Does the current standalone version work with public datasets in PRIDE, MassIVE, jPOSTrepo and iProX, or Universal Spectrum Identifiers (USIs) from ProteomeXchange?

[zxseason]

Hi developer,
When I used the proteomics study ID, for example '-b PXD000529', it shows no file associated with the ID. Does the current version works by automatically downloading the proteomics study or is there any additional steps to do that?

Thanks,

[wenbostar]

The data downloading url from the public databases was changed. Could you please try this new version https://drive.google.com/file/d/1_xKW7xYDl3bTZe5WyA57PdFJ0l9MRgKY/view?usp=sharing?

[wenbostar]

This is a known issue and has been fixed ba5d3e5.

[zxseason]

Thank you. BTW do I have to specify the modifications, for example TMT or iTRAQ myself by looking into the detail of the study or it is automatically retrieved by Pepquery from some metadata file?

[wenbostar]

You will need to look at the study to set these parameters based on the experiment.

[zxseason]

Thank you. I have another question. When I try to index some .raw files in a folder, I encountered Error: Could not find or load main class index, what does this mean?

[wenbostar]

Could you please send me your complete command line and the command line message?

[zxseason]

.Raw files in the folder. Why no file is converted and indexed? Thank you!

PS D:\pepquery-2.0.2> java -jar pepquery-2.0.2.jar index -i D:\proteomicsdownload\ -o D:\proteomicsdownload\PXD036238\ -p D:\pepquery-2.0.2\Thermo\ThermoRawFileParser.exe
2025-03-22 15:46:30 [INFO ] main.java.index.BuildMSlibrary[main:39] - Start analysis
2025-03-22 15:46:30 [INFO ] main.java.index.BuildMSlibrary[main:40] - -i D:\proteomicsdownload\ -o D:\proteomicsdownload\PXD036238\ -p D:\pepquery-2.0.2\Thermo\ThermoRawFileParser.exe
2025-03-22 15:46:30 [INFO ] main.java.index.BuildMSlibrary[buildLibrary:195] - Total MS/MS files: 0
2025-03-22 15:46:30 [INFO ] main.java.index.BuildMSlibrary[buildLibrary:206] - Used CPUs: 8
2025-03-22 15:46:30 [INFO ] main.java.index.BuildMSlibrary[buildLibrary:290] - Total spectra: 0
2025-03-22 15:46:30 [INFO ] main.java.index.BuildMSlibrary[buildLibrary:294] - Compress index files ...
2025-03-22 15:46:30 [INFO ] main.java.index.BuildMSlibrary[gzfiles:340] - Used CPUs: 8
2025-03-22 15:46:30 [INFO ] main.java.index.BuildMSlibrary[buildLibrary:296] - Compress index files done
2025-03-22 15:46:30 [INFO ] main.java.index.BuildMSlibrary[buildLibrary:299] - Delete all .mgf index files, keep .mgf.gz index files ...
2025-03-22 15:46:30 [INFO ] main.java.index.BuildMSlibrary[buildLibrary:314] - Delete all .mgf index files, keep .mgf.gz index files. Done
2025-03-22 15:46:30 [INFO ] main.java.index.BuildMSlibrary[main:121] - Total time used:0.00 min

[sophiachen1]

Hi @wenbostar ,
I am wondering if this issue is fixed? I had the same error "Could not find or load main class index" when I use "java -cp pepquery-2.0.2.jar index", however it seems working when I try "java -cp pepquery-2.0.2.jar main.java.index.BuildMSlibrary", which I learned from this post #31 (comment)
Thank you for your help!