Use the data analysis software supplied with the instrument. Alternatively, but not as good, save it in an alternate format such as ANDI, then use the aftermarket DA software.
have you ever heard of Virscidian? We use the Analytical Studio Reviewer (ASR) to process all our analytical and preparative data. We only need MassLynx for instrument control. The rest of the workflow runs only through Virscidian/ASR. The software is excellent and a major advantage is that Virscidian adapts the software exactly to your needs. You can have a look at their website. https://www.virscidian.com/
If you want to process the data on your personal PC, Install MassLynx on your PC but remember to disable automatic updates. Any time windows receives an update and restarts, MassLynx will need to be re-installed. We used to have a laptop that has no network connection so it doesn't receive updates. We installed MassLynx on this laptop and I used to copy the raw results from the computer that controls the LCMS after the run is done to an external hard drive. Then I put these raw results on the laptop to process them in TargetLynx. It is somehow labor-intensive to do so, but it saved me a lot of hassle because the computer that controls the LCMS is in the lab for sure, while the laptop is in the office, far away from the noise and chemicals.
One more advice, consider having JMP software. It is so powerful in dealing with spreadsheets and can generate figures and statistical calculations for you so easily.
In TargetLynx after you finish processing your raw data, go to File then Export then All Results and export to .txt file. The .txt file can be imported into Excel to make a spreadsheet, then the spreadsheet can be imported into JMP to manipulate the results, make graphs and tables, and do so much more with your results.
Target Lynx has most of the features that you need for processing your data. Once you set up, it takes a minute to get processed data. After that, you can export the results as a txt file or copy -paste to an Excel sheet.
I found this is more efficient and accurate than exporting the raw data for processing.
Please feel free to txt me if you need help for the process. Thanks.