The following table describes the parameters in the Consolidated Results table (for the "Find All Masses in the Run" task) or the Charge State Results table (for all other task types) on the Process and Review page for oligonucleotide analysis experiments.
Column | Description |
|---|---|
Columns marked with an asterisk (*) are only present in the Results table when the certain features are enabled in the experiment, as detailed below. | |
+/– (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:
|
Level | Indicates the level of information displayed as either component level (top-level) or raw data file-specific (lower-level). |
No. | Displays the number assigned to a specific component in the analysis. Component number is not related to table row number (see above). If you sort/filter results in the table, the assigned component number will remain unchanged for a component, although its row number within the table may change. |
*Alias Name | Identifies a component using the custom chain root aliases applied to theoretical digestion results. Only components that match a theoretical digestion component have an alias name listed in this column. You can edit the entries in this column by placing your cursor in the Alias Name box for the currently selected component row and typing a new alias name. If you added labels to your chromatogram, you can update the labels to reflect the changes you made in the Alias Name column by selecting the Refresh Alias button at the top of the Chromatogram pane. *This column is only visible when the Customize Results checkbox is selected on the Customize Results subpage of the Parameters page. |
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). |
Oligo Sequence | Displays the oligonucleotide sequence constituting an identified component. If a component is not identified, this column is empty (blank). |
*Start # | Displays the position of the first nucleotide in a theoretical digestion component. *This column is only visible when the Customize Results checkbox is selected on the Customize Results subpage of the Parameters page. |
*End # | Displays the position of the last nucleotide in a theoretical digestion component. *This column is only visible when the Customize Results checkbox is selected on the Customize Results subpage of the Parameters page. |
Mod | Displays the type(s) of modification(s) associated with an identified component. For a description of the notation used in the "Mod" column, see Modification notation. If there is no modification, this column displays “None”. If a component is identified but does not adhere to the expected activity of the ribonuclease you selected, this column displays “Nonspecific”. The modifications listed in this column may include the variable modifications assigned during processing, nonspecific modifications, and other modifications determined automatically by the application. In this case, the application lists variable modification first, followed by static modifications in parentheses. Multiple modifications are separated by commas (“,”). |
*Seq Length | Indicates the number of nucleotides in a theoretical digestion component. *This column is only visible when the Customize Results checkbox is selected on the Customize Results subpage of the Parameters page. |
*Nonunique Seq | Indicates the number of times the nucleotide sequence appears in the theoretical digestion results. *This column is only visible when the Customize Results checkbox is selected on the Customize Results subpage of the Parameters page. |
*Isomer Group | Indicates the group to which a particular series of isomeric nucleotide sequences belongs. *This column is only visible when the Customize Results checkbox is selected on the Customize Results subpage of the Parameters page. |
*Num of Isomer Seq | Indicates the number of isomeric nucleotide sequences of a particular mass that appear in the theoretical digestion results. *This column is only visible when the Customize Results checkbox is selected on the Customize Results subpage of the Parameters page. |
*Digest Position | Indicates the relative position of a particular nucleotide at which the theoretical digestion took place; based on the specific activity of the ribonuclease assigned to the theoretical digestion and intrinsically related to the theoretical component number listed in the alias name. For example, since RNase A cleaves the internal phosphodiester bonds of cytosine (C) and uracil (U) bases, for a theoretical digestion using RNase A, a digest position of 3 indicates that the theoretical digestion component resulted from RNase A acting at the third C/U-containing nucleotide in the target oligonucleotide sequence. For alias root “Chain1”, this theoretical component would have the alias name “Chain1_3”. *This column is only visible when the Customize Results checkbox is selected on the Customize Results subpage of the Parameters page. |
Site | Displays the location of the modification(s) listed in the Identification/Mod columns or the amino acid substitution(s) listed in the Identification/Mod columns for an identified component. For example, if the Identification column 1:G1-T17 = 5225.9300m(T2+Thiamine loss) for a component, the site of the thiamine loss modification is T2. If a component is not identified, this column in empty (blank). The application lists the sites for variable modifications first, followed by the sites for static modifications in parentheses. Multiple modifications are separated by commas (“,”). If the application cannot identify the exact site of a modification or if there are multiple candidate residues within a component, the application indicates an approximate modification site with a tilde (“~”). |
∆ 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. |
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). |
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 Amino Acids)/(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. |
Integration Type | Indicates the type of integration used to calculate the MS area for 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. |
M/Z | Displays the mass-to-charge ratio of the theoretical monoisotopic mass of a component. |
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). |
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”. |
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. |
Theor. Mass | Displays the theoretical monoisotopic mass for an identified component. If a component is not identified, this column is empty (blank). |
Missed Cleavages | Displays the number of missed cleavages involved in producing an identified component; intrinsically related to the activity of the ribonuclease selected for the experiment. |
Oligo | Displays the default oligonucleotide name (derived from the FASTA file) associated with an identified component. If you included random sequences in your target oligonucleotide sequence using the Random Sequence Generator in the Oligonucleotide Sequence Editor, randomized sequences are appended with “_randomized”. If a component is not identified, this column is empty (blank). |
*Ratio (Condition/Reference Condition) | Displays the following ratio for a component: Ratio = Avg MS Area (Condition)/Avg MS Area (Reference Condition) The Results table includes a Ratio column for each condition (excluding the reference condition) specified in the experiment. If the reference condition value is 0 for a component, this column displays “999.99”. *This column is only visible when multiple raw data files and conditions are used in an experiment. |
*Max Cond. | Displays the experiment condition with the highest ratio value. See the Ratio (Condition/Reference Condition) column for more information. *This column is only visible when multiple raw data files and conditions are used in an experiment. |
*Min. Cond. | Displays the experiment condition with the lowest ratio value. See the Ratio (Condition/Reference Condition) column for more information. *This column is only visible when multiple raw data files and conditions are used in an experiment. |
*Max MS Area | Displays the highest MS area determined for a component, considering all of the conditions specified in an experiment. *This column is only visible when multiple raw data files and conditions are used in an experiment. |
MS Area or Avg. MS Area: Condition | 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. |
*%CV: Condition | Displays the coefficient of variation (CV) for a component for a particular condition. %CV = (S ÷ A) × 100, where
The Results table includes a %CV column for each condition specified in the experiment. *This column is only visible when multiple raw data files and conditions are used in an experiment. |
Comment | Editable. You can enter comments (up to 128 alphanumeric characters and/or symbols) related to the selected component in this column. Comments entered in the Results table on the Process and Review page automatically appear in the Comment column of the Components table on the Modification Summary page (and vice versa). |