Loading and Organizing PTM Data

The following article contains a list of frequently asked question relating to loading data 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.

Loading Data into Scaffold PTM

What data formats can Scaffold PTM load?
Scaffold PTM can load files in the mzIdentML format. When loading an MZID file, you MUST have the associated MGF files (which Scaffold generates automatically when it generates a MZID) in the same directory as the MZID. Scaffold PTM also support quantitative PTM expeiments when a ScaffoldQuantML or SQML is exported from Scaffold Q+. When loading an SQML file, you MUST have both the associated MZID and MGF files in the same directory as the SQML.

Can I load MZID files from several different programs (such as Mascot, PEAKS, and Scaffold) all at once?
Scaffold PTM does not support combining mzIdentML files produced by different programs. Because each program groups proteins differently and Scaffold PTM performs no grouping on its own, Scaffold PTM cannot read the protein groups. Results from different search engines may be processed through Scaffold and the resulting MZID files may be loaded together into Scaffold PTM to resolve this conflict.

Can I export quantitative data from Scaffold Q+ to load into Scaffold PTM?
Yes, in Scaffold Q+, select ScaffoldQuantML Report from the Export menu to generate an SQML file and its associated MZID. This will export quantitative PTM data for analysis in Scaffold PTM.

How do I load multiple files at once?
To create an experiment with multiple files, or to add more files onto an existing experiment, click the Add button in the Organize View, next to the Loaded Files pane. This allows you to select multiple MZID or SQML files and load them all together.

Organizing Data in Scaffold PTM

What filters from Scaffold, Q+, or Q+S does Scaffold PTM retain?
Scaffold exports certain user-defined filters that Scaffold PTM loads with the MZID or SQML data. The Minimum Protein Probability, Minimum Number of Peptides, Minimum Peptide Probability, Required Modifications, and any custom or advanced filters are all included.

How do I select which MS Samples to display and analyze?
To select your MS Samples, simply check or un-check the box next to the MS Sample details in the MS Sample Data pane in the Organize View. This will toggle whether Scaffold PTM uses that MS Sample in its analyses.

Can I change the category names and details of my samples?
Yes, Scaffold PTM allows users to change the names of biosamples, categories and MS samples.  

Where can I set program preferences for Scaffold PTM?
To set your program preferences, click on the Edit>Preferences... menu. Here users can change modification colors, motif background, memory, processors and internet settings. 

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