PSD peak detection for
3.2 Peak Detection
3.2 Peak Detection
This section includes:
• Strategy for Mariner peak detection
• Strategy for Voyager peak detection
• Setting peak detection parameters
• Peak detection parameter descriptions
• Charge state determination and examples
3.2.1 Strategy for Mariner Peak Detection
This section gives some quick suggestions on how to approach Mariner peak detection. For details on peak detection, see Section 3.2.3, Setting Peak Detection Parameters.
Default peak detection values are listed in Section 3.7, Default Peak Detection Settings.
Strategy
When detecting peaks in Mariner data:1. Open the data file and observe the effects of the default peak detection settings.
If you are analyzing resolved isotopes, default settings should yield acceptable peak detection. The default resolution setting of 5,000 is optimized for masses below 3,000 Da.
2. If you are analyzing proteins, decrease the Mass Resolution setting.
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3. If peak detection is not acceptable, leave the Use Resolution Dependent Settings option enabled, and adjust the following global threshold parameters in the following order:
• %Base Peak Intensity—Use this parameter to eliminate peaks with an intensity below the specified threshold. This threshold is represented as a percentage of the intensity of the base peak.
• %Max Peak Area—Use this parameter to fine-tune noise discrimination on the baseline or noise spikes on peaks. This threshold is
represented as a percentage of the area of the peak with the largest area and is calculated above the local baseline.
To determine an appropriate threshold, display the Spectrum Peak list, note the area of the peak with the greatest area and the areas of unwanted peaks, and estimate the percentage to enter as the threshold.
Specifying a %Max Peak Area Threshold is particularly useful if the spectrum includes a rising baseline that would cross a %Base Peak Intensity Threshold and eliminate peaks of interest in one portion of the trace.
4. If peak detection is still not acceptable, adjust the remaining peak detection parameters, as described in Section 3.2.3, Setting Peak Detection Parameters.
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3.2.2 Strategy for Voyager Peak Detection
This section gives some quick suggestions on how to approach Voyager peak detection. For details on peak detection, see Section 3.2.3, Setting Peak Detection Parameters.
Default peak detection values are listed in Section 3.7, Default Peak Detection Settings.
Strategy
When detecting peaks in Voyager data:1. Open the data file and observe the effects of the default resolution-dependent settings.
Hint: To improve peak detection, you can calculate the resolution on a tall, resolved peak in the middle of the spectrum. If the resolution result differs by more than 50% from the default resolution setting, fine-tune the Resolution setting and reapply peak detection. For more information, see Section 6.3, Using the Mass Resolution Calculator.
2. To aid in peak interpretation, do all of the following:
• Baseline-correct—The Centroid% peak detection value is derived from a percentage of the peak height, which is measured from 0. For information, see Section 5.8.2, Using Baseline Correction.
• Noise-filter or smooth—Use the method appropriate for your data to remove noise spikes:
For more information, see Section 5.7, Noise Filtering/Smoothing.
Data Type Method
Linear Default or Gaussian smoothing Reflector Noise Reduction
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• Deisotope (reflector data only)—Peak deisotoping reduces the spectrum to a
monoisotopic centroided plot of the monoisotopic masses. This is useful in identifying overlapping isotope clusters. Make sure peak detection thresholds are set low enough to detect the monoisotopic peak before deisotoping. For more information, see Section 3.4, Deisotoping a
Spectrum. Deisotoping provides no benefit on linear data (non-isotopically resolved) or on PSD data (pure isotope data).
3. If peak detection is not acceptable, keep the Use Resolution Dependent Settings option enabled, and adjust the parameter associated with the observed problem:
Problem Suggested Actions
High-mass peaks not detected
Decrease Mass Resolution setting. The default Mass Resolution settings are optimized for masses below 20,000 Da.
Noise detected as peaks Increase the %Max Peak Area.
Decrease the Resolution.
Peaks of interest are not detected
Decrease the %Max Peak Area.
NOTE: %Max Peak Area is calculated above the local baseline and can compensate for problems related to a rising global baseline.
Low Mass Gate spike is identified as the Base Peak
Truncate the data to eliminate the Low Mass Gate spike, then reapply peak detection settings. See Section 5.9, Truncating a Spectrum.
Peaks detected before deisotoping are not detected after deisotoping
Set %Max Peak Area and %BP Intensity to 0 before deisotoping, deisotope, then reset thresholds to appropriate settings after deisotoping.
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4. If you see more than one of the problems listed above in a spectrum, you can adjust peak detection parameters for any or all detection ranges (referred to as setting parameters locally) by doing the following in the order listed:• Disable Use Resolution Dependent Settings.
• Click the Advanced tab.
• Select a detection region that is exhibiting the problem.
• Adjust the local settings to fine tune detection.
• Click OK.
5. If peak detection is still not acceptable, adjust the remaining peak detection parameters, as described in Section 3.2.3, Setting Peak Detection Parameters.
Partially resolved peaks not detected
If peaks represent two compounds, and you want both peaks labeled, do either of the following:
• Set %Max Peak Area to 0, then adjust the %Base Peak Intensity until peaks are detected.
• Click the Peak Processing tab, then change the default Integration Baseline Setting from
Valley-to-Valley to Valley-to-Baseline.
If peaks represent partially resolved isotopes, and you want to label and detect the average mass, decrease the Mass Resolution setting until the isotopic envelope is detected.
Problem Suggested Actions
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3.2.3 Setting Peak Detection Parameters
This section includes:
• Before you begin
• Setting chromatogram parameters
• Setting Basic Settings (spectrum data)
• Setting Peak Processing parameters (spectrum data only)
• Setting Advanced Settings (spectrum data only)
• Resetting Basic Settings
Before you begin
Before setting peak detection, read:• Section 3.2.1, Strategy for Mariner Peak Detection
• Section 3.2.2, Strategy for Voyager Peak Detection