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OpenReadout

spectra

spectra lists the scan headers of a mass-spectrometry run, or returns one spectrum’s m/z and intensity arrays.

openreadout spectra [OPTIONS] <FILE>

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.

Flags

Listing scans

  • --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). With --nth, the level to count in.
  • --polarity positive|negative: only scans of this polarity.
  • --rt 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.
  • --tol DA: precursor tolerance in m/z units. Default 0.01.
  • --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).
  • --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.

One spectrum

  • --scan N: this scan number as the instrument counts it (1-based in Thermo files).
  • --index I: this zero-based spectrum index.
  • --nth K: the K-th spectrum (from 1) of --ms-level. --ms-level 2 --nth 1 is the first MS/MS scan.
  • --centroid: the instrument’s stored centroid list instead of the profile, when a scan has both.
  • --exclude-flagged: Thermo .raw: leave out peaks the instrument flags as reference or background ions. Otherwise they are listed in extra.flagged_peaks.
  • --max-points N: return at most this many points. point_count still reports the full size.

Examples

Terminal window
openreadout spectra run.raw --ms-level 2 --count
openreadout spectra run.raw --ms-level 2 --precursor 445.12 --ppm 10 --csv > ms2.csv
openreadout spectra run.raw --ms-level 2 --nth 1 --centroid --json

Scan numbers

--scan N follows each format’s own numbering. For mzML it is the scan=N of the native id (else position + 1); for mzXML, scan/@num. For Bruker timsTOF, Waters and Sciex files it is the position + 1, and native_id says what the spectrum is (a frame, a PASEF precursor or window, a function and scan, or an MRM cycle and experiment). Per-format details are in Formats.

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

JSON

spectra (scan headers), spectra --scan (one spectrum).

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