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Topic: Post-identification issues (Read 243 times) previous topic - next topic

Post-identification issues

Hi, Hiroshi! Great thx for the MS-DIAL and all the work you guys do on it!

Have a couple of questions regarding post-identification with tab-separated file:

1) Does current version of MS-DIAL have limits on a size of the postidentification tab-separated text file? We are doing metabolomics on endogenous metabolites. In-house database is employed at some point, which contains around 800 entries for tailored identification process. When i try to load the complete list, i get a window "Loading libraries..." after pressing "Finish" button, which dissapears momentarily and nothing happens. I've reduced the list to around 300 entries, everything went well.

2) For the post-identification library, can the Formula/InChi/ be included there to get displayed in Basic Peak Property/Compound detail tabs?

3) As far as I understand, for postident you need to put masses of ionized species, right? So, the post-identification is only possible then for one peak with selected adduct -> can be overcome by having 5-6 rows with different probable adducts for single compound -> again, size limit problem.

Will it be possible in future to use neutral masses in post-ident, that the program searches through all combinations based on selected adducts?

Cheers and take care,
SG

Re: Post-identification issues

Reply #1
Hi Sergey Girel,
I suppose the problem is not the limitation of the size of the table. I have once encountered a similar problem, and I finally found that one of my entries had a wrong MZ, that was placing whitespace after the decimal point (e.g. 355. 0705 instead of 355.0705). Maybe you can check your list by something like bisection method.


Re: Post-identification issues

Reply #2
> Maybe you can check your list by something like bisection method.

Thx! I'll go for it, for sure can be a single parsing error which is easy to overlook.

Re: Post-identification issues

Reply #3
Maybe you can check your list by something like bisection method

Checked. The list is ideal.

So, problem is somewhere else.

UPD: there were some special symbols in the metabolite name fields, removed them -> it worked. I think, this is to mention somewhere in manuals, how the program handles different fields.

Re: Post-identification issues

Reply #4
Hi,

sorry for the late reply.
Well, I am sorry that I should improve the parser to let you know the issue in the text library you made more friendly.
Meanwhile,
about: 2) For the post-identification library, can the Formula/InChi/ be included there to get displayed in Basic Peak Property/Compound detail tabs?

Yes, see attached. You can add several meta data in the text library.
The column order must be followed, but you do not have to put all information. For example, CCS value can be excluded from the text library.

Thanks,

Hiroshi

Re: Post-identification issues

Reply #5
Arigato, Hiroshi-san!

Again, a couple of small questions (related):

1)Is isotopic pattern assessment being performed, if i give the formula as input for PostIdent? If not, would be very nice feature. I suppose, it should be easily accessible with the same chunk of code used in isotopic pattern evaluation for MS2 scans.

2) If isotopic pattern is being assessed in the core module, would it be possible to provide either top or top-5 formulas in feature table as general output. Otherwise going to MSFinder or Thermo FreeStyle (please, no!) tends to be very time consuming.

I myself have another means to get this information quickly, but it would be very convenient for other users.