Data Format Conversion Inquiry for MSstats Compatibility

[Chen Xi]

Hello, I would like to analyze data using MSstats. 

My data is TMT11 data. I performed the search using SpectraST and quantification using Libra in TPP, then converted the results to CSV format. My results contain the intensity of each channel. Can I use MSstats to analyze my results? If I want to manually modify the result file to make its format compatible with MSstats, how should I do it? Are there any functions in MSstats that can be used for this purpose? 

 

Thanks a lot for your help.

[Devon Kohler]

Hello,

Unfortunately we do not currently have a converter for your output. I would recommend checking out some of the example data included in the MSstatsTMT package to get an idea of the format you will need to convert your data into. The resulting dataset below should be a good place to start. You will need to extract the columns listed input.mq. Let me know if you run into trouble.

Devon

```

head(evidence)
head(proteinGroups)
head(annotation.mq)
input.mq <- MaxQtoMSstatsTMTFormat(evidence, proteinGroups, annotation.mq)
head(input.mq)

```