Skip to main content ↑ ↓

Messages

This section allows you to view all Messages made by this member. Note that you can only see Messages made in areas you currently have access to.

Messages - Sergey Girel

16
MS-DIAL / Re: Will the data of LC-MS be removed
> 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?
17
MS-DIAL / Re: Will the data of LC-MS be removed
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...
20
MS-DIAL / Profile data handling by MS-DIAL (orbi)
Working on annotation methodology, i've stumbled upon an issue with data handling. For instance, we have some big guys doing some good metabolomics (10.1021/acs.analchem.8b04698). The data in the abovementioned work were acquired on a good instrument with a good resolution and mass accuracy (i slightly doubt it was actually stable 0.1mDa, quite optimistic -). In centroid mode. Without any justification. Or i was unable to trace the explanation back to previous works of the group, this can also be an issue.

It is supposed, that centroid data should be equal in quality to those collected in profile mode. The only reason to use centroids should be data volume reduction. However, processing the data with MS-DIAL we can see and perfectly replicate  following: profile data produce less features than centroided, software employed is MS-DIAL or ProgenesisQI.

Workflow is standard (for MS-DIAL):

Acquisition -> MSConvert if prof. -> ABF converter -> MS-DIAL (full scan tolerance 0.3mDa) -> ... -> Data matrix for statistics
prof. / cent.         prof.->cent.

Sample: human plasma PP, identification/annotation via in-house DB)

There is some small difference if we produce centroids on the fly with the instument or with Thermo MSFileReader library. They adjust the algorithms slightly with each update and new RawFileReader API was introduced recently. But its negligible.

Big issue is, that we get 280 features in profile mode against 350 using centroids. Manual curation reduces the numbers to 220/250. The difference is still >10%. So, the devil should be somewhere in details. I assume, ABF converter simply extracts MS data array from .RAW files using Thermo API. If we are in profile mode, it should be simply datapoints against the scans. No problem here. Then, MS-DIAL performs centroiding on its own. 

The big question is, how MS-DIAL does the job: is it the same noise estimation + slicing algorithm used in chromatogram EIC extraction or something else?

Otherwise centroiding picks up all the shoulders and distorted peaks, creating too much garbage, which reduces S/N ratio, as it stated in Progenesis (with a recommendation to use profile data). I cannot be clear on Progenesis, what happens there, as it is proprietary black box. But more or less the same thing is observed also there.

P.S. i prefer profile data for different, but not completely unrelated, reasons (FTMS research).
21
MS-DIAL / Re: Post-identification issues
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.
23
MS-DIAL / Re: MS-DIAL Wish List for 2020-2021!
MS-DIAL

1) Normalization using peak areas
2) Semi-quantitation using again peak areas if internal standard and calibration measurements are present. Or, at least, approximation from internal standard if concentration is known.

MS-FINDER

1) I'll join to ElliottJP's post above - MS/MS fragment search in is-CID spectra.

GENERAL

1) To add some error messages upon crashes - to get at least a clue what caused the problem. Like in case with different separator settings in system  locale.
24
MS-DIAL / Re: Post-identification issues
> 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.
25
MS-DIAL / 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