DIANN report input

[aakendra11]

Since DIANN has changed their default report file output to .parquet, how can this file type be imported into MSStats Shiny?

[tonywu1999]

Hi,

We haven't gotten a chance to update MSstatsShiny to be able to upload the parquet file. My goal is to add it in MSstatsShiny by end of August, but that timeline is subject to change. I'll keep you posted if that timeline changes.

At the moment, only MSstatsConvert / MSstats supports the .parquet format through code. Here's an example with the latest release.

# For DIANN 2.0, set quantificationColumn = 'auto'
input_file_path_2_0 = system.file("tinytest/raw_data/DIANN/diann_2.0.parquet",
package="MSstatsConvert")
annotation_file_path_2_0 = system.file("tinytest/raw_data/DIANN/annotation_diann_2.0.csv",
package = "MSstatsConvert")
input_2_0 = arrow::read_parquet(input_file_path_2_0)
annot_2_0 = data.table::fread(annotation_file_path_2_0)
output_2_0 = DIANNtoMSstatsFormat(input_2_0, annotation = annot_2_0, MBR = FALSE,
use_log_file = FALSE, quantificationColumn = 'auto')
head(output_2_0)

Thanks,
Tony