Time series data analysis using spectronaut DIA data

[Sithurandi Ubeysinghe]

Hello MSstats team,

I am attempting to perform a statistical analysis of some DIA data, which I obtained after APEX proximity labeling of the Kappa opioid receptor at various time points following ligand stimulation. I was able to successfully export the data from Spectronaut after performing direct DIA analysis. However, I am having trouble using MSstat for the statistical analysis, as it is continuously giving me error messages. The MSstats report I downloaded is too large to attach here.

Could you please suggest a workflow or code to do this?

Thank you in advance.

Sithurandi

[Anthony Wu]

Hi Sithurandi,

Would you be able to attach a small subset of your Spectronaut report (along with the annotation file) and copy/paste the code you're running and the error message you're seeing?

Thanks,

Anthony

[Sithurandi Ubeysinghe]

Hello Anthony,

Thank you for your quick response. Please find the attached Spectronaut report, annotation file, and the error messages I got. I am new to R and MSstats, and I am worried that I am using incorrect random codes. I highly appreciate your help. 

Thank you so much for your assistance.

Best regards,

Sithurandi

[Anthony Wu]

Hi,

I tried using the input file provided and I wasn't able to reproduce your error.  Here's the code I used:

input = data.table::fread("Spectronaut_DIA_export.csv")

SpectronauttoMSstatsFormat(

    input,

    filter_with_Qvalue = TRUE, 

    qvalue_cutoff = 0.01, 

    removeProtein_with1Feature = TRUE,

    removeFewMeasurements = FALSE

)

It appears the main difference is that I didn't set the `annot` parameter because the experimental design information is already in the Spectronaut input file.  Let me know if you still encounter any problems.

Thanks,

Tony

P.S. I set `removeFewMeasurements` to FALSE because the file you gave me only has one MS run (if set to TRUE, it removes all peptides measured in only one MS run).