Exporting and Sharing Scaffold Results

The following article contains a list of frequently asked question relating to Scaffold's views and displays. 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 exports are available using Scaffold's Export menu?
The Export menu allows the user to view a drop-down list of options for exporting results.
The export options are as follows: Subset Database... | Spectra... | protXML... | mzIdentML... | Scaffold Batch... | Scaffold Batch Archive... | To Excel... |

Subset Database...: Produces a FASTA subset of the sequence database, containing only proteins identified in the biological sample. Select Filter Parameters to determine which identified proteins are included. (More restrictive parameters result in fewer proteins in the exported database.) The exported subset can facilitate a more thorough search for protein modifications with the original search engine.

Spectra...: Produces spectral files saved in different formats. The following provides information regarding the Spectra export parameters:

Set Export Parameters

All Spectra: This option will export all the spectra that were loaded in Scaffold to begin with.

Unmatched spectra: This option will export only the spectra that do not meet the filters criteria set by the user, to allow further targeted searches on these types of spectra.

Unmatched Spectra Criteria: Allows users to set the Minimum Protein Probability, Minimum Number of Peptides and Minimum Peptide Probability

High quality spectra: This option will select only those spectra that identify peptides with probabilities higher than 50% or if the peptide probability happens to be lower, the spectra has to be assigned to proteins that have a probability of at least 95%

File Type: Allows users to select the file type of spectral files from the following options: Concatenated DTAs | Individual DTAs | Mascot MFGs | Micromass PKLs | SEQUEST MS2s |

protXML...: Produces 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

mzIdentML...: Produces a standard data exchange file which the HUPO Proteomics Standards Initiative (Protemics Informatics Standards group) has specified for the analysis of proteomics data. Scaffold PTM and Scaffold perSPECtives use these exported *.mzid files to load data.

Scaffold Batch...: Produces an XML driver file (SCAFML) from which ScaffoldBatch takes its commands rather than the from the graphical user interface. This option on Scaffold's Export menu creates this driver file using the files and the options currently chosen in Scaffold. This file can be sent to a computer which has ScaffoldBatch to be run at a later time. These SCAFML XML files are often used as an interface between Scaffold and another program. For example, an add-on to Matrix Science's Mascot Demon is available from Proteome Software that uses a SCAFML to run Scaffold as soon as Mascot finishes analyzing a file. A number of labs have also created custom software that uses SCAFML files as an interface between a LIMS system and Scaffold.

ScaffoldBatch Archive...: Produces the SCAFML XML driver file along with all the files that it references into one package. This package contains the input files and the FASTA database. This allows you to send a single package of all these files to a remote computer and run ScaffoldBatch there.

To run ScaffoldBatch on this package,

  1. send this package to a computer which has ScaffoldBatch
  2. unzip and untar the package
  3. run ScaffoldBatch.

The unzip and untar step can easily be done on a Linux computer since these are standard Linux commands. On a Windows computer you may need a file compression utility to unpack this package. 

The Export menu also provides the users with numerous Excel reports the contents of which are enumerated below:

  • Publication Report: saves the information available in the "Publish" view
  • Protein Report: saves the information about the proteins identified by Scaffold
  • Peptide Report: saves information about the peptides identified by Scaffold
  • Spectrum Report: saves information about the spectra loaded into Scaffold
  • Current View: saves the information you are currently viewing in Scaffold
  • Complete: saves all of the statistical information about your Scaffold analysis to a folder with multiple Excel files. This will save information on the statistics and proteins identified in your analysis.
  • Samples Report: saves information about the current view on the samples page to an Excel file. It is important to note that this function only saves information on the current samples view. If you want to save information about the number of identified spectra, then make sure that the "Display Options" are set to "Number of Identified Spectra" and export.

Preparing and Publishing Results

What is the Publish view?
The Publish view is a tool to help scientists share their results. It contains pertinent information about your analysis and gives some example paragraphs that demonstrate ways of reporting Scaffold results.

Why are some fields highlighted red in the Publish view?
The red fields are entries that require additional information. You can insert comments into these fields by double-clicking then writing in the space. The example paragraphs will be updated as you add comments to the red fields.

How do I know what parameters were used?
Scaffold's Publish view contains information about the search engine and Scaffold parameters. If you cannot view the contents of a cell (because the entry is too long), right click and choose "copy selected cell". Then go to a spreadsheet and paste the contents of that cell into the spreadsheet and you will be able to see the entire cell's contents. Additionally the center slider bar can be dragged to the right to expand the cells.  

How can I share an analysis with colleagues?
The best way to share a Scaffold analysis with your colleagues is to save it as an .sf3 file, and send it to them. Simply have your colleagues download a free viewer 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 an Excel spreadsheet using Scaffold's Export menu. Simply pick which export you would like from the dropdown list. 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 go to Edit>Preferences>Password. 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.

How can I upload my Proteomics results for MCP publications?
Because Tranche is no longer supported, Scaffold has the ability to export mzIdentML files to submit your data to PRIDE.

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