Skip to content
OpenReadout

spectrum

spectrum returns one mass spectrum: its scan metadata, its most intense peaks with their charge states, and its m/z and intensity arrays. To list the scans of a run, see scans.

openreadout spectrum [OPTIONS] <--rt <MIN>|--scan <N>|--spectrum <I>> <FILE>

MCP: openreadout_spectrum.

Flags

  • --json: print the JSON wrapper instead of text.
  • --run N: run index, for files with more than one run (Sciex samples). Default 0.
  • --rt MIN: the scan nearest this retention time in minutes, of MS level 1 or --ms-level. Use it for the spectrum at a chromatogram’s apex.
  • --scan N: this scan number as the instrument counts it (1-based in Thermo files).
  • --spectrum I: this zero-based spectrum index, counted within --ms-level when it is given.
  • --ms-level L with --spectrum I: count I among the spectra of MS level L only. With --rt, the MS level of the scan. MS1 and MS/MS scans are interleaved, and --ms-level 2 --spectrum 0 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.
  • --lock-mass MZ|auto: Waters .raw: correct m/z with the lock-spray reference scans, MZ being the lock compound’s m/z (auto: the Lock Mass the file records). Each scan is multiplied by the reference over the lock peak measured in the lock-spray scans within 60 s of it; extra.lock_mass_correction gives the factor. Off by default: m/z are as stored. Against MassLynx’s own correction of the same runs the result agrees to about 2 ppm. chromatogram takes the same option for accurate-mass XICs.
  • --max-points N: return at most this many points, the most intense ones, in m/z order. point_count still reports the full size. MCP returns 1000 by default.

Examples

Terminal window
openreadout spectrum run.raw --rt 93.15
openreadout spectrum run.raw --scan 1200 --json
openreadout spectrum run.raw --ms-level 2 --spectrum 0 --centroid --json

Peaks and charge states

peaks lists the 20 most intense peaks of the whole spectrum (MCP top_peaks changes the number). In a profile spectrum the peaks are its local maxima; a centroided one is used as stored. For each peak the charge is the z whose isotope spacing, 1.00336/z, finds the most isotope peaks in a row above it (each at least 2 % of the peak, within 15 ppm or 0.003). monoisotopic_mz steps down the same pattern while the lower isotope is present, and neutral_mass_da is z × (monoisotopic m/z − 1.00728) in positive mode (+ in negative mode). A peak inside the pattern of a more intense one is not listed again. This is a quick reading of the pattern, not a deconvolution: overlapping patterns can give the wrong charge.

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.

JSON

spectrum.

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