The following table describes the information in the Results table on the Process and Review page.
The Results table for an Intact Mass Analysis experiment with target sequence matching enabled contains several additional columns. See Additional Results table parameters for target sequence matching experiments.
Batch experiments (or experiments with a single raw data file) contain two levels of results: Component and Charge state.
NOTE
Batch experiments (or experiments with a single raw data file) with drug-to-antibody ratio (DAR) feature enabled, have three levels (Component, Raw Data File, and Charge State) and the Results table is similar to the Results table for a multiconsensus experiment.
See Results table parameters (multiconsensus format experiments).
In the table header, "Avg/RT" refers to Average Over Selected Retention Time, "Auto PD" refers to Auto Peak Detection, and "SW" refers to Sliding Windows.
The columns in the Results table vary depending on the selected deconvolution algorithm (ReSpect or Xtract), deconvolution method (Average Over Selected Retention Time, Auto Peak Detection, or Sliding Windows) and other processing method parameters.
For each parameter described in the table below, a "Y" (for "yes") indicates that the parameter (column) appears in the Results table for a given deconvolution algorithm (ReSpect or Xtract) and associated deconvolution method (Average Over Selected Retention Time, Auto Peak Detection, or Sliding Windows).
NOTE
Because the BioPharma Finder application uses an updated algorithm, the calculated mass values in the Results table from this application might be slightly different from those reported by the Protein Deconvolution application.
Column | Description | Xtract | ReSpect | ||||
---|---|---|---|---|---|---|---|
Avg/RT | Auto PD | SW | Avg/RT | Auto PD | SW | ||
Component level | |||||||
+/− (button) | Select to show or hide the lower level of charge state information related to the currently selected component row. | Y | Y | Y | Y | Y | Y |
Row number (bolded) | The number assigned to each visible component row in the table. This sequential numbering does not change when you sort or filter the table. | Y | Y | Y | Y | Y | Y |
(Check box) | Selects/deselects a component row. To select/deselect the checkboxes for all component rows at once, select or clear the checkbox in the column header. If you filter the table, the following occurs:
| Y | Y | Y | Y | Y | Y |
Level | Indicates that the row is displaying component information (top level). | Y | Y | Y | Y | Y | Y |
Monoisotopic Mass | Displays a weighted average of the monoisotopic masses of each charge state. | Y | Y | Y | |||
Average Mass | Displays the mean mass value of a component determined after deconvolving a series of constituent charge states using the ReSpect algorithm. | Y | Y | Y | |||
Intensity | Displays the sum of the intensities of the peaks for a charge state. | Y | Y | Y | |||
Sum Intensity | Displays the sum of the intensities of the charge states (isotopic clusters) comprising a component. At the component level, sum intensities are measurements of the relative abundance of components. At the charge state level, sum intensities are the actual intensities of peaks in the m/z spectra. *Displays the sum of all the successive component peaks identified by successive Sliding Windows. | Y | Y | Y* | |||
Relative Abundance | Displays the relative abundance of the peaks in the sample that are above the Rel. Abundance Threshold (%) parameter specified in the processing method. The application assigns the most abundant peak (the largest value in the Sum Intensity (for Xtract) or Intensity (for ReSpect) column) in a deconvoluted spectrum a relative abundance of 100 percent. The number in the Relative Abundance column represents the Sum Intensity (for Xtract) or Intensity (for ReSpect) value for a particular peak divided by the largest value in the Sum Intensity or Intensity column, multiplied by 100. *For Auto Peak Detection experiments, this value is based on each peak. | Y | Y* | Y | Y | Y* | Y |
Fractional Abundance | Displays the fractional abundance of a component peak, which is the abundance for that peak relative to the total abundance of all peaks in the spectrum, expressed as a percentage. The sum of all fractional abundances of all peaks in a deconvoluted spectrum is 100 percent. *For Auto Peak Detection experiments, this value is based on each peak. | Y | Y* | Y | Y | Y* | Y |
Score | Displays the quality score of a deconvolved component. | Y | Y | Y | |||
Number of Charge States | Displays the number of detected charge states (isotopic clusters) for a given deconvolved mass. This is the same number as the number of rows at the charge state level, below the component level. | Y | Y | Y | Y | Y | Y |
Charge State Distribution | Displays the range of charge states detected for the component, from the lowest to the highest charge state. | Y | Y | Y | Y | Y | Y |
Average Charge | Displays the average of the charge numbers in the Charge State column. | Y | Y | ||||
Number of Detected Intervals | Displays the number of sliding windows within the specified tolerances where the application found the specified component. | Y | Y | ||||
Mass Std Dev | Displays the standard deviation (in Da) of the Delta Mass values for all the charge states of a component. | Y | Y | ||||
PPM Std Dev | Displays the standard deviation (in ppm) of the Delta Mass values for all the charge states of a component. | Y | Y | ||||
Delta Mass | Displays the difference between the mass of the component and the mass of the highest-intensity component. | Y | Y | Y | Y | Y | Y |
Scan Range | Displays the scan range of the Sliding Windows deconvolution for a component. | Y | Y | ||||
Start Time (min) | Displays the start of the retention time (RT) range (in minutes) of the averaged source spectrum for the given component. *For Sliding Windows experiments, displays the start of the RT range that the Sliding Windows deconvolution covered. Note: For mixed MS and MS/MS data, the start time of the range might not necessarily be the first full MS scan that was used to generate that component. | Y | Y | Y* | Y | Y | Y* |
Stop Time (min) | Displays the end of the retention time (RT) range (in minutes) of the averaged source spectrum for the given component. *For Sliding Windows experiments, displays the end of the RT range that the Sliding Windows deconvolution covered. Note: For mixed MS and MS/MS data, the end time of the range might not necessarily be the first full MS scan that was used to generate that component. | Y | Y | Y* | Y | Y | Y* |
Apex RT | Displays the retention time (RT) for the chromatographic peak when a component has a calculated XIC. Visible only when the Calculate XIC checkbox is selected in the processing method. For Sliding Windows experiments, displays the RT for the chromatographic peak from the abundance trace. | Y | Y | Y* | Y | Y | Y* |
Charge state level | |||||||
Row number (bolded) | The number assigned to each visible charge state row in the table. This sequential numbering does not change when you sort or filter the table. | Y | Y | Y | Y | Y | Y |
Level | Indicates that the row is displaying charge state information (lower level). | Y | Y | Y | Y | Y | Y |
Charge State | Displays the specific charge state for a selected component. Charge state refers to the imbalance between the number of protons and the number of electrons in a molecular species (or an ion adduct). | Y | Y | Y | Y | Y | Y |
Calculated Monoisotopic m/z | Displays the mass-to-charge ratio of the calculated monoisotopic mass for a specific charge state. | Y | Y | ||||
Monoisotopic Mass of Charge State | Displays the detected monoisotopic mass for a specific charge state. | Y | Y | ||||
Most Abundant m/z | Displays the mass-to-charge ratio of the most abundant isotope (or the height of the tallest peak in the isotopic distribution). | Y | Y | ||||
Charge Normalized Intensity | Displays the ratio of the intensity of a specific charge state divided by the highest intensity charge state for a component. | Y | Y | ||||
Fit % | Displays the quality of the match between a measured isotope pattern and an averagine distribution of the same mass. This column displays a value between 0 and 100 percent. A fit factor of 100% means that the observed peaks in the measured isotope profile are identical to those in a theoretical averagine distribution and that any missing peaks fall below a restrictive threshold. | Y | Y | ||||
Fit % Left | Displays the quality of the match between a measured isotope pattern and an averagine distribution one Da smaller than the calculated monoisotopic mass. | Y | Y | ||||
Fit % Right | Displays the quality of the match between a measured isotope pattern and an averagine distribution one Da larger than the calculated monoisotopic mass. | Y | Y | ||||
Intensity | Displays the intensity of a specific charge state (isotopic cluster). | Y | Y | Y | Y | ||
MZ Centroid | Displays the centroid position of the charge state (isotopic cluster). | Y | Y | ||||
Calculated Mass | Displays the mass associated with the MZ Centroid parameter value. | Y | Y | ||||
Measured Average m/z | Displays the average mass-to-charge ratio of a charge state (isotopic cluster) in the source spectrum. | Y | Y | ||||
Measured Average Mass | Displays the average mass calculated from the measured mass-to-charge ratio and the charge state. This value represents the deconvolved mass for a particular charge state. | Y | Y | ||||
Delta Mass (Da) | Displays the difference between the average mass for a component and the calculated mass for a specific charge state (in Da). | Y | Y | ||||
Delta Mass (ppm) | Displays the difference between the average mass for a component and the calculated mass for a specific charge state (in ppm). | Y | Y |