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How ProMass for Xcalibur processes data step-by-step

This overview describes how ProMass processes data automatically. If you want to manually process individual spectra, please refer to the instructions for processing a clipboard spectrum.

1. The user sets up an Xcalibur sequence with a valid ProMass-enabled Qual processing method and optional ZNova parameter string(s).
2. The user either runs a sequence and selects post-acquisition processing, or batch reprocesses a sequence.
3. The processing method creates a results file (.RST file) in the data file path for each data file processed.
4. ProMass gets chromatographic peak definition from the results files.
5. ProMass averages scans that are defined by each peak in the Xcalibur results files.
6. ProMass writes out an ASCII (text) file containing sample, chromatogram, and mass - intensity information for each spectrum averaged in the chromatogram.  A ProMass ASCII data file is created for each raw data file processed.  These text files are saved in the data file path.
7. ZNova reads each ProMass ASCII data file and processes (deconvolutes) all of the averaged spectra present in each text file.
8. ZNova generates graphics files, text-based results files, and an html report for each data file processed.
9. ZNova produces a summary index.html file in the results directory summarizing all of the files that were processed into that same directory.