Conversion and preprocessing#

Often mass spectrometry data needs to be converted or preprocessed. quantms checks your input files and automatically decides on necessary steps.

Mass spectra processing: Raw conversion#

The RAW data (files from the instrument) can be provided to quantms pipeline in two different formats: (i) RAW files - instrument files; (ii) mzML files (HUPO-PSI standard file format). quantms uses the thermorawfileparser to convert the input RAW files to mzML and all the following steps are built in top of the standard mzML.


Automatic RAW file conversion is only supported from Thermo Scientific.

Additionally to file conversion, the Raw conversion step allows the users to perform an extra peak-picking step openmspeakpicker true for those datasets/projects where peaks can be extracted using the Thermo RAW API. Read more about the OpenMS peak picker algorithm here . When bruker .d files are provided, quantms provides an optional parameter convert_dotd to convert .d to mzML (default false).

Mass spectra statistics: Quality metrics extraction#

The mass spectrum file can be parsed and generates a set of statistics about the file by script , and then passed to the pmultiqc module to perform quality control visualization. including as follow columns:

  • SpectrumID

  • MSLevel

  • Charge

  • MS_peaks

  • Base_Peak_Intensity

  • Retention_Time

  • Exp_Mass_To_Charge

  • AcquisitionDateTime