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21
MS-DIAL / Re: Will the data of LC-MS be removed
Last post by Sergey Girel -
It does not depend on software, it's common issue - what do you want to see as a feature and how robust it should be.

Then i would set Peak count filter to and N% detected in at least one group in initial evaluation to 0%, or better - do chromatogram similarity heatmap in something like R/XCMS, then Peak count to 0 and N% detected to 80%.

Again, you urgently need pooled QC for such investigation.
24
MS-DIAL / Re: Will the data of LC-MS be removed
Last post by Sergey Girel -
> Our experiment was divided into two groups (normal group and model group), UPLC-Q/TOF-MS was used to collect data.

Do you have biological or measurement replicates for each sample in your group or it is simply X measurements, each from different specimen?
25
MS-DIAL / Few questions about MS-FINDER
Last post by Sukis -
Dear Hiroshi Tsugawa,
I have a few questions about using MS-FINDER, could you please help?
1. Does it allow deleting files from the file navigator? I think it will be very nice to have this function.
2. Does it allow exporting results as .MSP file without peak annotation?  I understand that the peak annotation is helpful to get cleaner spectra when building a library. But sometimes the spectrum seems to be overcleaned that the cleaned spectrum is not representative.
3. when exporting .MSP file from MS-LIMA, the obtained .MSP file has descriptions about each peak that is annotated by MS-FINDER. I have tried that, this .msp file can be used for MS-DIAL, but I am just thinking this information seems not necessary for a library no? can we export the .msp file without these descriptions?
 

all the best,
Qizhi Su
26
MS-DIAL / Processing CCS files from Waters Vion ?
Last post by Sukis -
Hello everyone,
MS-DIAL now is capable to process ccs profile. Does anyone have experiences to work with Waters Vion ccs file (UNIFI)? how can I export data from UNIFI and then process them in MS-DIAL?


best regards,
Qizhi Su
27
MS-DIAL / Re: Will the data of LC-MS be removed
Last post by Bei-bei -

Thank you very much for your help.

How should I set the alignment parameters? Please explain in detail because I have just started to use this software.

Our experiment was divided into two groups (normal group and model group), UPLC-Q/TOF-MS was used to collect data. We want to find out the difference metabolites (the difference in quality, not in quantity) between the two groups through MS-DIAL software.
29
metaXCMS / Not able to access metaXCMS result
Last post by suprama@bu.edu -
Hi,
I have done pairwise comparison of my LC-MS raw files in positive mode using the XCMSonline and now want to compare the pairwise job data visa metaXCMS. Fo me the jobs are running fine but when I click on the number of overlapped metabolites on the Venn diagram, I am getting an empty result table. Clicking on individual set of data doesn't return results either. Attaching the screenshots - First image is of the Venn diagrams and second is of the empty table. Any help would be truly appreciated.

Many thanks
Suprama

30
MS-DIAL / Re: Will the data of LC-MS be removed
Last post by Sergey Girel -
It depends on your alignment settings.

I suppose, you have these two datasets as groups. If you put 0 to Alignment/N% detected in at least one group, your feature for sure will make it to the list.

Again, how your data are actually organized? # of groups, biological or measurement replicates, etc...