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MS-DIAL / Re: How to Specify Column Polarity and use Retention Index for ID
Last post by James -
Hi Justin,

I don't know of a way to do this within MS-DIAL, so I would untick the 'use retention information for scoring' box in the Identification tab of the parameter settings, and then compare the calculated retention indices with your putatively identified compound RIs manually.

If there are so many compounds that it isn't feasible or efficient to do it manually, the webchem R package has functions for searching online databases for RI information of the compounds in your dataset and allows you to specify column polarities and retention index types - meaning you could specify only polar Kovats retention indices and then quickly screen for big differences.

MS-DIAL / Re: The best result of same annotation compound with different retention time
Last post by berrytf -
You have to go in and make a judgement call on which one is correct. Do you have a standard to compare it against to verify the expected RT? That would help resolve it. Otherwise you can open the data in MS-Dial and take a look to see if you have any representative MS2 to make a judgment call on based on the similarity to a known standard another group produced. Hopefully it's not just the loss of the sodium. Your %Fill for the last two denote that it was found in every sample at those RTs. Not sure if that helps either, but it might be an indicator.

There isn't enough information to go on here, but we could tell you how to better narrow it down with a bit more information.
MS-DIAL / Adduct-based filtering of featurelist
Last post by FalcoB -
Hello at all,
I´m interested in reducing the number of features of my raw feature list. The steps I´am currently doing are the following:
- MS-Dial data processing: using parameters "peakcount filter" & "N% detected"
- MS-Dial data processing: elimination of blank features (by applying a specific limit value for sample average/blank average ratio)
- manually after data processing: elimination of features by QC-specific filters (using specific limit values for missing rate and CV value)

By performing these steps, I can reduce the number of features from ca. 10.000 (or more) to about let´s say 4000-5000. But there are still redundant features, i.e. adducts!

So my question: Is there a simple way to (semi-)automatically delete all the adducts from the feature list in MS-Dial? How would be a reasonable way to do this?
As I remember right, in XCMS "peak grouping" at least facilitates eliminaton of adducts. In MS-Dial, somehow similar information is given in the column "post curation result" within the aligned feature list, but based on these data you are not able to delete all adducts from the list in a reasonable time.

Unfortunately I´m not experienced in programming. So, I would prefer using a tool that does not require deep knowledge in programming. However, can someone recommend any tool?

One additional question. Just to be sure, the isotopes are excluded automatically from the aligned feature list in MS-Dial?

MS-Dial version: 4.90

Best regards
MS-DIAL / How to Specify Column Polarity and use Retention Index for ID
Last post by JMS -
We are doing nontargeted analysis by GC-MS (single quad) and because our analytes are relatively polar, we are using a polar (Innowax) GC column. We have an alkane standard chromatogram so we can calculate Kovats RI values for our peaks.

However, can we specify in MS-DIAL that we used a polar column in our analysis for the purposes of library matching? I know that many library entries may not have polar RI values. Basically, I don't want the identification to use nonpolar RI scoring to discount spectral matches on the MS side (at minimum) and would like to use the polar column RI values as a confirmation of the identity, if possible.

Any ideas?

MS-DIAL / MRMPROBS Crashing When Importing Converted Thermo LC-MS/MS mzML Files
Last post by TM -
I am encountering a problem with the MRMPROBS software when I try to import mzML files that have been converted from Thermo raw files (LC-MS/MS). The software crashes upon this operation.

Additionally, when I press the "Finish" button in the reference options, the software abruptly terminates. I am struggling to understand the underlying cause of these issues.

I would appreciate your assistance in resolving this problem. Could you provide any insights or solutions for this issue?

I look forward to your response.

MS-DIAL / Linux add export parameter for choose export raw data matrix of Area or Height
Last post by Ruth -
   MS-DIAL is the most excellent software that I have used. MS-DIAL can not only support analyze in Linux but also process the MSE spectral data.  So I am very approciate your work. I am trying to use MS-DIAL to identification and annotation the metabolites.
   Recently, I found the Alignment msdial result (the raw matrix) is the matrix of Height, but I am in need of the matrix of Area instead of the matrix of Height, cause I feel Area data is more accurate than Height data. So could you please update your software of Linux platform which include the parameter to choose which type of raw data matrix to export, Height or Area.
   By the way, this is how I do in Windows version to get the Area data, I want to have the same Area data in Linux, too. Could you please help me about this requirement?


MS-DIAL / Re: Question about Bruker QTOF raw data in MS-DIAL
Last post by hdecoevo -
I received an answer to the above question from the ABF converter developer, and am posting it in case it helps others. The converter currently can't process .tdf or .tdf_bin files because CompassXtract does not recognize them. There is a new converter in the works designed to do so, but a release date hasn't been announced. For now it seems it isn't possible to process IMS data in MS-DIAL, and files should be converted to a more general format (like mzXML) directly from Bruker software.
MS-DIAL / Batch alignment in MS-DIAL 4.92
Last post by Hzamora14 -
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.

MS-DIAL / Re: Question about Bruker QTOF raw data in MS-DIAL
Last post by hdecoevo -
A quick revision to my previous post - I realized my error (trying to drag and drop the .tdf file, rather than the .d folder from Bruker). But unfortunately, the ABF converter is still telling me it can't convert the .d file folders to .abf because CompassXtract isn't installed. I've installed, uninstalled, and reinstalled it multiple times now. Has anyone else had this issue?