Uploading data
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      Preparing SomaLogic ADAT Data for Upload to Mass Dynamics

      Uploading Somalogic data into Mass Dynamics

      This FAQ provides guidance and an example R script for transforming SomaLogic ADAT data into a wide-format table with intensities. The output is a *.csv file that can be uploaded to the Mass Dynamics platform.

      Sample data: https://somalogic.com/datadelve-statistics/

      Expected SomaLogic Input Format

      • A .adat file exported from SomaLogic assays.
      • Each sample contains protein measurements (intensities) for a set of analytes uniquely identified by AptName.

      Required fields or derived columns:

      • SampleId

      • PlatePosition (to uniquely identify calibrators/QC samples)

      • Intensity values (in columns prefixed with seq.)

      • Analyte metadata: AptName, UniProt, EntrezGeneSymbol, TargetFullName

      Prepare the Data for Mass Dynamics

      • Read the ADAT file into R using read_adat() from the SomaDataIO R package.
      • The ADAT file is in a wide format but with samples as rows and analytes as columns. To make it suitable for Mass Dynamics the file needs to be converted to a wide format where analytes represent rows and samples are the columns.
      • Analyte metadata are retrieved and merged with the measurement data using getAnalyteInfo() and a join on AptName.

      R Code snippet to prepare the data

      Upload to Mass Dynamics

      1. Upload the intensities_somalogic.csv file

      2. Follow the steps to select the columns containing protein intensities

      3. Map protein metadata as follows:
      • AptName-> ProteinGroup
      • Uniprot -> ProteinIds
      • EntrezGeneSymbol -> GeneName
      • TargetFullName -> Description

       

      4. Follow the steps to upload the experiment design 

      Code in text format

      library(SomaDataIO)

      library(dplyr)

      library(tidyr)

       

      # Read SomaLogic ADAT file

      my_adat <- read_adat("path/to/your_data.adat")

       

      # Retrieve analyte metadata

      analyte_infos <- getAnalyteInfo(my_adat)

       

      # Convert wide-format intensity data to long format to retrieve intensities

      my_adat_long <- my_adat %>% 

        pivot_longer(cols = starts_with("seq."), names_to = "AptName", values_to = "Intensity")

       

      # Join long data with analyte metadata

      my_adat_long <- left_join(my_adat_long, analyte_infos, by = "AptName")

       

      # Create unique sample name using SampleId and PlatePosition

      my_adat_long <- my_adat_long %>% 

        unite(SampleName, SampleId, PlatePosition, sep = "-", remove = FALSE)

       

      # Pivot to wide format: one row per protein, one column per sample

      intensities_table <- my_adat_long %>%

        pivot_wider(

          id_cols = c(AptName, UniProt, EntrezGeneSymbol, TargetFullName),

          names_from = SampleName,

          values_from = Intensity

        )

       

      # Write to CSV

      write_csv(intensities_table, "path/to/intensities_somalogic.csv")