Exporting and Sharing Results Using Scaffold Q+

The following article contains a list of frequently asked question relating to collaboration using Scaffold Q+. 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 

What is the ScaffoldQuantML Report?
This option exports SQML and MZID files for loading quantitative data in Scaffold PTM. See the Scaffold PTM documentation for more details on this option.

What is a protXML file?
A protXML is an open file format for storage of protein identifications inferred from MS/MS data and their subsequent protein-level analysis. There are several different methods to infer protein identifications from database search results; one of them is ProteinProphet. For more information about the structure of protXML files please check the following publication: Molecular Systems Biology 1:2005.0017

What do the Export>To Excel options export?

  • Publication Report: lists the data analysis information that is required for publication in a number of the proteomics journals. This report is a copy of the information on the Quantitative Publish view.
  • Samples Report: echoes Scaffold's Samples view and contains the following: Protein Identification Probability, Percentage of Total Spectra, Number of Identified Spectra, Number Unique peptides and Number of Unique Spectra.
  • Samples Report With Isoforms: reports the same values as the Samples Report, but includes Protein Family grouping expansions.
  • Quantitative Peptide Report: lists and details all the peptides passing the current filter settings as well as quantitative values. 
  • Quantitative Spectrum Report: lists and details all the spectra passing the current filter settings along with quantitative values.
  • Raw Data Report: creates a tab delimited file containing the raw data values pre-normalization as well as the normalized values.
  • Statistical Analysis Report: this report is created only when the user applies a statistical test. For each protein in the Quantitative Samples list, the report provides the summary for the selected statistical test and the assumption testing results. The data used to compute the test statistics is also included listed by category.
  • Protein Accession Number Report: lists all the proteins passing the current filter settings. Its purpose is to provide a easy way to look up the protein description for each accession number.

Preparing and Publishing Results

What information is contained in the Publish view?
The Publish view is a tool to help scientists share their results. It contains pertinent information about your analysis and gives example paragraphs that demonstrate ways of reporting Scaffold Q+ results. From here, you can also export supplemental reports that contain potentially important protein and peptide information.

How can I share an analysis with colleagues?
The best way to share a Scaffold Q+ analysis with your colleagues is to save as an SF3 file, and send the file to them. Simply have your colleagues download the free Scaffold Q+ viewer here and they will be able to view your analysis. The free viewer allows your colleagues to see everything that you see, and gives them a good understanding of your analysis parameters.

Another way to share your results is to export them to a spreadsheet. To export your results to a spreadsheet use Scaffold's Export menu and choose the most useful export. Exporting Scaffold results to a spreadsheet is a good way to share results, but spreadsheets are slightly more difficult to use than Scaffolds user interface, because the large amount of information on the spreadsheet can make it unwieldy.

Can I control the data I share with colleagues?
You can password protect your Scaffold settings in a SF3 file. To password protect your analysis use the Edit>Preferences>Password pathway. You can set your password to whatever you want and choose OK. Check the items you wish to password protect and click Apply. Your settings are now password protected. This can only be done in Scaffold, not from within the Scaffold Q+ module.

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