File Preparation

Examples of each data type can be found under test data in the github repository.

PreProcessed Data Folder

Raw data is generated by vendor instruments. This data is commonly encoded in a propriatory format. It is recommended to first process this data with PNNL PreProcessor. All raw/Preprocessed data must be together in an encompassing folder, some raw data types such as Agilent (.d) are folders themselves, these must still be isolated in an encompassing folder. See more details in section titled “Upload your files” below. Supported file types can be found on the proteowizard website.

IMS Metadata Folder

This data is generated alongside and paired with the raw data by some vendors. It includes information such as instrument specifications, temperature deviations between runs, and electrical current changes. This is required for stepped field experiments and optional for single field experiments. Including this data for single field experiments improves accuracy of CCS value predictions.

Feature Data Folder

Feature files are generated by Mzmine or DEIMoS. Features, also known as peaks, are predicted based on signal-to-noise ratio of drift time, intensity, and mass/charge (m/z) ratios.

Target List File

This excel file is required for stepped field experiments. This contains the following columns: CompoundID, CompoundName, ExactMass, UniqueID4RawFileNames, Adduct_mz, Ionization, ExpectedCCS.

This must be created by the user with known molecules/standards and neutral masses in order to compare with sample data and calculate CCS values. Singlefield Target List File can be generated from the SteppedField CCS table output using this script.

Metadata File

This hidden metadata file is generated from PreProcessed data and includes the following metrics: RawFileName, AcquiredTime, InstrumentName, IonPolarity, Well, Cartridge. This is generated in and required for the AutoCCS step.

Calibrant File

This text file includes calibrant information for single field experiments. Calibrant information includes: CCS values, mass(m), charge(z), m/z, and ionization.