The following table describes the information in the Intact Fragmentation Results table on the Process and Review page.
Column | Description |
|---|---|
Peak level | |
+/– (button) | Select to show or hide the lower level of proteoform information related to the currently selected peak row. |
Row number (bolded) | The number assigned to each visible peak row in the table. This sequential numbering does not change when you sort or filter the table. |
Level | Indicates that the row is displaying peak information (top level). |
Protein Name | Displays the protein sequence specified for each peak in the processing method. |
Peak # | Displays a number for each peak. This number matches the peak number specified in the processing method. |
Start Time (min) | Displays the retention time (RT) start time (in minutes) specified for each peak in the processing method. |
Stop Time (min) | Displays the retention time (RT) stop time (in minutes) specified for each peak in the processing method. |
Number of Proteoforms | Displays the total number of processed proteoforms for the experiment. |
Proteoform level For a single raw data file or batch experiment, the results are from processing one raw data file. For a multiconsensus experiment with multiple loaded raw data files, the results are from processing the combined files. | |
+/– (button) | Select to show or hide the lower level of raw data file-specific information related to the currently selected component row. |
Row number (bolded) | The number assigned to each visible peak row in the table. This sequential numbering does not change when you sort or filter the table. |
Level | Indicates that the row is displaying proteoform information (lower level). |
Identification | Identifies key characteristics of an identified proteoform and any applied modifications. Displays the name of the proteoform, followed by the modification site and modification type (in parentheses) that were identified for an individual proteoform, if available. Commas separate multiple modifications and their sites in the identification. For example, "Rituximab_C4(Oxidation), N35(Deamidation)" indicates the following:
If there are no detected modifications to the proteoform, the site and modification portions are empty. |
Modifications | Displays the type(s) of modification(s) associated with an identified proteoform. The modifications listed in this column are the same as those listed in the Identification column. If there is no modification, this column is empty. |
Site | Displays the site(s) of the modification(s) associated with an identified proteoform. The modification sites listed in this column are the same as those listed in the Identification column. If there is no modification, this column is empty. |
Ions Matched | Displays ratio of the total number of identified ions divided by the total number of ions submitted for searching for each proteoform. For example, "80/400" indicates:
|
Fragmentation Explained (%)* | Displays the percentage of identified ions divided by the total number of ions submitted for searching. For example, if the Ions Matched column displays "80/400", then the value in this cell is 100×(80/400) = 20%. *For multiconsensus results from multiple loaded raw data files, this value appears at the raw data file level, not at the proteoform level. |
Residue Cleavages (%) | Displays a percentage representing the number of identified residue cleavage sites divided by the total number of residue cleavage sites. |
−Log P-Score* | Displays the −log10(P-score) value, which is the probability of obtaining at least as good of a match between the observed fragment list and a sequence as by chance. The P-score is a measure of confidence in the validity of a match. A low P-score means that it is unlikely that random chance caused the association. When the deconvolution algorithm returns no results and no fragment ion is identified, this column displays "Infinity" since the P-score is 0. *For multiconsensus results from multiple loaded raw data files, this value appears at the raw data file level, not at the proteoform level. |
PCS* | Displays the protein characterization score (PCS) that uses shuffled protein sequences to create a decoy distribution to compare against the actual results. The more the actual results differ from the decoy distribution, the higher the PCS value. *For multiconsensus results from multiple loaded raw data files, this value appears at the raw data file level, not at the proteoform level. |
Activation Type* | Displays the fragmentation type specified for each peak in the processing method. *For multiconsensus results from multiple loaded raw data files, this value appears at the raw data file level, not at the proteoform level. |
Theoretical Monoisotopic Mass | Displays the theoretical monoisotopic mass for a proteoform based on its protein sequence. If the proteoform is not identified, this column is empty. |
Raw data file level The data listed for this level are the results from processing the individual raw data files loaded for the experiment. The columns at the raw data file level display the same information as the corresponding columns at the proteoform level, except the information is from one raw data file instead of from the combined results in the case of a multiconsensus experiment. The additional columns included at the raw data file level are described below. | |
Level | Indicates that the row is displaying raw data file information (lowest level). |
Raw File Name | Displays the name of the raw data file. |
Condition | Displays the condition assigned to the raw data file on the Top Down Analysis page. If no condition is assigned to the raw data file, this column is empty. |