##### Peaks

##### Masses & intensities

##### Ion types

a | a-H2O | a-NH3
b | b-H2O | b-NH3
c | c-H2O | c-NH3
x | x-H2O | x-NH3
y | y-H2O | y-NH3
z | z-H2O | z-NH3
z° | z°-H2O | z°-NH3

##### Fixed PTMs

##### Protein sequence

###### Precursor mass:

###### Protein molecular mass: 0

###### Mass Error: 0

|  | ###### Da

All peaks Matched peaks Not matched peaks |  |  |  |

Scan | Peak | Mono mass | Mono m/z | Intensity | Charge | Theoretical mass | Ion | Pos | Mass error | PPM error
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---

#### Theoretical fragment masses

#### Add a fixed PTM

To add a fixed PTM, select "C:57.0271464" or "C:58.005479" and click the "+" button.

#### Add a custom PTM

To add a custom PTM, enter an amino residue and mass. Click the "+" button to apply.

Amino acid: Mass: Ptm name:

## Help

#### Peaks

The text area contains a list of peaks, each of which is represented by an m/z value and an intensity separated by a space. The user can copy, paste, and edit the list as text.

#### Masses and intensities

The text area contains a list of deconvoluted masses, each of which is represented a monoisotopic mass, an intensity, and a charge state separated by spaces. The user can copy, paste, and edit the list as text. If the intensity is unknown, a default value 1 can be used. For example, the user can add a monoisotopic mass 10000 Da with charge state 10 by inserting a line "10000 1 10" into the text.

#### Fixed PTMs

To add a fixed PTM, select "C:57.0271464" or "C:58.005479" and click the "+" button.

#### Protein sequence

The text area contains a protein sequence, which the user can edit as text. A mass shift or modification on the protein is represented by a number enclosed by brackets. For example, the user can insert "[79.9663]" into a sequence 'MPRSLKKGPF' to obtained a modified protein "MPRS[79.9663]LKKGPF", which has a phosphorylation site on the 4th amino acid.

After the user click the "Submit" button, an annotated protein sequence will be shown. Alternatively, the user can click the amino acids in the annotated protein sequence to add mass shifts.

## Error!

#### Invalid amino acid in the protein sequence.

### Help

- Drag: Press the left mouse button and drag.
- Zoom in/out of the m/z value: Place the mouse cursor below the x-axis and use the mouse wheel to zoom in or out.
- Zoom in/out of the intensity: Place the mouse cursor above the x-axis and use the mouse wheel to zoom in or out.

##### Applied variable ptms

##### Total list of variable ptms

Mass shift value: