Plot Properties and Processing tab define parameters that are applied for the traces, injection, or raw data file. The following table describes the parameters in the Plot Properties and Processing.

Parameter

Description

Injection/Raw data

Displays the name of the injection or the raw data file.

Select a Raw File for the Active Trace icon ()

Opens the Ardia repository folder.

Detector

Displays the detector type based on the information in the injection or the raw data file. Available detector types:

  • MS: Detects MS data.
  • A/D card: Detects data from an analog-to-digital converter.
  • PDA: Detects wavelength scan data from a photodiode array detector.
  • UV: Detects data from a UV detector.
  • Analog: Detects data from an analog detector.
  • MS Trending: Detects the instrument status readings for the mass spectrometer.

Scan Filter

Displays the filter to apply to the injection or the raw data file. The application auto-senses the metafilters (including SRM or compound-filters) in the injection or the raw data file in this order: MS, MS2, ETD, HCD, and then the individual scan filter list.

Trace Type

Displays the trace type, which is based on the different detector types as follows:

  • For MS: TIC, Mass Range, Base Peak, or Neutral Fragment.
  • For A/D card or Analog: The relevant trace.
  • For PDA: Total Scan, Wavelength Range, or Spectrum Maximum.
  • For UV: UV trace.
  • Trace type for MS trending: Instrument status parameters.

Ranges

Specifies the m/z ranges of the displayed spectrum. Available only when you select Mass Range under Trace Type.

Default mass tolerance for different mass analyzer types:

  • FTMS: 5.00 ppm
  • ITMS: 0.50 amu
  • TQMS: 0.50 amu
  • SQMS: 1.00 amu
  • Sector: 5.00 ppm
  • ASTMS: 5.00 ppm
  • Unrecognized: 0.50 amu

Range: 0.00−1,000 ppm or 0.00−10 amu; units: amu, mmu, or ppm.

Default: 5 ppm.

Mass Tolerance

Specifies the mass tolerance for the m/z of the specified ion.

Default: 5 ppm.

Units

Specifies the following units for the Mass Tolerance parameter:

  • Atomic mass units (amu)
  • Millimass units (mmu)
  • Parts per million (ppm)

Default: ppm

Formula

Displays the chemical formula or the peptide sequence of the compound to be analyzed in the injection or raw data file.

Edit icon ()

Allows users to edit any of the following:

  • Chemical formula: Specifies the IUPAC nomenclature for a chemical formula.
  • Peptide: Specifies the one-letter amino acid abbreviations for a peptide sequence.
  • Charge: Specifies the charge of the adduct ion or peptide.
  • Adduct: Specifies the adduct for the simulated spectrum.

NOTE The adduct box is unavailable when the charge is 0, or if the field is blank.