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Messages - WenYu

3
MS-DIAL / Support for Lipidomics analysis in the Console app?
Hi, we're having some problems analyzing the lipidomics data with the console app. The feature identification for lipids apparently is lacking as compared to the GUI app. Looking thro the source codes, it seems to me that the "Lipidomics" specific functions are not enabled. Am I correct?

For example, the "Target" param is not recognized by the console app. Therefore, Target: Lipidomics has no effect. The support for the solvent type or lipid types seems to be missing as well.

 Are we on the right track?

Thanks!
Wen
4
MS-DIAL / Re: MS-DIAL 4.48 for IMS samples (Agilent)
Hi Ana,

We've recently worked on a set of Agilent-IMS files for 60 samples with the Ms-dial console app. The total run time was about 12-24 hours starting IBF files, depending on the disk and CPU configuration.

We are using a custom build of the console app with IMS support. Thanks to Hiroshi and Yuki for their help on making it possible!

Wen
5
MS-DIAL / Re: when linux version of MS-DIAL will be released
Hi Hiroshi,

Thanks so much for your reply! The concern about the vendor software is totally understandable.

We do have most of the instruments in our labs, so we should have the arrangement to use the vendor specific functionality. For data pipeline, we usually convert the raw files to mzML or IBF first. Thus the console app can start with these standard file formats, instead of the vendor files.

Looking forward to contribute as much as we can. Please contact me at wen.yu@astrazeneca.com for follow-up.

Wen
6
MS-DIAL / Re: when linux version of MS-DIAL will be released
Hi Yuki,

Thank you for your kind reply! The MS-dial and its console app have been instrumental for our studies. We are very grateful for what you've provided for the community.

Is there a possibility we can contribute the to the development of the Linux version of the console apps? We'd love to put some time and resource on the app, and possible enhance it to support the sample grouping, ion mobility support, for example.  

Wen
7
MS-DIAL / Ion mobility support in MsdialConsoleApp?
Is ion mobility data supported in the console app? We have data from IMS-QTOF instrument. However the parameters for the Console app don't seem mention the ion mobility or CCS tolerance.

Thanks!
8
MS-DIAL / Re: when linux version of MS-DIAL will be released
The Linux version will be super useful, especially for large dataset and for pipeline automation. Would you be releasing the source codes and compilation instruction as well?

One of the feature we'd like to request for in the console app is the ability to supply the sample definition (sample order, groups, etc) in a file.

Thanks!
Wen
 
9
MS-DIAL / MsDialConsoleApp: Sample attributes and Target Omics
Hi, while most of the arguments have one-to-one mapping from the GUI app, two of the arguments seems to be missing.

1. The "target omics" to specify whether lipidomics or metabolomics is intended.
2. The sample types and other attributes are set to default for every raw files in the folder. Is there a way that we can prepare the sample list separately and attach it to the search? We'd like to specify different sample types and other attributes that are appropriate for the experiment.

Thanks for the MsDial team for such wonder tool.

Wen
11
MS-DIAL / Re: IBF convertor from command line
Hi Sukis,

We are using the timsTOF instrument from Bruker. The "*.d" raw files it produces can be converted flawlessly to *.ibf files when we drag-n-drop the file folders onto the IBF converter. We'd just like to run this step in a script from the command line if possible.

Thanks!
12
MS-DIAL / IBF convertor from command line
Hi everyone,

Is it possible to run the IBF converter from the command line without the GUI? We'd love to batch convert the timsTOF files as a part of a pipeline.

Thanks!
Wen Yu