DIANN 2.2 data format

[xuel12]

Starting DIANN2.2, they replaced the report.tsv with report.parquet. Can the MSstatsConverter update accordingly so that new version of the software could be still compatible?

Thanks.

[tonywu1999]

Hi,

First, you can read the file using the arrow library. Then, the DIANNtoMSstatsFormat function has an argument called quantificationColumn that you can set to auto to use the format of the parquet file. I believe that is what you'd be looking for, but let me know otherwise. Example below:

library(arrow)
library(MSstatsConvert)
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,
                                 use_log_file = FALSE, quantificationColumn = 'auto')

Thanks,
Tony