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Topic: Batch alignment in MS-DIAL 4.92 (Read 721 times) previous topic - next topic

Batch alignment in MS-DIAL 4.92

Hi all,

Does MS-DIAL handle batch alignment for GC-MS data?

I know you are asked to indicate the batch ID in the project settings, but I am not clear if that information are used for doing batch alignment during the process.

Thanks!

Re: Batch alignment in MS-DIAL 4.92

Reply #1
Under the parameter tab there is a check box for 'execute with RT correction' at the bottom of the options. You can input alignment information there to aid the program along in the process.

Re: Batch alignment in MS-DIAL 4.92

Reply #2
MS-DIAL automatically aligns all extracted peaks. I don't think the batch information is taken into account in that process. You have to set the RT window in the alignment tab high enough to catch any RT drift from batch to batch and then it will recognise those peaks as the same feature. If not you will get multiple features with the peaks split between them. My students have tried various RT windows up to about 0.5 mins, dpending on how bad their batch effects are. The problem here is when you have isomeric pairs and the alignment mismatches them. There's no perfect solution so you have to accept some compromises. If you want to get the most out of the data you have to go through your entire data set peak-by-peak to correct dodgy alignments and integrations.

I would be careful with RT correction. I have found it introduces artifacts.
http://www.metabolomics-forum.com/index.php?topic=1900.0

 

Re: Batch alignment in MS-DIAL 4.92

Reply #3
MS-DIAL automatically aligns all extracted peaks. I don't think the batch information is taken into account in that process. You have to set the RT window in the alignment tab high enough to catch any RT drift from batch to batch and then it will recognise those peaks as the same feature. If not you will get multiple features with the peaks split between them. My students have tried various RT windows up to about 0.5 mins, dpending on how bad their batch effects are. The problem here is when you have isomeric pairs and the alignment mismatches them. There's no perfect solution so you have to accept some compromises. If you want to get the most out of the data you have to go through your entire data set peak-by-peak to correct dodgy alignments and integrations.

I would be careful with RT correction. I have found it introduces artifacts.
http://www.metabolomics-forum.com/index.php?topic=1900.0


Thanks for the info. We've had some difficulty in reconciling a large batch of LC-MSMS data in which some subsets of collected samples shifted in RT by ~0.5 minutes or so. Trying to correct the data with the alignment wizard hasn't been super successful on our part, partly because the documentation for that process is poor and limited. If you don't do it then it the consequences are as you mention a larger than expected number of referenced ID matched hits spread over different %fills because the software appears to think that the shifted RTs and related reference QC samples are different analytes than the 'correct' samples and their respective QC samples. A thought was also to drop the QCs from the messed up samples, but it doesn't appear to do much to improve upon the issue. Your other post is helpful, but also frustrating because I feel like this should be a capability of the MS-Dial software, yet the options available to correct it either don't work or there isn't enough documentation information available, specifically for the alignment wizard, to devise a solution within the program itself. MS-Dial is an awesome program when it works, but when it doesn't it can be frustrating.

Re: Batch alignment in MS-DIAL 4.92

Reply #4
I very much empathise. It is a fantastic tool but it's not perfect. If you have the chance you can raise an issue on their GitHub or make suggestions on the Twitter feed. They had a thread asking for suggestions for improvements in MS-DIAL 5.
https://github.com/systemsomicslab/MsdialWorkbench

Are all the RTs shifted by 0.5 mins, or is it a progressive change across the batch? If the former you can convert your data to mzML and use Python to shift the RTs for the dodgy batch by a fixed value to align the peaks badly. I had to use this hack recently.