Nothing "wrong" with the software. This is a training issue. You need to be trained first in how to use the software. Their are a LOT of important screens, features and parameters to setup and configure just for one method or analysis. Learning which parameters are important and which ones require correct setup is best done on-site, with the help of a professional who is experienced in using the same system you have. It takes several years of hands-on experience with any HPLC system (under guidance) just to attain a basic level of HPLC training. Many more years are needed to perform method development. Learning each of the different vendor's CDS packages though only takes several days of professional instruction, with follow ups, to have a basic understanding of the software features.

Regarding any observed "truncating" or cropping of chromatograms. This would be due to you setting up the system to show your data (or collect your data) in this way. You could have set the stop time too early or set the system to only initially show you results up to a specific time point. It is unclear exactly what your issue is from your post. The HPLC system only does what you instruct it to do. If you are only referring to post-acquisition chromatograms, then you just need to set the Data Acq parameters to show the time axis used in the original method (then it will default to autoscale the times for you). If you are referring to the truncating of an active method or analysis, then you need to use the "EDIT Entire Method" feature to step you through the various method screens (for your method) until you see the one where you set the time settings to over-ride the pump stop times. Do not over-ride the settings. Always set the PUMP TIME to be the stop time, then all of the other modules will sync to it (unless you over-ride it).

Regarding your comment; "All peaks are still visual but at different retention times", indicates that your method has changed (% composition, flow rate etc), equilibration is not adequate or their is a hardware problem (e.g. a leak).

Please ask your teacher for help (that is what you pay the school for). Have a professional who is experienced in using the same HPLC system you have review your method to find the errors you made or clarify the confusion you are having. Everyone needs help in learning these systems and having someone experienced (hire them if needed) to train you is an excellent investment.

You can set the stop time to 30min before running the sample and then run or you can adjust the data acq parameters by using the offline software. There you can go to more settings options and can select the "use ranges option". This will vary depending on your software. There you can adjust the X axis (time range) as well as y axis

William Letter , First of all, I want to thank you for your detailed description. I'm indeed a yet unexperienced student.

In my problem I used the word 'cropping' which didn't describe the problem perfectly. A better word would've been compressing. Whenever I (or the teacher) run a random aquisition method the running chromatogram shows a retention peak at 12 minutes, but after the run, when I collect my data and check this in an excel or pdf file (doesn't matter which one) the same peak is then compressed and visual at 8 minutes. In addition to that, the complete duration of this acquisition method was 50 minutes, but the X axis stops at 30 minutes. (and compresses every peak into this 30 minutes). I've used different aquisition methods aswell as methods that used to give 'normal' chromatograms before, but all with the same result. I even ran the exact same acq. method on 2 HPLC's (exact same model) at the same time. One HPLC's chromatogram was perfect, with normal retention times and a X axis till 50 minutes. The other one however gave again different/compressed retention times and a X axis till 30 minutes. I already asked my teacher for help, but they don't know what is causing the problem either. That's why I tried the question here. Ill add photo in which I show the used method and the compressed chromatogram.

Dear Sander Punt

Apart from the advice given earlier, if the problem is new to your research group (also to your teacher), I will recommend creating your method starting from an existing one and your acquisition parameters as well. Please do all these changes in the offline mode as advised by Tharindra Weerakoon

Please set a similar stop time(50min) in the detector setting as well. I am sure that you have kept 30 min in detector stop time. Please change to 50 min.

Sander Punt, issue is not with the HPLC system, it is with how YOU have set up the software and method on the system. Start with a fully checked out and maintained HPLC system. Next, create a brand new METHOD (do not use an earlier method. Your methods may be corrupt. Use as an example, the default.M in the system for this purpose). Use the ChemStation's 'Edit Entire Method' menu feature to step through all of the key screens to build the new method. When finished, use the "Save AS" feature to save the method with a unique name. Next, run a true blank sample analysis on this NEW method and save the data (BTW: a "blank" is the mobile phase). Review the results.