Get CCS values
For HDMSE data (with IMS), CCS values can be retrieved from the UNIFI API.
The API call requires passing m/z values, charges and retention times. Therefore, it is not recommended to use it for all peaks present in raw data to avoid excessive requests and unnecessary CCS calculations (e.g., for fragments or isotopes).
The conversion should be performed for a limited number of detected
peaks. Detected peak lists can be obtained after peak detection by any
software or algorithm. The DEIMoS Python
library can be easily used with MS data converted with
arcMS to Parquet format. It can perform peak detection to
obtain a reduced list of peaks for which CCS values can then be
retrieved.
The conversion operation is based on drift time calibration of an HDMSe result. It is possible only if CCS calibration was performed. It will convert bin index values to CCS calibrated values, expressed in angstrom squared.
The convert_bin_to_ccs() function can be used as
follows:
convert_bin_to_ccs(arrow_data)It takes an Arrow table object containing the sample data as input.
This table must include the necessary columns: bin,
mz, and rt, and the metadata must contain the
id of the sample. The function returns the same Arrow table
with an additional ccs column.