1. MassMatrix PC Graphical User Interface (GUI) Manual
GUI Version 0.1.0? or later
Version number?
February 2017

2. MassMatrix PC GUI
Main Navigation Tab Panel

3. MassMatrix PC GUI – Go to Search Engine
Click “Database Search” tab to go to the search engine.

4. MassMatrix PC GUI – Search Submission
Step 1: Drag and drop the data files in this area that you want to search.
Note: Multiple data files can be selected.
Step 2: Specify all the search parameters and quantitation parameters (if you are doing quantitation searches) in the search form. Please refer to the help file “MassMatrix Search Form Help” in the “Help & Manual” page or the link below for the details about all the parameters.
Step 3: Click “Submit Search” button to submit the search.

5. MassMatrix PC GUI – Results
Click “Jobs & Results” tab to go to the jobs & results page. The jobs & results page lists all the search jobs & results that you have.
To view search result of a job: Double click in the table,
or click in the table to choose an entry then click
"View Search Result" button.
To reload: Click "Reload" button.
To cancel queued or ongoing search jobs, or to delete finished jobs: Click ROW LABELS to select rows in the table, then click "Cancel/Delete Job" button to cancel the jobs or remove them from the table.
Search log and status of the job
View your results in the internet browser or go to the result folder.

6. MassMatrix PC GUI – Settings
Tabs for settings
Click “MassMatrix Settings” tab to go to the MassMatrix settings page. This allows you to upload your own databases and configure the search engine, such as specifying custom modifications, enzymes, amino acids, crosslinks, iTRAQ/TMT purity correction, SILAC quantitation methods.

7. MassMatrix PC GUI – Settings: Protein Databases
Click “MassMatrix Settings” => “Protein Databases” tabs to go to protein database configuration page.
To rename a database: Double click in the table, or click in the table to choose an entry then click “Edit” button.
To delete databases: Click ROW LABELS to select rows in the table, then click "Delete" button to delete the databases.
To add protein databases: Drag and drop database files to this area, or click “Add” button.

8. MassMatrix PC GUI – Settings: Modifications
Click “MassMatrix Settings” => “Modifications” tabs to go to modification configuration page.
To add a modification: Click “Add” button.
To edit a modification: Double click in the table, or click in the table to choose an entry then click “Edit” button.
To delete modifications: Click ROW LABELS to select rows in the table, then click "Delete" button to delete the modifications.

9. MassMatrix PC GUI – Settings: Add/Edit A Modification
Specify the full name of your modification.
Specify the label of your modification. The label of the modification will be used in the result report.
Specify the chemical formula of the modification (click the link below for chemical formula syntax). Mass shift will be calculated automatically according to the chemical formula.
Specify the modification sites. Multiple sites may be specified.
Click the "Submit" button to submit the changes or click the "Cancel" button to cancel the change.

10. MassMatrix PC GUI – Settings: Enzymes
Click “MassMatrix Settings” => “Enzymes” tabs to go to enzyme configuration page.
To add an enzyme: Click “Add” button.
To edit an enzyme: Double click in the table, or click in the table to choose an entry then click “Edit” button.
To delete enzymes: Click ROW LABELS to select rows in the table, then click "Delete" button to delete the enzymes.

11. MassMatrix PC GUI – Settings:
Add/Edit An Enzyme
Specify the full name of your enzyme.
Specify the sense of the cleavages.
Choose the cleavage sites. Multiple sites can be selected.
Click the "Submit" button to submit the changes or click the "Cancel" button to cancel the change.

12. MassMatrix PC GUI – Settings: Amino Acids
Click “MassMatrix Settings” => “Amino Acids” tabs to go to amino acid configuration page.
To edit an enzyme: Double click in the table, or click in the table to choose an entry then click “Edit” button.
Note: only J, O, and U amino acid residues are editable amino acids.

13. MassMatrix PC GUI – Settings: Edit An Amino Acid Residue
Edit the full name, 3-letter name, and chemical formula of the amino acid (click the link below for chemical formula syntax).
Click the "Submit" button to submit the changes or click the "Cancel" button to cancel the change.

14. MassMatrix PC GUI – Settings: Cross Links
Click “MassMatrix Settings” => “Cross Links” tabs to go to cross link configuration page.
To add a cross link: Click “Add” button.
To edit a cross link: Double click in the table, or click in the table to choose an entry then click “Edit” button.
To delete cross links: Click ROW LABELS to select rows in the table, then click "Delete" button to delete the cross links.

15. MassMatrix PC GUI – Settings:
Add/Edit A Cross Link
Specify the name of the cross link.
Select the two link sites.
Specify the chemical formula of the cross linker (click the link below for chemical formula syntax). This will be used to calculate the mass shift to the peptides caused by the cross link.
Click the "Submit" button to submit the changes or click the "Cancel" button to cancel the change.

16. MassMatrix PC GUI – Configuration
Click “Configuration” tab to go to the configuration page. The configuration page allows to request and add a license, change the maximum number of search jobs running simultaneously on your computer, and view search and error logs.

17. MassMatrix PC GUI – Help & Manual
Replace contact info on GUI with into on last slide
Click “Help & Manual” tab to go to the help page. The help page has all the online help files. Click on the buttons to go to those online help files. Online help files are import resources about how to use and configure the MassMatrix suite and how to interpret your results.

18. Contacts
For more information about the MassMatrix search engine and results, please contact us:
MassMatrix, a dba of Creatively Alive, LLC
Columbus, Ohio United States