The following table describes the parameters in the Charge State Results for the "Find All Masses in the Run" task table on the Process and Review page for oligonucleotide analysis experiments.
Column | Description |
|---|---|
+/– (button) | Shows/hides raw data file-specific (lower-level) information related to the currently selected component row. |
Row number (bolded) | Displays the row number of the table. This number corresponds to the number of currently visible rows in the table; it is not assigned to a specific component. If you sort/filter results in the table, the row numbers will remain unchanged while the filtered/sorted components that populate the rows change |
(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:
|
Identification | Identifies key characteristics of an identified oligonucleotide component and any applied modifications. For example, 1:G1-T17 = 5225.9300m(T2+Thiamine loss) indicates the following:
If a component is not identified, this column is empty (blank). If a component is nonunique (found elsewhere within the full oligonucleotide sequence), the descriptor “[nonunique]” follows the listed modifications. In some situations, a combination of low resolution, large component mass, or high component charge state may prevent the application from resolving the monoisotopic mass (m) of a component. In this situation, the average mass (a) will be used in the Identification column notation. For example, 1128.27a is the average mass for a given component. Due to low resolution, the application cannot calculate the monoisotopic mass (m) for this component and displays a value of 0 in the Mono Mass Exp. column of the table. Therefore, in the Identification column, the average mass 1128.27a is used in the notation, rather than the monoisotopic mass (m). |
Charge St. | Displays the charge state of a 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). |
M/Z | Displays the mass-to-charge ratio of the theoretical monoisotopic mass of a component. |
RT | Displays the peak retention time (RT) for a component. If the experiment involves multiple raw data files, the retention time displayed in this column is the retention time associated with the first raw data file. Additionally, at the raw data file-specific information level, RT Start and RT End columns display the start and end time points of the retention time range for each individual raw data file. |
MS Area | For an experiment with a single raw data file, displays the MS area for a component for a particular condition. For an experiment with multiple raw data files, displays the average MS area for a component for a particular condition, considering all of the individual raw data files used in an experiment. |
Best ASR | Displays the best average structural resolution (ASR) value available for an identified component, considering all of the individual raw data files used in the experiment. The value displayed in this column is the best ASR value (value closest to 1.0) out of all the raw data files for the component. ASR = (Number of Nucleotides)/(Number of Bonds Found + 1) Each raw data file used in the experiment has its own associated ASR which can be viewed by expanding the selected component row to view raw data file-specific information. The Best ASR value is also displayed on the Fragment Coverage Map of the Mapping page. |
ID Type | Indicates the type of MS data the application used to identify a component.
If a component is not identified, this column is empty (blank). MS2 data provides more confidence than full-scan data in identifying a component. When the experiment involves a single raw data file, this column displays the same ID Type at both the component level and raw data file-specific level. When the experiment involves multiple raw data files, the ID Type used for each individual file can be viewed by expanding the selected component row to view raw data file-specific information. |
∆ ppm | Displays the mass difference between the theoretical monoisotopic mass (Theor. Mass) of the component and the experimental monoisotopic mass (Mono Mass Exp.) of an identified component. ∆ ppm = [(Mono Mass Exp. – Theor. Mass) ÷ Theor. Mass] × 106 If a component is not identified, this column is empty (blank). If the application cannot confidently determine the Mono Mass Exp. value for a component, it will use the Avg Mass Exp. to calculate ∆ ppm. |
Mono Mass Exp. | Displays the experimental monoisotopic mass for a component. This mass is based on the exact mass of the most abundant isotope of each element in a molecule. If the application cannot confidently determine the Mono Mass Exp. of a component, this column displays a value of “0”. |
Theor. Mass | Displays the theoretical monoisotopic mass for an identified component. If a component is not identified, this column is empty (blank). |
Avg. Mass Exp. | Displays the experimental average mass for a component. This mass is based on the average atomic weight of each element in a molecule. |
Conf. Score | Indicates how closely the predicted and experimental MS spectra match for an identified component using a percentage scale (between 0 and 100%).
If a component is not identified, this column is empty (blank). |