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21
MS-DIAL / CAN NOT download MSDIAL metabolomics MSP spectral kit
Last post by Amberrr -
Me and my colleagues couldn't download the 3rd one online database "ESI(+)-MS/MS from standards+bio+in silico (16,995 unique compounds)", while we can download the other three successfully.
It shows "403 Forbidden" on page when we try to download it.
23
Courses and training / [Course] Workflow4Experimenters 2023
Last post by yguitton -
Processing, statistical analysis, and annotation of metabolomics data is a complex task for experimenters since it involves many steps and requires a good knowledge of both the methodology and software tools. The Workflow4metabolomics.org (W4M) online tool suit provides a user-friendly environment with advanced computational modules for building, running, and sharing complete workflows for LC-MS, GC-MS, FIA and NMR analysis. Such features are of major values for teaching computational metabolomics to experimenters, and previous courses using W4M since 2014 have been very successful.

For this new session, the proposed format evolves:
- From 06 to 10/03: theoretical sessions in videoconference from 10AM to 12PM each day
- From 20 to 24/03: practical sessions and tutoring, with the 1st hour of each day dedicated to short reminders and participant questions (following the theoretical session).

Info: https://workflow4metabolomics.org/w4e2023

Pre-Registration: https://sondages.inrae.fr/index.php/114793?lang=en (deadline 31/12/2022)

Goals: During this course, participants will learn how to use the W4M infrastructure to analyze their own dataset. Online sessions will be dedicated to methodology and tools. Face-to-face sessions will be devoted to tutoring. For these practical sessions, the participants will work on their own data (prerequisite for the training is to have a data set).

Date:
from March, Monday 6 to Friday 10 2023: 10-12 am (Paris hour): theoretical sessions
from March, Monday 20 (lunch time) to Friday 24 (lunch time) 2023: practical sessions
24
Mass spectrometers / Re: ms dial library problem
Last post by agentfourtea7 -
Hello, I recently installed MSDial to interpret the chromatographic profile of phenolic extracts from fruit samples. However, on my notebook, I can't buy MS2 spectrum with msdial library. It appears as follows:

I downloaded the library for compounds in negative mode and inserted it as recommended by the tutorial. Also installed MSFinder. However, when I click to search in MS Finder the program closes.
I can check all peaks, but it is impossible to compare with the libraries.
My version is Windows 11 Home Single Language - 21H2.

I face the same issue, perhaps better to use MSDial version 4.9 or higher, but not 5. However, for me even loading libraries in MSFinder does not help as I get no annotations or IDs. Sometimes clicking MSFinder from MSDial crashes them both.
26
MS-DIAL / Re: How to do multiple regression or PCA in MS Dial?
Last post by agentfourtea7 -
PLS-DA may be better for this since it is supervised. Anyway, this can be done by assigning Class ID ['option' tab in toolbar],
 normalizing (must assign class first; I prefer LOWESS + an internal standard)[data visualization tab], then doing stats in the tool that is also under the data visualization tab (can't remember name off the top of my head).

Take care,
Triston


Great tip, what I struggle to understand is for PLS-DA it requires a y-variable to be defined, would you know how that's done?
27
MS-DIAL / Re: Peak detection: Amplitude calc
Last post by triston.groff -
If you have some prior knowledge of features before hand, your best bet is to determine this in the vendor software. You just need to determine a suitable cutoff to call "noise" that you have some confidence is a lower intensity than a low-intensity biological peak. There is no right or wrong, one size fits all. You must examine your data before setting the MS-DIAL parameters because they may not be appropriate for every analysis.
29
MS-DIAL / Combining DDA and DIA
Last post by MaxFeuerstein -
Dear Hiroshi and dear MS-DIAL team,

I plan to combine DDA and DIA for some future experiments (e.g., DDA for pooled QCs, DIA/SWATH for samples) and I was thinking about a workflow similar to R-based DaDIA approach (10.1021/acs.analchem.0c05022).
I really like the software, so I wanted to ask if it's possible to align DDA and DIA data in MS-DIAL?
As far as I understand it, it's only possible to decide batchwise if data is processed as DDA or DIA and it's not possible to align both data types in a straightforward manner.
Do you plan to implement the possibility to analyze mixed batches of DDA and DIA data in future releases, e.g., by selecting datatype for each file in the sample list and align DDA and DIA files in the end?

Thanks a lot for your great work and best regards,
Max
30
MS-DIAL / Re: How to do multiple regression or PCA in MS Dial?
Last post by triston.groff -
PLS-DA may be better for this since it is supervised. Anyway, this can be done by assigning Class ID ['option' tab in toolbar],
 normalizing (must assign class first; I prefer LOWESS + an internal standard)[data visualization tab], then doing stats in the tool that is also under the data visualization tab (can't remember name off the top of my head).

Take care,
Triston