The following table describes the parameters for the Xtract deconvolution algorithm in the Peak # − Deconvolution Parameters pane on the Component Detection page.

The Xtract deconvolution parameters are enabled on either the Intact Fragmentation page (for MS2 spectra) or the Intact Deconvolution page (for full-scan MS spectra).

These parameters are similar to the parameters used for intact mass analysis, but are specific to a selected peak.

Xtract parameters on the Component Detection page



Deconvolution Algorithm

Select the Xtract (Isotopically Resolved) option.

Parameters (Xtract)

m/z Range

Specifies the range of m/z values used as input for the deconvolution. You can use this parameter to select a narrower range. The deconvolution algorithm ignores the portions of the spectrum outside this range.

The range value comes from the first (or only) raw data file loaded for the experiment. You can edit the range as needed.

Output Mass Range

Specifies the range for the displayed masses on the x axis of the plots in the Deconvoluted Spectra panes on the Process and Review page.

Output Mass

Determines whether the Xtract algorithm returns a single peak at either the monoisotopic mass or the monoisotopic MH+ mass for each of the detected components.

  • M: Specifies that the results file contain a single peak for the monoisotopic mass for each of the detected components. This option generates masses without adducts.
  • MH+: Specifies that the results file contains a monoisotopic MH+ mass for each of the detected components. This option generates masses with adducts.

S/N Threshold

Specifies a signal-to-noise (S/N) threshold, x, above which the Xtract algorithm considers a measured peak to be a real (accepted) peak. The Xtract algorithm ignores peaks below this threshold.

Any spectral peak must be x times the intensity of the calculated noise for that spectrum before the Xtract algorithm considers the peak.

Rel. Abundance Threshold (%)

Specifies a relative abundance threshold below which the application filters out data for analysis.

This option sets a threshold as a percentage of the most abundant component in the spectrum. The most abundant peak in the deconvoluted spectrum has a relative abundance of 100 percent, and all other peaks are calculated relative to that one.

In the Results table on the Process and Review page, the application shows only those components that are greater than or equal to this relative abundance threshold in the deconvoluted spectrum. For example, if the highest peak has an absolute abundance of 1000 and the relative abundance threshold is 1 percent, the application filters out all peaks below an absolute abundance of 10.

For this value, 0% displays all results and 100% displays only the most abundant component.

Charge Range

Specifies the charge state range to be deconvolved, from the lowest charge state to the highest.

For example, if you set this parameter range from 2 through 5, the Xtract algorithm considers only charge states 2 through 5 for deconvolution. It ignores charge states 1 and higher than 6.

Min. Num Detected Charge

Specifies the minimum number of charge states required to produce a component. No components with less than this minimum number appear in the deconvoluted spectrum.

This parameter must be an integer greater than or equal to 1.

Isotope Table

Specifies the type of isotope table to use in the deconvolution.

Isotope tables simulate the distribution of isotopic peaks, in m/z, for different monoisotopic mass candidates. The Xtract algorithm chooses the monoisotopic mass with the best fit between the theoretical and the observed isotope distribution.

To generate an isotope table, the application uses a chemical formula to describe the type of molecule. You can select one of the following formulas:

  • Protein: Uses an averagine formula to generate the isotope table.
  • Nucleotide: Uses an elemental formula typical for nucleotides to generate the isotope table.
  • Sequence Specific: Use a sequence specific isotope table for experiments multiple protein sequences.

Advanced Parameters (Xtract)

Visible only when you select the Show Advanced Parameters checkbox; these parameters typically do not need to be modified.

Calculate XIC (checkbox)

When selected, the application calculates the extracted ion chromatogram (XIC) for each detected component.

Enabling this parameter can result in a much longer analysis time, so you might avoid using it with complex data or with data where XIC data is unnecessary.

The Calculate XIC checkbox is inactive (gray) on the Intact Fragmentation page for processing MS2 spectra.

Fit Factor (%)

Measures the quality of the match between a measured isotope pattern and an averagine distribution of the same mass.

Enter a value between 0 and 100%:

  • 0% means that the measured isotope profile does not match theoretical averagine isotope distribution.
  • 100% means that the measured isotope profile is identical to the theoretical averagine isotope distribution.

Remainder Threshold (%)

This parameter is used when the Xtract algorithm attempts to resolve overlapping isotopic clusters; specifies the peak height threshold for smaller overlapping isotopic clusters as a percentage of the height of the most abundant isotopic cluster in the overlap region.

For example, if an isotopic cluster in a spectrum has an abundance of 100 and you set the Remainder Threshold parameter to 30%, the Xtract algorithm ignores any overlapping clusters with an abundance less than 30.

Consider Overlaps

When selected (default), the Xtract algorithm is more tolerant of unexpectedly high peak intensity for a theoretical isotopic cluster, due to the possible presence of overlapping isotopic clusters contributing to the peak intensity.

Because this option can lead to increased false positives, select it only in cases where you expect overlapping isotopic clusters in a data set.

Resolution at 400 m/z

Defines the resolution of the source spectrum at an m/z value of 400.

Select one of these options:

  • Raw File Specific: The application automatically uses the resolution from each raw data file loaded for the experiment to process the deconvolution for that particular file.
  • If the acquisition used more than one resolution, the application takes the first resolution value from the raw data file.
  • With this option, you cannot edit the resolution value; however, you can process multiple raw files acquired at different resolutions.
  • Method Specific: You must specify the resolution in the processing method to process the deconvolution for all of the loaded raw data files in the experiment.
  • By default, the application displays the resolution value from the first (or only) raw data file. If the acquisition used more than one resolution, the application takes the first resolution value from the file.
  • With this option, you can change the resolution value for this method; however, the application processes all of the raw data files using the same resolution. If the files were acquired at different resolutions, this option might not be suitable.
  • Only use this option when instrument method information is not available in the raw data file. When the resolution information is not available, the application uses a default resolution of 12374. If this resolution is not appropriate, you can modify the resolution value.

Negative Charge

When cleared, indicates the data was acquired in positive charge mode during the electrospray ionization (ESI) process.

When selected (default), indicates the data was acquired in negative charge mode.

MS spectra of samples containing nucleotides (such as DNA or RNA) are often collected in negative charge mode.

Do not select the Negative Charge checkbox if your data was acquired in positive mode. Results will not be usable.

Charge Carrier

Specifies the adduct ions introduced during the electrospray ionization (ESI) process. Adduct ions convert neutral molecules into ions.

  • H+ (1.00727663): Specifies the addition of hydrogen ions (protons).
  • K+ (38.9631585): Specifies the addition of potassium ions.
  • Na+ (22.9892213): Specifies the addition of sodium ions.
  • Custom: Specifies the addition of a charge carrier other than hydrogen, potassium, or sodium. When you select this option, a box opens so that you can type the mass of the custom charge carrier.

In negative mode, these ions correspond to losses rather than adducts.

Minimum Intensity

Specifies a minimum intensity threshold to filter out possible background noise, even when you set the S/N Threshold parameter to zero.

Expected Intensity Error

Specifies the permissible percentage of error allowed in calculating the ratio of the most abundant isotope to the next isotope higher in mass in the isotope series.