Collaboration using Scaffold Software

Scientific disciplines, like proteomics, are inherently a collaborative effort. As the individual aspects of research become more complex, it will become increasingly difficult for an experiment to be carried out by an individual or even a small group. Often, the individual running the mass spectrometer, the one processing the data, and the one analyzing the results are not the same person or even at the same institution. To this end, Scaffold Software is designed with collaboration in mind.

Proteome Software provides a Windows, macOS, or Linux compatible free Viewer for each one of our programs. Simply send a saved Scaffold file to a collaborator. Once they download the Viewer they can open the file and visualize the results. For data analysis, this means that everyone involved can view the data using our intuitive User Interface, no need for one group to be viewing a Scaffold file and another to be stuck with Excel spreadsheets.

Core facilities derive great benefit from our free Viewer model as it allows them to distribute results to all of their customers using a common program and interface. This makes answering customer questions easier. Also, if your customer familiar with Scaffold is doing their first PTM-centric experiment, they will spend less time learning the Scaffold PTM interface and get right to analyzing data. Scaffold files with sensitive data can be password protected and individual views can be hidden if deemed appropriate. Customers can even apply GO and pathway annotations along with statistical tests after the file has been delivered, saving core facility time.

Excel spreadsheets are still valuable and in fact, all of our programs allow for the exporting of results in a format that can be opened by Excel. Need some advanced statistical analysis that Scaffold does not support? Export the data and send it to a colleague for processing in R.

Publication, the end goal of most studies, is also a method of collaboration and Scaffold Software aims to make it as simple as possible. As sharing data has become a major part of the process, Scaffold's mzIdentML and MGF exports play a role in the publication of proteomics data. These exports are directly compatible with PRIDE and can be exported from a Viewer by either a customer or colleague. All of the chart and graph images that you see in a Scaffold file can be exported in formats that are appropriate for a manuscript, poster or presentation. Finally, the Publish View contains experimental metadata needed to start writing the methods section of a publication.

We hope that adding these collaborative features will make science easier for both researchers and core facility staff. If you are interested in any of our programs for DDA or DIA proteomics, or small molecule analysis, request an evaluation and try Scaffold Software in your lab for free for 14 days.


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