The Spectrum Properties Filter node sets thresholds for the data that you pick to analyze. The node performs a function similar to that of the Spectrum Selector node but is included separately so that you can use separate thresholds in different branches of a branched workflow. You can also use multiple nodes in series to filter on multiple criteria, for example, to filter on more than one signature ion for a given PTM, such as glycosylation.

The following table describes the parameters for the Spectrum Properties Filter node.

NOTE

If you specify both a retention time range and a scan range, the application combines them into a single filter criterion; that is, it processes a scan only if it simultaneously falls within the specified retention time range and the specified scan range.

Spectrum Properties Filter node parameters

Parameter

Definition

Spectrum Properties

 

Lower RT Limit

Specifies the lower retention-time limit. If you set this value to 0.0, the application uses the lowest available retention time.

Range: 0–no maximum; default: 0

Upper RT Limit

Specifies the upper retention-time limit. If you set this value to 0.0, the application uses the highest available retention time.

Range: 0–no maximum; default: 0

Lowest Charge State

Specifies the minimum precursor charge state below which spectra are filtered out.

Range: 0–no maximum; default: 0

Highest Charge State

Specifies the maximum charge above which peptides are filtered out.

Range: 0–no maximum; default: 0

Min. Precursor Mass

Specifies the minimum mass limit of a singly charged precursor ion to be processed, in daltons.

Range: 0–no maximum; default: 0 Da

Max. Precursor Mass

Specifies the maximum mass limit of a singly charged precursor ion to be processed, in daltons. If you set the value to zero, the application applies no upper limit to the precursor mass.

Range: 0–no maximum; default: 0 Da

Spectrum Properties Filter

First Scan

Specifies the scan number of the first scan to process. If you set this number to 0, the application uses the first available scan.

Range: 0–no maximum; default: 0

Last Scan

Specifies the scan number of the last scan to process. If you set this number to 0, the application uses the last available scan.

Range: 0–no maximum; default: 0

Ignore Specified Scans

Activates the Edit Parameter Text for Ignore Specified Scans dialog box so that you can enter a single scan or a range of scans to exclude from processing.

To specify a single scan, enter its number in the dialog box.

To specify a range, place a hyphen between the starting scan and the ending scan, for example, 2000–3000.

For multiple entries, place a semicolon (;) between each entry, or place each entry on a separate line.

Thresholds

Total Intensity Threshold

Specifies the minimum total intensity that a tandem mass spectrum must have in order to pass the filter.

Range: 0–no maximum; default: 0

Minimum Peak Count

Specifies the minimum number of peaks that a tandem spectrum must have in order to pass the filter.

Range: 1–no maximum; default: 1

Filter Spectra by Peak Properties

Filter Mode

The settings determine whether the follow criteria are used to select or eliminate spectra:

  • Pass Through Matching Spectra (default)
  • Eliminate Mating Spectra

Peak Masses

List of masses or mass ranges (each entry typed on a separate line) to detect in filtering. Mass ranges must be specified by typing, for example, 1000–2000.

Neutral Loss Masses

List of mass differences used for the detection of neutral losses (each entry typed in a separate line).

Match Tolerance

The match tolerance used during peak based filtering.

Minimum value = 0.00 Da;
Maximum value = (unchecked)