I have no experience with Shimadzu instruments/software but there should be an option or checkbox for that (maybe called "peak data" vs full spectrum or profile mode.) 

If you can use proteoWizard (see https://xcmsonline.scripps.edu/docs/fileformats.html )

you can select centroidization during conversion.

The mzXML format is highly recommended.

Hi, 

As mentioned above by Salvatore, you can use proteowizard  MS convert. You might need a R script and write your code to convert the data if data is acquired in pos/neg mode. 

If you want I can help you write the script, just send me one file so that I can write the script accordingly ([email protected]). 

Gisele, Step-by-Step:

1. open LabSolution Main program

2. open Postrun Analysis explorer or 

From the Main menu of Realtime Analysis software, select Data Analysis.

3. Open your data folder and select the data file for processing.

4. open window Spectrum View

5. click checkbox from Display Spectrum Type profile or centroid 

enjoy

Thank you so much for the help guys..

I tried proteoWizard, but I couldn't transform my data, because of the extension (*.lcd).

In LabSolution, I did the selection centroid in spectrum view, I saved the file and the conversion (mzData or mzXML), but anyway after conversion, my data is still in profile mode.

can you choose convertion into cdf?

Hi Jean-Charles

Yes, I tried netcdf conversion, but the same problem occurs..

I think you must get back to the vendor and ask for a script or a patch that allow you to the conversion in the centroid mode. I'm not familiar with shimadzu, but they should be able to do that,

good luck

Yes, I'm trying with Shimadzu.. 

Thank you!

If you can convert to netcdf you should be able to take those files and convert them with proteowizard's msconvert to centroid mode (called peak picking in msconvert).