Exporting and Sharing Results from Scaffold PTM

The following article contains a list of frequently asked question relating to exporting and sharing results in Scaffold PTM. For specific questions not covered in our documentation we are available by telephone Monday through Friday from 8 AM to 5 PM PST. Our toll free number is 1-800-944-6027. Additionally support can be contacted via email at support@proteomesoftware.com.

Exporting Results

How do I use the Export SQL Table to Excel... option?
The SQL export feature gives users the ability to write custom SQL queries for the interrogation of their Scaffold PTM data which can then be saved to an excel spreadsheet. 

What if I don't know SQL? Can I get help from Proteome Software?
Of course. Our team of support staff is always willing to help. Contact us at support@proteomesoftware.com, toll-free at 800-244-6027, or by filling out a support ticket on our website.

What is the easiest way to publish and share the results I've found in Scaffold PTM?
The Scaffold suite of programs strive to make collaboration easy. The Export dropdown menu has numerous different Excel exports that allow researchers to share results. Scaffold PTM is available as a free viewer that allows collaborators to share SPTM files. Simply have colleagues download a viewer here. You can then send them a copy of the Scaffold PTM file and they can view data without the need for a license. 

The Publish view condenses experimental parameters in an easy to view and export table for submitting to a journal for publication. 

What exports are available in Scaffold PTM?
The following reports are available for export

Current View Report: The Current View report contains the information that is displayed in the current view. This report is applicable for all views.

PTM List Report: The PTM List report mimics the PTM List View. Each row in the report represents a protein in the PTM List table. The modifications displayed in the columns depend on the filter settings specified in Min Localization and Visible Modifications.

Spectrum Report: The Spectrum report details all the spectra included in the MZID files loaded in the experiment. Each row represents a spectrum matching a peptide. 

Filtered Spectrum Report: The Filtered Spectrum report details all the spectra respecting the current filter settings included in the MZID files loaded in the experiment. Each row represents a spectrum matching a peptide.

Motifs Report: Exports information included in the table appearing in the Motifs view including: Modification, Motif, Motif Score, Enzyme, Enzyme Type, Citation, Surrounding Sequence, Accession, Name, Site, Best Ascore, and Localization Probability.

PTM Counts Report: The protein report details all the proteins passing the current filter and threshold settings. This report is designed to be used as part of the supplemental information supporting a journal article. The report header rows identify the data and how it was created, which is the same information that is contained in the Publication report. Then there is a single report entry for each protein in every sample. For example, if there are 3 samples each with the same 12 proteins, there will be 36 rows in this report.

Publish View Report: The Scaffold PTM Publish View displays general and detailed information about the data loaded in the current experiment usually required for publication in a number of proteomics journals.

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