Error analysing "combined modified peptide.tsv".

[Prashant-OIST]

Hello,

I am analyzing "combined modified peptide" files generated using the FragPipe workflow through the online FragPipe Analyst. However, I keep encountering an error. My file contains both "Intensity" and "MaxLFQ Intensity" columns, and I want to analyze the "MaxLFQ Intensity" data with variance normalization.

Could someone guide me on how to resolve this issue?

PS: I faced a similar issue when analyzing the "combined peptide" file, which only worked after repeated attempts. However, other peptide files, such as "S/T/Y" or "combined modified," fail to work entirely.

Thank you,
Prashant

[RaquelVaya]

Hello Prashant,

The error you’re encountering is likely due to modifications made to the TSV file. For example, if you changed the column name from 1_1_MaxLFQ intensity to A_1_MaxLFQ, you’ll need to update the annotation file accordingly and ensure the names match. Alternatively, when adding the file in MS Fragger, you can modify the name directly instead of selecting the custom/consecutive mode in the groups/replications settings.

Although I’m not entirely sure if this is critical, I’d recommend avoiding the deletion of any columns. However, if you want to remove specific proteins, that should be fine (I think).

I hope this helps!

[Prashant-OIST]

Hello Raquel,

Thank you so much for your suggestions. However, I have carefully checked the files multiple times, and the column names and annotation file names seem to match perfectly. Additionally, I have used the same annotation file for the "protein.tsv" analysis, and it works perfectly every time.

I am unsure where the error could be. I have not deleted any columns and have been using the files as generated.

I would appreciate any help in figuring out the issue.

[RaquelVaya]

Hi @Prashant-OIST,

Do you also have the same issue with the combined peptide instead of the modified peptide? I’m sorry, I’m running out of ideas.

Best,

Raquel

[Prashant-OIST]

Hi @RaquelIQS ,

I am having the same error when analyzing "MaxLFQ Intensity" with "combined peptide." However, normal "Intensity" analysis works fine and does not generate any errors. On the other hand, when using "combined modified peptide," I get errors while analyzing both "Intensity" and "MaxLFQ Intensity."
I truly appreciate you taking the time to think about this issue, but unfortunately, I have not been able to find a solution yet.

[hsiaoyi0504]

@Prashant-OIST We don't officially support the combined_modified_peptide.tsv yet, but feel free to email me (yihsiao@umich.edu) your data then we can test a bit how to support that.

[Prashant-OIST]

Dear @hsiaoyi0504, Thank you so much for your message and guidance. I wanted to let you know that I was able to successfully perform the analysis by locally downloading the Fragpipe Analyst on Linux using the codes provided on the website. however, I did not perform myself but sought some assistance to get it done.
Once again, thank you for your help and support!