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Fus protein scaffold and client3/1/2023 This view displays this information at the protein level along with quantitative bar charts, volcano plot, Venn diagram, and GO term charts.įigure 4. The Quantify View: Scaffold displays quantitative values based on spectrum counting, or precursor intensity values.The Similarity View shows how proteins are assembled from the identified peptides The Similarity View: Here users can see which peptides are assigned to which proteins, where there are shared peptides and which proteins are excluded from the Scaffold experiment due to the principle of parsimony.įigure 3.The Proteins View: Contains information related to the individual selected protein including the peptides identified (with search engine scores), sequence coverage and spectrum visualizations.The Samples View complete with GO terms, fold change calculation and T-test added All of this is given at the experiment level (for all files loaded into Scaffold).įigure 3. The Display Options dropdown menu allows users to toggle between displaying protein identification probability, various quant types, and percent coverage. Peptide and protein level thresholding and filtering can also be done here. The Samples View: This protein-centric display gives information about proteins identified, GO terms, and quantitative values.BioSamples may be organized into categories through the Scaffold Viewer, however. A Scaffold viewer does not allow users to add additional MS Sample files to a Scaffold file nor can MS Sample files be reorganized into different BioSamples. The Load Data View: Displays the organization of MS Samples into BioSamples along with information relating to search engine parameters, such as fragment and peptide mass tolerance and the searched FASTA database.Scaffold is divided into 7 distinct views: Scaffold focuses predominantly on displaying protein and peptide identifications and quantitative information along with additional metadata such as gene ontology terms via the NCBI or UniProt (see Applying GO Terms). If you received a finished Scaffold file from a core facility these steps will already have been completed. The following document goes into detail about the steps involved in creating a Scaffold file. These open an in-program version of the User Guide which can be queried to get quick answers. Additionally, users will notice blue question mark buttons in various locations around the program. For answers to detailed questions the Scaffold User Guide is available from the Help menu. This document provides a high-level explanation of features. Close and reopen Scaffold to save the settings. Before viewing data for the first time in Scaffold open the Edit > Preferences > Memory tab and allocate about 80% of your systems total RAM (in MB) to Scaffold. Scaffold users will see an increase in performance when the program has access to more RAM. Selecting "Always Viewer" will ensure you are not prompted for a key each time you run Scaffold As this guide is primarily intended for users who will run Scaffold in viewer mode only, when prompted for a key by Scaffold, tell the program to continue permanently in viewer mode.įigure 2. Once the installer has completed, you can run Scaffold for the first time. ![]() In most cases the default settings are recommended Click Next > to work through the installer. The first page of the Scaffold installer. Once the file has downloaded double click to run the installer.įigure 1. Installers for Scaffold viewers can be found here, select the proper program, operating system and system architecture (32-bit vs 64-bit) and choose Download Now. The following documentation provides a quick-start guide for first time Scaffold Viewer users and provides a short introduction to the data available in the Scaffold file you have received. Often researchers receive their processed data in the form of a Scaffold SF3 file from a core facility or collaborator.
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