Proteobench / ProteoBench

ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows. https://proteobench.cubimed.rub.de/
https://proteobench.readthedocs.io
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new support for i2MassChroQ using Sage instead of X!Tandem #417

Open OlivierLangella opened 1 month ago

OlivierLangella commented 1 month ago

Is your feature request related to a problem? Please describe. no problem, many thanks for the new web user interface ! it is well done. i2MassChroQ is already supported, but I had to add new parameters in the metadata specific to the Sage identification engine. Those new tags in the metadata csv file are not taken into account yet.

Describe the solution you'd like So I've reported the main Sage parameters in the metadata file. The new parameters dedicated to sage are present in this file :

Module_2_DDA_quantification/search_results/i2MassChroQ/i2m_and_sage/Project parameters.tsv

in the dedicated cloud.

Additional context The result is interesting and I would like to publish it image with relevant metadata

Thanks a lot ! Olivier

mlocardpaulet commented 4 weeks ago

thanks, we should definitely make this work. Is it normal that there are no values in the FDR fields?

OlivierLangella commented 4 weeks ago

Hello @mlocardpaulet ! oh no, that's a bug... thanks I'll check this

OlivierLangella commented 4 weeks ago

I've checked the file, here are the FDR fields reported :

i2m_psm_fdr_threshold_target    0.006
peptide_fdr 0.008561447245
protein_fdr 0.009234643907
psm_fdr 0.005999419143

is this the right fields or is there an other field ? https://github.com/Proteobench/ProteoBench/blob/369dd02231560e3d5be7c624d06ebf3bb45b6484/proteobench/io/params/i2masschroq.py#L33

OlivierLangella commented 1 week ago

Hello @mlocardpaulet , is this field OK or am I missing something ? Thank you Olivier

mlocardpaulet commented 1 week ago

yes, these are OK :). It is just that these are empty in the parameter file in the cloud.

OlivierLangella commented 1 week ago

Oh that is weird, when I download the file in the cloud, I get this :

langella@piccolo:~/Téléchargements$ cat /tmp/Project\ parameters.tsv  | grep fdr
i2m_psm_fdr_threshold_target    0.006
peptide_fdr 0.008561447245
protein_fdr 0.009234643907
psm_fdr 0.005999419143

in the directory "i2m_and_sage". Tell me if it is the case for you, otherwise I'll just put the file elsewhere.

Thanks again Olivier

mlocardpaulet commented 1 week ago

Oh that is weird, when I download the file in the cloud, I get this :

langella@piccolo:~/Téléchargements$ cat /tmp/Project\ parameters.tsv  | grep fdr
i2m_psm_fdr_threshold_target  0.006
peptide_fdr   0.008561447245
protein_fdr   0.009234643907
psm_fdr   0.005999419143

in the directory "i2m_and_sage". Tell me if it is the case for you, otherwise I'll just put the file elsewhere.

Thanks again Olivier

Oh no! You are right. Sorry. I don't know what I did to not see these 🤦 It looks all good. Sorry for the wasted time.