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Messages - Sergey Girel

2
MS-DIAL / Retention times for lipids in Fiehn articles and MS-DIAL
Hi all,

should RT´s for lipids in MSDIAL-TandemMassSpectralAtlas-VS68-Pos.msp (latest version) correspond to those published in https://doi.org/10.1021/acs.analchem.7b03404 ?

Fiehn article states RT 2.23 min for LPC 18:0, which i also similarly detect with his method. MSP file above, however, has RT of 6.75.

If this is correct, so that MSP retention times should be like this, then two questions:

1) Lipidomics processing in MS-DIAL 2.xx, does it have Fiehn RTs?
2) Derivation of RTs in VS68 - measurement or in silico?

Thx in advance for clues!
3
MS-DIAL / Re: MS-DIAL 4.60 was released.
Thx Hiroshi for your great work!

So far everything works fine. Checking some of my steroid test datasets with recent in-house DB version and realized one thing - it would be great to have a separate functionality for postIdent, which allows for a choice of postIdent list entry for the annotated feature (similarly to Compound search for MS2 annotation).

Sometimes comes a situation, where two closely eluting isobaric compounds are annotated with the same record, because it's eluted slightly closer and gained higher score. For now it's a tedious process of manually opening the list, sorting on RT and looking what could be nearby.
4
MS-DIAL / Re: Processing of big datasets
Hi, Ondrej!

Problem solved, actually. It was the ToF data itself, after some preprocessing it was possible to get to results in a reasonable time. But still, MS-DIAL in its current form is, unfortunately, not that much capable to deal with these profiles and associated data volumes.
5
MS-DIAL / Re: Show ion table
Had the same, especially with big ion tables.

Often it helps to cancel ion table building and simply start it again.
7
MS-DIAL / Re: Post-identification issues 2
The whole adduct detection output appears completely broken to me, as output like on the picture (see attached) makes completely no sense.

Why even something with a difference in RT of 0.12 min could be mapped as an adduct of a feature at 9.54... This time i've left only M+H+ adducts in post-ident text file.
8
MS-DIAL / Post-identification issues 2
Hello, guys!

I've noticed some weird thing with post ident. What i want to have, is an ability to identify all possible adducts for my metabolite library. So, the postIdent .txt file has a separate entry for each adduct for each metabolite. Like this:

Code: [Select]
18-Hydroxycortisol	379.21152	6.22	[M+H]+		C21H30O6
18-Hydroxycortisol 401.19346 6.22 [M+Na]+ C21H30O6
18-Hydroxycortisol 417.1674 6.22 [M+K]+ C21H30O6
18-Hydroxycortisol 396.23807 6.22 [M+NH4]+ C21H30O6
18-Hydroxycortisol 361.20204 6.22 [M+H-H2O]+ C21H30O6
18-Hydroxycortisol 348.19148 6.22 [M+H-2H2O]+ C21H30O6
18-Hydroxycortisol 383.1828967 6.22 [M+Na-H2O]+ C21H30O6

MS-DIAL output - attached. To all these masses the adduct [M+H]+ is attributed wrongly.

How to overcome?

Thx in advance!
SG


 


10
MS-DIAL / Re: Disabling fill gaps
Fill% has, in principle, nothing to do with gap filling itself. It is an occurence across samples in group. If MS-DIAL was able to determine a feature in 3 samples of 5, then this value will be 0.6 or 60%.

Gap filling can help to increase this count, searching automatically in a certain range of the known feature with eased parameters. Hiroshi can, of course, correct me.
11
MS-DIAL / Re: Processing of big datasets
Hi, Ondrej!

>  I would suggest to explore a small subset of your files to get the real impression what is worth the time, and optimize the parameters. E.g. when I tried a lower threshold (20,000 -> 1,000) with ~700 abf files, the gain was ~24,000 -> 27,000 peak spots for extra 15 hours of calculations (1.5 -> 16.5 h).

Already done exactly like this. This processing session is as optimized as possible. And i need the guys deep in the forest for these experiments. Threshold is under 1E3 counts.

> but the alignment and gap filling take the most of the processing time

Let's wait for new MS-DIAL architecture -)

> so plug in a UPS if you are afraid of the power failure

It was a constructed situation. I, personally, have everything and more.

> You will find small alignment files being processed during the "limbo time", most probably

Which exactly temp folder? Peaklists from gap filling are stored in separate folder within the project location. Resource monitor only showed handles for pagefile and DLL's afterwards. Apparently, the steps after gap filling are going through RAM. There is "Gap filling: 385/385" now and stays like this. 2 cores of 16 are regularly at 100% load, around 140 Gb of memory are still commited to MS-DIAL and at some point around 800 Mb RAM block becomes modified and then goes again to the "in use" state.

It simply wonders me what is then calculated, which takes more time than gap filling. In my experience it was always the longest processing step.

Best,
SG
12
MS-DIAL / Processing of big datasets
Hello, community!

I have almost managed to push a set of 385 Q-ToF measurements (around 200 Gb of centroid data :-) through MS-DIAL v. 4.24. It has for now finished gap filling (required ca. 90h) and does something in limbo for another 24h. App is responding, something is being written on HDD from time to time and there is also some dynamic in RAM. But quite small one. Only one-two cores of 16 are involved at 100% load from time to time. Don't know when it'll be done, but already excited to see the results.

In this run one of our in-house databases had been used for metabolite identification. However, we got another idea and would like to check with another database. Is there a possibility to go through another post-ident run on existing ion table without experiencing a whole sequence of peak picking / alignment / gap-filling / finalization again?

IIRC MS-DIAL always does this when new alignment instance is created. And it would take another week again, i guess, if there is no way around it. Another important thing also arises - let's say i suddenly got power shortage during processing in gap filling stage. Is there some possibility to start from the point where everything stopped?
13
MS-DIAL / Re: Project File Path
Hello, Biswapriya!

If you can mount your cloud storage as a network drive or folder alias with sufficient permissions to read/write, then no problem at all.
15
MS-DIAL / Re: Will the data of LC-MS be removed
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.