Bruker ultrafleXtreme MALDI-TOF/TOF compatibility

[Sine Yener]

Dear all group members,

I am currently working on triglyceride analysis with MALDI-ToF/ToF. For the moment only MS without fragmentation. I would like to use LipidXplorer to process my data. Since I have been dealing with many peaks, I would like to clean my mass spectra as much as possible. In particular, to use the deisotoping function.

- I followed the instructions and installed LipidXplorer on my computer. 

- I converted my raw files (Bruker fid) by using MS Convert into mzML and/or MzXML format.  

However I got stuck in the Import Settings. I have some questions related to this:

1. Does the .ini file depend on the type of the mass spectrometer?

2. I cannot see the configuration file options when I scroll down the menu. How can I access these files? 

Should I find them from the MALDI?

3. I have run my samples in automated mode. I have one mZML file containing almost 75 different spectra. Does it influence the data processing?

Should they be uploaded as separate files rather and a list? 

4. I am not sure how to select the other parameters under the configuration settings. In particular for the timerange parameter. 

I tried to run the program by skipping this but I received an error message.

Since I am new to this field, I would appreciate your help!

Thank you very much in advance!

Best regards,

Sine 

[Jacobo Miranda Ackerman]

HI Sine,

we replied directly to your email,

we are happy to help...but in general,

if you have a question and can provide the relevant files, please do so.

when you have a specific problem, please provide the steps and resources to reproduce the problem.

if you cant share the data, let us know so we can find a way to help.

this will help us give a quicker and better response to your issues.

Kind regards

Jacobo

[Dr. Ronny Herzog]

Dear Sine,

this is Ronny, the developer of LipidXplorer.

I can might be able to help you with some general answers:

(1) The *.ini file contains several settings. Each individual setting should comply with a mass spectrometer and its settings. We used LTQ Orbitrap Velos, QStar and other Thermo mass spectrometers with individual settings. Each machine and setting is reflected as a single entry in the *.ini file.

(2) In the top text field you select the *.ini file. Click on "Browse" and find the default *.ini file ("lpdxImportSettings_tutorial.ini"). This includes some example settings for Thermo Orbtrap mass spectrometers.

I cannot help you with settings regarding Bruker instruments. It depends on how you set your acquisition and other things. Maybe someone else in this forum can help you.

(3) If your mzML contains 75 spectra of different samples, then this won't work with LipidXplorer. It assumes that all spectra within a mzML file belong to  a single acquisition and it will average them into a single spectrum. So, you have to split this file into 75 individual mzML files.

(4) The time range let you filter spectra from a single acquisition according to the time points of there measurements. Each spectrum within a mzML file should have a "retentionTime" parameter. It does not matter if you used a LC or if you did shotgun. In LipidXplorer you can set a certain time range which lets you include only those spectra whose "retentionTime" is within this time range. If you still get an error message, feel free to post it here. I can help you, if I see the concrete Problem.

I hope this helps so far. Don't hesitate to ask.

best regards,
Ronny

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Dr. Ronny Herzog
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[Sine Yener]

Dear Ronny,

Thank you for your answer! It is indeed very helpful. 

1. I will contact the technician of the MALDI-ToF to see if I can get the necessary .ini file. Or if someone has experience on this can help me out.

3. For the moment I have one single file containing 75 different spectra. I am trying to find a way to split them or to convert them separately if it is possible.

Otherwise, I need to acquire the mass spectra separately.

As soon as I have an update/able to fix the issues, I will post here.

Thank you again. 

Best regards,

Sine

26 Temmuz 2017 Çarşamba 10:22:25 UTC+2 tarihinde Dr. Ronny Herzog yazdı:

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