Formatting issues with experiment_annotation.tsv for DIA

[enonimos]

Hello, I have been testing FragPipe-Analyst with DIA data from DIA-NN and generating the experiment_annotation file as outlined in the DIA tutorial section here: https://github.com/MonashProteomics/FragPipe-Analyst/tree/main/docs I have run into two formatting issues related to the experiment_annotation file.

First, when I leave the full paths in the "file" column of the annotation and the DIA report (diann-output.pg_matrix.tsv), then i get the following error: If I remove the path, leaving just the filename, in both the annotation file and DIA report, that message is gone.

Once that was resolved, I received a second error. After testing, I realized that the labels in the sample_name and condition columns cannot start with numbers. Once they were changed, the error message was resolved.

I have uploaded the original annotation file that I thought would be compatible, and the "fixed" annotation that allowed import of the data. experiment_annotation_fixed.txt experiment_annotation_original.txt

I hope this helps as you continue to develop Analyst, thank you for the developmental efforts! Todd

[hsiaoyi0504]

@enonimos Thanks for the feedback. Could you send a copy of files you are using to yihsiao@umich.edu? I will take a look soon.

[hsiaoyi0504]

Based on my test sample_name column could contain values start with number, but condition column couldn't.

[hsiaoyi0504]

The fixes have been included in the MonashProteomics/FragPipe-Analyst@568a3c350783d0894a538996816b69a80773b3e4 and been available in v0.19. For the experiment_annotation.tsv mentioned here, the file path doesn't match to the columns of protein group file. It might because the files have been moved after running the DIA workflow. Simply updated the file fixes the issue.

[enonimos]

I missed the differences in file path, sorry about that. Thank you.