Basic interactions
Fragmentation Table Browser including three parts:
- Tool Bar: gives user to modify some parameters.
- Fragmentation Table: shows peptide fragmentation ions match the spectra.
- Errors Differ Chart: shows the matches between theoretical digestion masses of the peptide and the peaks of the fragment ions for the spectra / peptide selected.
Tool Bar: There are three components on the tool bar:
Tool Bar Component | Description |
Comment Label | Shows current type of fragment ions matching. |
Choose Ion Type | Choose one type of ions pair. Such as A_X means show A and X fragment ions in the Fragmentation Table. The default choosed value is B_Y ion pair. |
Range(Da) | Choose error differ interval range from 0.1Da to 1.0Da in the Errors Differ Chart. Default value is 0.5Da |
Fragmentation Table: shows peptide fragmentation ions match the spectra. Highlight on the table cell means there exists a fragment ion matching. When you click the cell, system will give an box annotation on the Errors Differ Chart.
Ion Type | Description |
y | Y ion |
y++ | Doubly charge Y ion |
y° | Y ion with loss of water |
y°++ | Doubly charge Y ion with loss of water |
y* | Y ion with loss of ammonia |
y*++ | Doubly charge Y ion with loss of ammonia |
Errors Differ Chart: shows the matches between theoretical digestion masses of the peptide and the peaks of the fragment ions for the spectra / peptide selected. When you click one point on the chart, the according matched the Fragmentation Table cell background will become grey color.
Display Manual Annotations
If there exist fragment ion matches which stored in the PRIDE database, system will show these manual annotations to user. At this context, Tool Bar's Comment Label component will display "Show manual annotations" message, and Range(Da) component not display.
Display Auto Annotations
If there not exist fragment ion matches in the PRIDE database, system will using peptide spectrum matches (PTM) algorithms to generate some annotations automatically, and show them to user. At this context, Tool Bar's Comment Label component will display "Show auto annotations." message, and Range(Da) component will display.
Errors
If delta mass over charge of peptide great than 1 Da, which means the spectra mass is not reliable. Thus, Fragmentation Table Browser hide the Tool Bar, Fragmentation Table and the Errors Differ Chart, only show "Delta m/z is too large, no fragmentation table!" message.