Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Sharing result reports

Mascot search reports are generated on the fly by the Mascot server. This provides great flexibility, allowing a report to be re-formatted easily. The reports also make extensive use of HTML hyperlinks, allowing you to ‘drill down’ to other views of the data, such as the Protein View or the Peptide View.

However, these same features make it difficult to share the result reports with colleagues or customers who do not have on-line access to the Mascot server. This help page discusses some of the options that are available if you want to share result reports with a third party.

Saving a report from the web browser as HTML

All web browsers allow you to save the current HTML document to a file. This is a useful option for a peptide mass fingerprint (PMF) search or a small MS/MS search (<1000 proteins).

The key step is to choose a report format where all the relevant sections have been expanded. Many pages include links and buttons that expand content on demand. Unless you expand every item manually, the expanded content will not be captured in the saved file.

Saving PMF report as HTML

Example PMF report shipped with Mascot: Peptide Mass Fingerprint Example

  1. Open the results report in Mozilla Firefox, Google Chrome or Microsoft Edge.
  2. Mascot displays PMF results as Protein Summary or Concise Summary. Switch to the Concise Summary.
  3. All the expandable sections are expanded by default.
  4. Save it as a complete web page. For example, in Firefox, right click on the page, choose Save Page As and set “Web Page, complete” as the save type.

This produces a file Protein Summary Report (Peptide Mass Fingerprint Example).htm and a directory Concise Summary Report (Peptide Mass Fingerprint Example)_files, which contains any images used by the HTML file.

Limitations: Only the protein and peptide listings in the summary report are saved. This method does not save the Protein View pages. Click to open the Protein View for each protein hit, then save each one as an HTML file.

Saving MS/MS report as HTML

Example MS/MS report shipped with Mascot: Yeast example (CPTAC study 6)

  1. Open the results report in Mozilla Firefox, Google Chrome or Microsoft Edge.
  2. Mascot Server 3.0 and later default to the Protein Family Summary report.
    *Older versions may display the report as Select Summary. Switch from Select Summary (master_results.pl) to Protein Family Summary (master_results_2.pl) by editing the URL.
  3. Under the Proteins tab, select to display all protein families on a single page.
  4. Under the Proteins tab, click Expand All to display all peptide matches.
  5. Save it as a complete web page. For example, in Firefox, right click on the page, choose Save Page As and set “Web Page, complete” as the save type.

This produces a file ___data_F981142_msr_.htm and a directory ___data_F981142_msr__files, which contains any images and Javascript files used by the HTML file.

Limitations: Only the protein and peptide listings in the summary report are saved. This method does not save Protein View and Peptide View pages or the machine learning quality report. The links to expand duplicate peptide matches or lower scoring matches to a query won’t work.

Saving a report from the web browser as a CSV table

Report Builder, included in the Protein Family Summary report, makes it very easy to create a list of confidently identified proteins.

Printing to a PDF document

Printing a Mascot HTML report as a PDF document is possible. We don’t recommend it for searches containing more than a few proteins, because the number of pages makes the file difficult to browse.

Follow the instructions above to create the HTML report, then instead of saving as HTML, choose to print as PDF. The best print settings depend on your web browser (such as: portrait/landscape, scaling, printing embedded graphics).

Mascot Security

Mascot security allows you to provide limited or ‘read only’ access to your Mascot Server. This can be the ideal solution for a core service facility. Customers can access the search log, but only see their own searches listed. They can view all the standard reports and exports for their searches, but not run new searches or access search results belonging to users in other groups. For more information:

Mascot Distiller

Mascot Distiller can be used as a free project viewer. First, use Distiller to perform peak picking, submit searches, import the results, and optionally perform quantitation. Then, send the raw file and project file to your colleague. They can download Distiller for free and study every aspect of the search and quantitation results without needing online access to the Mascot Server. All stages of Distiller processing can be automated using Mascot Daemon, so this is ideal for large projects, with many raw files.

Exporting in a standard file format

Mascot search results can be exported in standard file formats, mzIdentML and mzTab. Free, open source tools like PRIDE Inspector can be used to open and visualise results in these formats.