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Free COMPASS Sandbox

A 'sandbox' version of COMPASS is available online.  While it is not the full, licensed version of the software, potential users can:

  • Test if COMPASS' computational tools would facilitate discovery in their research

  • Explore several projects and workbooks built to analyze real, published data

  • View how projects are laid out and experiment with COMPASS' interactive visualization tools 


The information below is designed to help you navigate the data and software tools.


Sandbox data. The COMPASS sandbox is currently populated with data analysis derived from publicly available data from a published research report. This data is available in two projects, both of which contain comparative analysis of proteomics data derived from the NCI60 cancer cell line panel. The first project, SandboxIntro, contains two workbooks that compare data across the NCI60 brain cancer cell lines. The second project, NCI60-FullStudy, contains workbooks that compare the data across the entire NCI-60 panel and is organized by cancer type.


COMPASS analysis has been performed using two different comparison selections. Workbooks designated with the number 1 (i.e. brain1) compares all cell lines to the first listed, such that the first cell line acts as the reference cell line for all comparative analyses. Workbooks designated with the number 2 (i.e. brain2) performs comparative analysis between adjacent cell lines in the list. Parameter settings of the workbooks are otherwise identical.


All projects have been structured to identify signals with differential expression for a subsequent targeted mass spec molecule identification campaign. The end result is a downloadable file containing coordinates of differentially expressed MS1 features targets. In short, COMPASS searches all of the data for insights related to the biological difference under study, rather than performing identification before these insights as is performed during typical LC-MS/MS workflows.


Data sources. The original data analyzed in the COMPASS sandbox is found on the PRIDE proteomics database (reference number PDX005946). Briefly, replicate extracts from individual cell lines of each cell line in the NCI60 panel were prepared for proteomics analysis before LC-MS/MS. There are 12 or more replicate samples per cell line for comparison.


Functionality. The COMPASS sandbox allows users to visualize project data. However, it does not grant access to full analytical capabilities; users cannot alter analysis parameters that would alter the project workbooks.


Further, a Molecule Dictionary file has not been uploaded into this project. Such a file contains identification information derived from MS2 analysis of specific MS1 precursor ions selected for fragmentation and mass spectrometry during the initial run. Had such a file been uploaded, COMPASS would indicate when the datapoints it selects for analysis have corresponding MS2 identity information.


Support. Please see our support pages, which contain instructions for each COMPASS software module. Also, COMPASS’ internal help bubbles are fully functional; hover over them for quick tips or click on them for more detailed information.

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