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21
MS-DIAL / How to find the internal standard by using MS-DIAL
Last post by Atekton -
Hello,
I want to ask how I can find the internal standard using MS-DIAL.
I try to construct both .msp and .txt files about the Precursor m/z and the information which was necessary for identification.
But I can find the metabolite (internal standard) in my data.

Thanks for any suggestion
22
Courses and training / [COURSE] Introduction to Nutritional Metabolomics 2023
Last post by Jan Stanstrup -
Course dates
26. June 2023 - 30. June 2023

Place: Copenhagen

Info, sign-up, program:
https://phdcourses.ku.dk/DetailKursus.aspx?id=110456&sitepath=NAT

Content

The course will provide a general overview of LC-MS based untargeted metabolomics from study design to results and will be exemplified with its specific application in nutrition. It will be delivered using a mixture of lectures, hands-on data preparation and analysis, computer-based practical sessions, and discussions. Visits to wet labs and instructions on human sample preparation procedures is included but there is no practical lab work.

The students will go through common steps in a typical metabolomics study using a real-life case. This case study includes plasma (or urine) samples from a nutritional intervention. The sample preparation and analysis on UPLC-QTOF has been conducted and the students will further process and analyze the acquired data with various freeware tools (e.g. R, XCMS, MZmine etc). They will finally work on identification of relevant metabolites using manual analysis assisted by several web-based databases and structure elucidation tools. The course will conclude by presentations of reports generated by the students based on the case study.

The students should expect a fairly technical course with a strong focus on the hands-on data analysis abilities and data interpretation skills. Programming skills are not a prerequisite for entering the course and students are guided through the exercises. However, for students that are not familiar with R we expect them to explore the self-study curriculum based on short videos and texts that cover essential programming concepts.
The project work has a high workload and hence evening work can be expected during the course week.


23
MS-DIAL / Maximum of 8 samples processing in MS dial
Last post by Timas93 -
Hi,
As long as I only include a maximum of 8 samples/datafiles MS dial seems to process my samples as expected, but as soon as I include more than 8 datafiles it suddenly interrupts the process and terminates the program without any error message. Since it is working fine with a maximum of 8 files there shouldn't be anything with my parameters nor the alignment with alkanes as I am trying to implement.

Has anyone experienced something similar or has any clue what may cause this issue?

// Tim
24
MS-DIAL / Re: Reifycs Analysis Base File Converter Error
Last post by Timas93 -
Which kind of raw files are you using, or which vendor? In Chemstation, you need to export your files into AIA files before you can convert them to .aif files.

It should be straightforward, but make sure that you are converting your files into the right directory as well.

// Tim
25
MS-DIAL / Reifycs Analysis Base File Converter Error
Last post by sofcolag -
Hello,
I have installed Reifycs Abf (Analysis Base File) Converter  as well as CompassXtract (V 3.2.201).
Still, upon attempting to convert the files the file converter indicates that there is a conversion error: "Conversion Failed. Check your PC condition. CompassXtract should be installed." I found user SallyKH posted abpout the same error on August 23, 2022 but no solution was proposed. Would appreciate any guidance to address the error message.
Thank you.
28
MS-DIAL / Re: Version 5.1.22 Takes considerably longer than 4.90
Last post by lefelit -
Indeed the latest MSDIAL version (5.1...) is using far more RAM memory to process the data. My computer has 32GB DDR4 RAM and 5.1 uses 97% while version 4.9 only 27% of it. I am strangling to get assigned ID for DG and TG with 5.1. I revert back to 4.9
29
MS-DIAL / Re: Cannot import Sciex Wiff Files in 5.1.22
Last post by berrytf -
Oops,

In my haste I accidentally mixed up my file types. The Sciex .wiff raw files I was searching for were actually .mzXML files. Upon double checking the correct folder containing the .wiff files the program is behaving as expected. Let this be a lesson to double check the file type.

I'm still not getting any ref matched IDs or even suggested though when I parse the files with similar project parameters. Going back and comparing to v4.9 using the same raw files and the same in house library. Its really confusing.
30
MS-DIAL / Peaks not aligning in MS-Dial without error message
Last post by CRoper -
Hi everyone,
I'm hoping someone might be able to help me solve a problem I'm having with lipidomics data in MS-Dial.

When I process the data to identify the lipids and align the peaks (in negative ion mode), I receive no error messages. However, upon looking at the alignment results, I can see that many of the peaks are not actually aligned (see screenshot), and it seems to be worse the higher the retention time. I have tried increasing the retention time tolerance, but that didn't help. Any advice or suggestions would be much appreciated. I ran this same dataset through positive ion mode and didn't have any issues.

Best,
Christine