MSstats with M/L/H SILAC data

[Claus Pelikan]

Hey MSstats team,

First of all thanks for the great software! 

I am currently analyzing some SILAC data with three labels. Since I used MSstats before I wanted to give it a try, but as mentioned elsewhere MSstats is currently not capable of analyzing this kind of data. 

Therefore two questions:

1. Do you plan on implementing a SILAC pipeline into MSstats anytime soon?

2. If not could you recommend a way to handle SILAC data so I could use one of the current MSstats pipelines? I was thinking to split the label data and treat the different labels as different samples, do you think this is a viable approach?

Thanks in advance!

Best,

Claus 

[Devon Kohler]

Hi Claus,

There currently is not a specific SILAC pipeline, however we have used MSstatsTMT to analyze SILAC experiments in the past. I am not sure what your exact experimental design is, however you should be able to treat each sample as a "mixture", with the heavy and light cells as "channels". See below for a table of what I mean. With your data in the correct format you can simply follow the standard MSstatsTMT pipeline.

Mixture (Sample)   Channel Condition
1 channel.H       Treatment
1 channel.L    Control
2 channel.H        Treatment
2 channel.L    Control
3 channel.H   Control
3 channel.L       Treatment

We have seen that SILAC experiments can be underpowered, due to a low number of replicates, so if you see few significant proteins after modeling that may be why. Let me know if you have any questions!

Best,

Devon