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.
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:
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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; |