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1
MS-DIAL / Batch job error
Last post by Angrist -
dear Developers
During the MS Finder search on all MS/MS events (including the identified ones) I received the following error:

Batch job was desorbed by the following error: Object reference not set to an instance of an object

what does it mean? what are the measures to avoid it again? the processing time is very long, even if I indicated in the configuration a time out of 1 min (structure finder stopped at 255075933 after 2 day..)
all the best
andrea
3
MS-DIAL / MS/MS spectra selection for library matching - MS-DIAL 4.24
Last post by DeFelice -
Hi Hiroshi,

I am processing time-course data right now (but this is applicable for all studies).  I am finding a number of features with poor spectral matching in the alignment result, but when I check the "Spectrum reference file name" column I find the spectra are commonly from samples with very low levels of the metabolite.  If I then go to a file with high levels of that same feature I find a very highly scored match.

So my question is:  Is there a way to force MS-DIAL to select the MS2 spectra (in the aligned peaks list) from the sample with the most intense response?

Perhaps a relevant note:  This feature found using an mz-RT list.

Thanks,
Brian
4
MS-DIAL / Re: convert lbm to lbm2
Last post by pennoca -
Hi Rico,

Is it possible to read this file in R?

I want to check if a specific Lipid is covered by the default library.

thanks you for the info

best regards, carlos.
5
MS-DIAL / Re: Retention Time in text files - Missing peak start and missing peak end
Last post by Hiroshi Tsugawa -
Hi Tony,

please do
1. Export -> Peak list result
2. Choose "txt" for export format
3. Choose "centroid" or "deconvoluted" for spectra type
4. Set your directory and files that you wanna export

Again, in the alignment result, MS-DIAL does not have the function to export the retention times of peak left- and right edges.
But you can check the edge's retention times for each peak of each file by the above way.
Thanks,

Hiroshi
6
MS-DIAL / MS/MS QC's for ID only
Last post by !ndium -
I have a lipidomics QC sample prepared by pooling equal amounts of each sample. The QC sample is injected up front and analyzed by data dependent MS/MS for lipid identification five times using a rolling exclusion list (QTOF). Then the samples, interspersed with periodic injections of the QC sample, are analyzed using MS1 only. Both the MS/MS and MS1 analysis data files are defined as a QC type in MS Dial. Is there a way to differentiate between the QC MS/MS data files and QC MS1 data files? The MS1 QC data is desired for data processing while the QC MS/MS data files are for ID only.

Is there a way to remove the QC/MSMS and blank from the aligned bar chart plots after processing for presentation purposes?

I have not used MS Finder yet, but can the QC MS/MS data files be used in MS Finder to ID lipids after MS Dial processing?

Thanks.
7
MS-DIAL / Spectra extraction for database creation
Last post by Noelia -
Dear all, we are using MS-DIAL 4.24 v for the extraction of MS and MS2 spectra in MoNA format (.msp). Our files are acquired in an Agilent QtoF 6560 by direct injection.  We have some questions:

1. In the beginning we were fragmenting 4 precursor ions per cycle resulting in a low number of scans per peak. Thus, the software didn´t pick our compound of interest and we couldn´t extract the spectra. Is there any procedure to pick up peaks with a low number of scans? After increasing the number of scans the software was able to pick up the compounds.
2. If we are applying several (up to 3) collision energies in the same file, is it possible to obtain different extraction features files for the different CE?
3.  For the identification of the peak, do we have to use the alignment result file or the individual compound file?
4. Once in MS-Finder, can we export batch files in MoNA format (.msp)?

Thanks
9
MS-DIAL / MS-DIAL (version 4.16) MSP database selection and mass tolerance
Last post by semo519 -
Dear users,

I encounter an issue of the MSP database selection in metabolomics in MS-DIAL as follow,

I performed the plasma metabolomics test and followed the MS-DIAL paper (nature method, DOI:10.1038/NMETH.3393). The polar metabolites extraction and LC-MS conditions were similar to the paper description.

My MS data (Waters, Mse data)  was processed by MS-DIAL and the MSP database file was chosen All Public (please see the attached figures). The ref. matched metabolites are around 400. However, the ref. matched metabolites are 0 when I chose the Fiehn HILIC database. (Because I used HILIC column and follow similar LC-gradient). Why is so large difference by using two databases and at least some metabolites should be overlap?

In addition, another important value is Accurate mass tolerance (MS1). When I put 0.025 Da (follow tutorial), the ref. matched metabolites are 0 but I put 0.05 Da, the ref. matched metabolites are around 400. I checked my MS raw data, the mass accuracy could be 0.025Da tolerance but not sure why the MS-DIAL can't recognize it well.

Any comments and suggestions are all welcome and hope the experienced user could help me solve them.

Thanks for your attention

Best,

Bingpeng
10
MS-DIAL / Re: Exporting Error
Last post by JeanFroment -
Hi Hiroshi,

thanks for the detailed answer. I have exactly the same problem and you described the situation I am in. Now, I am not sure I understood what I could do to export the "alignment result B" (obtained with the MSP file B). Should I just start a new project using the same parameters so the feature list won't change (I hope) but this time it will look for annotations with MSP file B?

Cheers
Jean