Procedure
- Select the appropriate neutral loss ion checkboxes in the Neutral Losses area of the Fragments area.
NOTE
The application only calculates water neutral loss fragments if side chains contain the potential neutral loss groups of aspartic acid, glutamic acid, serine, or threonine. It only calculates ammonia neutral loss fragments if side chains contain the potential neutral loss groups of lysine, asparagine, glutamine, or arginine.
The following table lists the neutral loss ions that you can select.
Ions | Description |
|---|---|
–H2O | Neutral loss ion that has lost water (–18 Da) |
–NH3 | Neutral loss ion that has lost ammonia (–17 Da) |
–2H2O | Neutral loss ion that has two water losses (–36 Da) |
–2NH3 | Neutral loss ion that has lost two ammonia losses (–34 Da) |
–CO | Neutral loss ion that has lost (–28 Da) |
–HCOOH | Neutral loss ion that has lost (–46 Da) |
Modification Loss | Any neutral loss associated with an identified PTM |
- Select the Neutral Losses tab in the ion table.
The following figure shows the Neutral Losses page of the Peptide Spectrum Match Identification Details view.
| No. | Description | No. | Description |
|---|---|---|---|
1 | Neutral losses | 3 | Sequence of amino acids that compose the peptide |
2 | Fragment number |