I'm seeing a noticeable number duplicate annotations for the analytes generated from Compound Discoverer. Specifically, there are cases where the molecular weight are the same, but some (or all) of the retention times are different.
What is the best way of handling such cases during downstream analyses?
Last post by Ondrej -
Dear Hiroshi, I have a problem with MRMPROBS when processing large datasets (30+ samples and 20,000+ MRMs). Everything works fine until I save the project. Then I can not open it again (quite often).
Application: MRMPROBS.exe Framework Version: v4.0.30319 Description: The process was terminated due to an unhandled exception. Exception Info: System.Runtime.Serialization.SerializationException at System.Runtime.Serialization.ObjectIDGenerator.Rehash() at System.Runtime.Serialization.ObjectIDGenerator.GetId(System.Object, Boolean ByRef) etc.
It is difficult to get the info what is actually wrong. Could you please add a debug console or some other kind of warning or log file to the next version? Thank you. Best, Ondrej
i maybe wrong, but there is no peak left- and right retention times in each processed after the peak list export. There is only retention time (RT averaged) for each peak and each sample given, but I cannot see any peak start/peak end.
"Annotated Compound Table" This is actually the utility to check the duplicated annotations in the result. Currently, "Identified" and "Annotated" mean the ones of "Ref.matched" and "Suggested", respectively. (sorry, I will fix the header name accordingly in the next version) Num spots means, for example, if the number is 3, three peaks have the same InChIKey (actually, based on the first 14 characters) information in the result.
"Spot Relation Table" Actually, each peak spot is linked to other spots by some properties (within similar retention times): (1) same metabolite, but different adduct forms (2) similar chromatogram peak shape (3) the precursor ion peak is included in the MS/MS spectrum of higher'm/s peak (4) similar metabolic profiles. You can check the linkages by the spot relation table. Thanks,
the current version of MS-DIAL does not provide the edge RT for the alignment result. You can check the peak left- and right retention times in each processed file by export -> peak list export function. Sorry for your inconvenience.
1. You processed your data with e.g. MSP file A for peak annotation, and then, created an alignment result A. 2. Then, you reprocessed your data (in the same project) with MSP file B for peak annotation, and then, created an alignment result B. 3. Then, you tried to export the alignment result of "A".
If yes, the outofrange exception is due to the difference of MSPs. Although the MSP ID stored in the alignment result A is for MSP file A, your current project (.mtd2 file) now contains the information of MSP file B. When the file sizes of MSP file A and B are different, this kind of error will be occurred.