derivative metabolite profiling, analyzing standards of sugar compounds like glucose and galactose is needed to validate the results because they have very similar RI/RT values.
Then, you may use the library like "All records with Kovats RI" that contains experimental/predicted RI values. Not all of RI values should be compatible with your experimental data, but the annotation using this wider coverage library will be helpful for your annotation pipeline.
sorry, I cannot understand your situation. If your data was obtained by negative ion mode of ESI, you should choose "Negative" mode in the start up window of MS-DIAL.
also make sure, the direct import for MS raw data is only available in Windows GUI application. This is because the API for reading MS data was built in .net framework environment (you do not have to understand this) in the MS vender's side. In future, it may be improved to be used in any type of OS. Also, although I wrote the parser of Bruker's MS data, I recommend to convert Bruker's .d file into abf (for normal LC-MS) or ibf (for ion mobility data) for the rapid data retrieving in MS-DIAL application at this moment.
Dear Kyra and all, as I noticed at the previous update, the msdial in mac/linux is currently available as the command line application. If you use the GUI app, you have to use Windows OS. You can run the msdial console app of mac/linux with the "-p" option that creates the project folder which can be opened in the Windows GUI application.
And Sergey,
thanks for the suggestions. I also recently think the same demand in my private research. I will create the functionality in the next update. Thanks,
sorry for this issue. It is because that two lbm2 files are contained in the same ms-dial folder. I just forgot to delete one of them...I reuploaded the same ms-dial kit containing only the latest library file (lbm2). Thanks,
The MS raw data of SCIEX (.wiff, .wiff2), Thermo (.raw). Agilent (.d), and Waters (.raw) can be imported directly without any data conversion. SWATH-MS type acquisition in SCIEX WIFF1/WIFF2 and Thermo RAW was validated. AIF type acquisition in Agilent data was validated (The abf file format for Waters MSE is still needed. However, it will be fixed soon). Raw data of Agilent and Waters can be imported by "drag and drop" of the analysis files in the analysis file import window. The option "N% detected in at least one group" was added to GCMS project. SIRIUS .ms format was supported as a peak list export option. The peak picking algorithm was improved (see http://www.metabolomics-forum.com/index.php?topic=1609.0). Lipidomics platform (including MS/MS search function) was improved. The function of "gap filling by compulsion" was fixed (see http://www.metabolomics-forum.com/index.php?topic=1469.0).
