Sciex Mass Spec Error

[Former user]

Hi, I receive this error when I use lipidhunter, after converting .wiff.scan to .mzml using MSConvert. May I ask what solution i may use, it looks ok in SeeMS but I get the error "!! Sorry, an error has occurred, please check your settings !!" when I try to run an "Extract MS level" on the .mzML file.

Warm regards, Pandiyan

[Zhixu Ni]

Hi!

Thank you for using LipidHunter! The current version we did not check the compatibility of mzML converted from Sciex data. If you have some sample data file using DDA, please try to convert to mzML and send me both raw files and corresponding mzML to us. please also provide us the screenshot of the MSConvert with your conversion settings. If you would like to share your files to us, please put the files to Google Drive, One Drive, other online storage so we can have a look.

Thank you for choosing LipidHunter for your Lipidomics analysis!

Best wishes,

Zhixu Ni

[pandiyan1]

Hi Zhixu,

Thank you for your reply. Here is the link to download the .wiff file, .wiff.scan file and the corresponding .mzml file. The screenshot of MSConvertGUI settings is also there. Really appreciate you having a look to see how it can be made compatible. https://drive.google.com/open?id=0BxfGp-9GXGsSV1VOY1lOMXU1MHc

Warm regards, Pandiyan

[Zhixu Ni]

Hi Pandiyan!

Thank you for providing us your test data files.

I had a look of the files, and here are some instructions.

When you convert your files, please use this setting to get one mzML with MS and MS2 information for all steps:

with this settings, you do not need to convert a separate MS1 only mzML.

After conversion, you can start LipidHunter and chose "Thermo" mode for data processing. It is important to work in "Thermo" mode, since mzML converted from SCIEX files have different data structure to mzML converted from Waters files.

If you manage to run a 1 min test, you can change the time window to the actual time window you interested in, e.g. 5~20 min.

There is a bug that it cannot merge the MS1 precursor files from SCIEX data. However, you can open the excel output and select columns of m/z and i for bulk search.

Please use "Thermo" mode for Step II as well.

I managed to run step I and II from this file. However, it appears to me that there are too less good MS2 spectra with bulk identification. LipidHunter is entirely based on MS2 spectra, please check your DDA settings, and maybe try with another file.

I strongly recommend to use data with PE standards in negative ion mode to test.

Best wishes,

Zhixu Ni

[pandiyan1]

Hi Zhixu,

Thank you so much for your help.

Unforunately, I am still getting the same error Here are my settings I just left it at the default setting. Apologies as I am very new to this. Really appreciate if you could let me know why I am getting this error.

Warm regards, Pandiyan

[Zhixu Ni]

Hi Pandiyan!

Please use the select file button in the settings tab to select the default configuration files before you start.

You have to find these files in the folder named "ConfigurationFiles" under LipidHunter folder.

e.g. D:\APPs\LipidHunter\ConfigurationFiles\FA_list.csv

and then press save above settings as default to save the locations of these files to LipidHunter.

I would recommend you to download our user guide and test files to run the tutorial step by step to make sure the software is fully functional. After that you can start with your own data.

Please find these files from https://bitbucket.org/SysMedOs/lipidhunter_exe/downloads/

Best wishes,

Zhixu Ni

[pandiyan1]

Hi Zhixu,

Apologies, I feel like I did all the steps correctly but it still wont resolve the error and I'm not sure why. Here are the new settings I used.

Nevertheless, I still received this error

May I ask why this is the case?

Warm regards, Pandiyan

[Zhixu Ni]

Hi Pandiyan!

Can you tell me if you have already successfully run the test data we provided according to the user guide?

If you failed in any step with the test data we provided, that means something wrong with the LipidHunter you have downloaded. In this case, please delete your current LipidHunter and try to download agian.

The test files and sample output can be downloaded from: https://bitbucket.org/SysMedOs/lipidhunter_exe/downloads/LipidHunter_TestFile.zip

If you successfully processed the test data and got the report file with images, then probably is the file conversion issues.

Please check the version of your ProteoWizard and try the mzML file I converted from your files using ProteoWizard version 3.0.9134 (64bit)

Please download the files before November 17 2017: https://speicherwolke.uni-leipzig.de/index.php/s/sI7hPbFopsblU3r

If you can process this file, please try to change your ProteoWizard to the latest version or try to find the version 3.0.9134 (64bit).

Please try to avoid spaces in the folder names, we observed certain bugs on some windows systems and working on that. in your case, try to use "URECA2017", "URECA_2017", or "URECA-2017" instead of "URECA 2017".

Best wishes, Zhixu Ni

[pandiyan1]

Hi Zhixu!!

Thank you so much for your help! Yes I have tried the test file and it runs fine! I am downloading your converted mzml file now. will let you know how it goes!

Also, changed my folder names to remove blanks already.

Warm regards, Pandiyan

[pandiyan1]

Hi Zhixu,

It seems like its a conversion problem. I used proteowizard 3.0.11537 (latest version) to convert the .wiff file myself and then run Lipidhunter and it failed. However, when I used the file you converted, it worked. However, I can't seem to find 3.0.9134 version of proteowizard online. May I know if there is a copy of it you can share with me or otherwise, is there a workaround for the latest version.

Warm regards, Pandiyan

[Zhixu Ni]

Hi Pandiyan!

It's good to know that the file finally works for you!

The problem is you cannot download version 3.0.9134 from ProteoWizard project website any more, and I am not sure if I am allowed to send you my installed version.

The alternative way is to download version 3.0.10158 from ProteoWizard project website:

http://teamcity.labkey.org:8080/viewLog.html?buildId=380712&buildTypeId=bt83&tab=artifacts

I suggest you to uninstall your old ProteoWizard, restart your computer and then install the following version:

http://teamcity.labkey.org:8080/repository/download/bt83/380712:id/pwiz-setup-3.0.10158-x86_64.msi

I have already tested this version of ProteoWizard, it was working fine and the converted .mzML file from your .wiff data is compatible with LipidHunter.

Please let me know if you succeed with ProteoWizard version 3.0.10158 or not.

If this version works, please keep the installation file for your later projects.

Best wishes,

Zhixu Ni