visualization for fractionated samples

Question

visualization for fractionated samples

Closed this issue 3 years ago · 8 comments

Dear PDV developers team,
I would like to visualize the MSfragger results for a fractionated sample. In this case I only have 1 pepxml file and 2 mzML raw spectra. How can I use PDV for this visualization? Unfortunately the PDV 1.7.3 gives an error message when I tried to import both raw files. Please see the attached image.
Thanks

Answer 1 · 2021-06-28T08:46:53.000Z

Hi,
Could you please try to input the *.tsv file generated by MSfragger? PDV should support multiple mzML files with that result file. Please let me know if it still doesn't work.
Kai

Answer 2 · 2021-06-29T16:22:42.000Z

Thanks for getting back to me.
I forgot to mention that I am using the "Nonspecific-HLA" workflow in FragPipe. I tested the PDV1.7.3 and it failed to visualize the results from a single file. Can PDV help with the none-specific HLA peptide searches?
I am happy to share a sample file in case you are interested.
Thanks

Answer 3 · 2021-06-30T07:35:04.000Z

That's great. Could you please share your data(FragPipe result file, pepXML and tsv, and spectrum files) with me?

Answer 4 · 2021-06-30T14:45:28.000Z

Please find all the FragPipe output + the mzML file in this zipped file:
https://www.dropbox.com/s/1ugug9ykb6e812r/test-PDV_HLA.zip?dl=0

Answer 5 · 2021-07-01T06:57:41.000Z

Thanks. I will take a try.

Answer 6 · 2021-10-26T15:48:05.000Z

@fazeliniah, could you try the new version of PDV (v1.7.4)? I downloaded the file test-PDV_HLA.zip and it could be loaded into PDV (v1.7.4) for visualizing.

Answer 7 · 2021-10-26T15:55:32.000Z

@fazeliniah, below please find a screenshot about how to load the files input PDV:
Identification File: psm.tsv
Spectrum(s) File: *.mzML

Answer 8 · 2021-10-26T15:57:37.000Z

Thank you so much for your effort. It is working on my side now. Appreciate all your help with this.