Hello,

I have a SILAC mass spectrometry protein data. It is the output of Thermo ProteomeDiscover.

The file format is *.msf. and is a SQLite DB file.

Which R package can work on with this kind of data?

Thank you in advance for great help!

Best,

Yue

I don't know any R packages that can parse PD' SQLite file (I don't even know if it's documented - I would keen to know). An alternative, is to export your data in a tabular format from PD and load it into R as a SummarizedExperiment object with QFeatures::readSummarizedExperiment().