scans

scans lists the scan headers of a mass-spectrometry run without decoding any peaks: scan number, MS level, retention time, polarity, precursor m/z and charge, isolation window, activation, collision energy, filter string and the stored total ion current. To read one spectrum’s arrays, see spectrum.

openreadout scans [OPTIONS] <FILE>

MCP: openreadout_scans.

It reads Thermo .raw, mzML (also .mzML.gz and mzMLb), mzXML, imzML, Bruker .d, Agilent .d, Waters .raw, Sciex .wiff, ANDI/MS .cdf and ChemStation .ms. IR, Raman, UV-Vis and NMR spectra are traces: see trace.

Flags

• --json: print the JSON wrapper instead of text.
• --run N: run index, for files with more than one run (Sciex samples). Default 0.
• --ms-level N: only scans of this MS level (1 = full scans, 2 = MS/MS).
• --polarity positive|negative: only scans of this polarity.
• --rt-range START:END: retention-time window in minutes. Either side may be empty (5:, :12.5).
• --precursor MZ: only MS/MS scans whose precursor m/z is within the tolerance.
• --precursor-tol DA: precursor tolerance in m/z units. Default 0.01.
• --precursor-ppm PPM: precursor tolerance in ppm instead.
• --charge Z: only precursors of this charge state.
• --activation METHOD: only this activation (HCD, CID, ETD, case-insensitive).
• --scan-filter TEXT: only scans whose filter string contains this text.
• --offset N: skip this many matching scans. Default 0.
• --limit N: list at most this many matching scans. Default 50, or every match with --csv. All matches are still counted.
• --count: only count the matching scans per MS level.
• --csv: write the matching scans as CSV to stdout, one row per scan.

Examples

openreadout scans run.raw --ms-level 2 --count
openreadout scans run.raw --ms-level 2 --precursor 445.12 --precursor-ppm 10 --csv > ms2.csv

Chromatograms and peak areas are in analyze chromatogram and analyze peaks.

JSON

scans.

Run openreadout scans --help for the full help of your installed version.