PDV export to text

[treko90]

Hello, is it possible to export the peptide's b/y fragment assignments into the csv file? When analyzing many peptides, complementary machine readable output would help in reporting

[KaiLiCn]

Yes.

You could export all or selected PSMs report to the txt file by clicking the Export menu on the top left.

Then, you could specify the save path and which information you want in a popup dialog:

Kai

[treko90]

Thank you for a quick reply! This exporting seems to export total numbers of b and y ions, I meant exporting the txt file with the annotation of specific detected fragments like: b3+: 335Da, y1: 150, y2: 250 and so from the command line

[KaiLiCn]

Hi, you are right. I just updated the code to allow users export the detail annotations. Please try this pre-release version: https://www.dropbox.com/scl/fi/0y73hyi4mso9czr91c3v6/PDV-2.1.1.zip?rlkey=9zfpg60div176g0fua1viuyoq&st=g0vuc02e&dl=0 .

You could select the "Annotations" in the same place. There will be three more columns "ions", "ions_mz", and "ion_ints" in the report file. Let me know if you see any issue.

Kai

[treko90]

I see that the new option called fragspectrum and Annotations appeared. Export works when I select to export all the spectra but the export of the selected spectrum produces an empty file.

Is it possible to export from command line to process multiple files in batch? I didn't see an option in PDV-2.1.1.jar -h