Failed to pares Spectrum file, Please check your spectrum file

[shenghao003]

Hello, When I followed the operation method of Visualize FragPipe result and tried to use PDV-2.1.0 to import the search results of Fragpipe, the following error occurred. How should I solve it?

Thanks!

[KaiLiCn]

Hi,

Which format of your input spectral files? PDV has been integrated into FragPipe. When you finish your search, you could open the PDV inside the FragPipe directly.

Please let me know if you have issues to run PDV inside the FragPipe.

Kai

[shenghao003]

Thank you for your reply, because I am using the linux version of Fragpipe.the format of the input file is as shown below(psm.tsv and *mzML).

Thanks.

[KaiLiCn]

I see. Do you have GUI on your Linux machine? I see you can open PDV here. If you want to open your result after finishing searching or open it in different places, it's still possible inside FragPipe. 1. Change the spectra raw file path in "fragpipe-files.fp-manifest" file which locates in your result folder. 2. Specify the result folder's new path in "Output dir" in "Run" panel and click "Open FragPipe-PDV viewer" directly without re-running it.

We added more features in the FragPipe-PDV and did many optimizations. So I highly recommend open the FragPipe result in that way.

Please let me know if you have any issues.

Kai

[shenghao003]

Sorry, My Linux machine is configured for executing large tasks only and does not accommodate the installation of a GUI, hence the necessity to utilize a standalone tool like PDV for importing search database results.

[KaiLiCn]

I see. I didn't test stand-alone PDV for the new FragPipe result. But for your situation, I can show you another way to run FragPipe-PDV.

If you have the whole FragPipe search result folder, you can try to run FragPipe-PDV in CLI. Here is the way:

1. Download the latest version of FP-PDV including lib.zip here: https://github.com/Nesvilab/FragPipe-PDV/releases
2. Unzip lib.zip file and put the lib in the same folder of FP-PDV-1.2.2.jar.
3. Use this command line: java -jar FP-PDV-1.2.2.jar your_result_folder_full_path thread_num
4. We just updated a comprehensive tutorial for FP-PDV: https://github.com/Nesvilab/FragPipe-PDV/blob/V1.2.2/FragPipe-PDV%20tutorial.pdf

Please let me know if you have any issues.

Kai

[shenghao003]

Thank you very much, but I still want to ask if using PDV software alone can support the results of Fragpipe database search?

[KaiLiCn]

Yes. It supports. I am not sure the reason of the issue without your data.

How many mzML files you used in the search? Based on the screenshot, you import only one mzML file. If you have multiple ones, please import them all together. I will also test the result from the new version of FragPipe.

Thanks.

[shenghao003]

There is only one mzML file.

Thanks.