Organizing Data in Scaffold perSPECtives

The following article contains a list of frequently asked question relating to organizing data in Scaffold perSPECtives. 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.

Using Attributes

What are attributes? How do I use them?
Attributes are characteristics assigned to loaded samples that provide experimental information about them. Samples can be grouped together as control or treatments and then further refined with various attributes within groups. Once attributes are defined statistical analysis can be performed to help draw meaningful conclusions about your experiment. Attributes can easily be added, removed, or changed which allows for perSPECtives flexible organizational scheme.  

How do I create new attributes?
Simply use the Add Attribute button on the right side of the Organize view, this will create a new attribute group. From there you can define different attributes with that group. For example if you were investigating different drug doses you could create a dose attribute group and then define the actual amounts within that group. Attribute groups are color coded for ease of view and these colors can be changed by the user by right-clicking and editing the already defined attribute group. Once in the Edit dialog click on the color box to change it. 

How do I organize the attributes of my experiment?
Scaffold perSPECtive's Organize view allows for the manipulation of attribute groups. Once groups are defined the can be applied to the samples loaded using by dragging attributes into the Organize view table or right-clicking individual files and adding them. 

Where do I change which attributes summarize my proteins?
Clicking on a sample in the Organize view table allows you to modify the attribute assigned assigned to it. Each column representing a different attribute can be changed independently. The same dropdown menu also allows for the addition of a new attribute within a group. Groups can be edited by right-clicking in the attributes tree table on the right.   

I've already set up my experiment with attributes in another program. How do I import them?
Please see Import Attributes file... on page 56 of the perSPECtives User's Guide for detailed instructions on the use of attributes files. 

Filters and Displays

Does perSPECtives have a protein filtering option?
Scaffold perSPECtives has numerous filtering options including stared protein, GO term, and p-value filtering. The Advanced Filter dialog allows for more complex filtering including by modification, taxonomy, protein sequence, identified peptide sequence and spectrum ID/title. Search boxes can be configured to use regular expressions using the Edit > Preferences > User Interface menu. See the next entry for information about FDR filtering.

Where do I set Target FDR or Number of Peptide thresholds for my data?
Experiments that contain decoy identifications can be thresholded using false discovery rates. Users have two options for thresholding by FDR values: FDR Thresholding (which is adjustable) or MZID-specified Thresholding (which simply uses the thresholds set in the program that wrote the MZID). The Edit > Preferences > Analysis menu allows users to set target protein and peptide FDR values as well as the minimum number of peptides needed for identifications.

How can I select which information columns to display in a table?
Users can remove columns from the Samples view. Selecting View > Show/Hide Columns will bring up a menu that displays all the columns currently visible. Uncheck the column name to hide it. Additionally the same menu can be accessed bu clicking the column button in the top right corner of the Samples view. 

How does perSPECtives cluster my data?
Scaffold perSPECtives has numerous protein clustering options detailed in chapter 9 of the User's Guide

What does Clear User Peptide Validation mean?
Users have the option to manually invalidate peptide identifications if they find them suspect. The Experiment > Clear User Peptide Validation option allows the changes to be reverted when the changes are not satisfying to the user. 

 

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