Question about MSstatsPTM R package

[Clarissa Braccia]

Hi,  

I am really interested in the use R package MSstatsPTM for the data analysis of a project we are currently working on in our lab. 

 

I’m working with MaxQuant output and trying to load the data using MaxQtoMSstatsPTMFormat, but I’ve encountered some difficulties.
Initially, I received the following error from R:

 

Error in .checkAnnotation(annotation, labeling_type) :   Extra columns included in the annotation file that are not required.     This can cause problems in the converter dependencies. Please     only include the following columns in the annotation file:                  Run, Raw.file, Condition, BioReplicate, IsotopeLabelType

 

After that, I created an annotation file containing only the required columns, but then encountered a new error:

Error in .handleFractionsLF(input) :   ** MSstats suspects that there are fractionations and potentially technical replicates too. Please add Fraction column to the input.

 

If I try to remove the Fraction column, I receive the first error. 

 

Would it be possible to kindly ask for your help in troubleshooting this issue? If helpful, I’d be happy to share the annotation file I prepared.

Thanks in advance, 

Clarissa

[Anthony Wu]

Hi Clarissa

Would you be able to share your annotation file and a small subset of your maxQuant quantitation file and then I could have a look and troubleshoot the issue?

Thanks,

Tony