Our lab's relationship with Proteome Software has been most rewarding, and Scaffold has become an integral part of our workflow.
Arthur Moseley, Duke University School of Medicine
As a core lab, one of our missions is to educate and empower end users: Scaffold is ideal for this purpose. Scaffold presents results in an intuitive ... format and the free Scaffold viewer enables researchers to view and analyze their own data.
Allis Chien, Stanford University
[Scaffold] Elements has allowed us to perform fast identification and relative quantification of high resolution shotgun metabolomics data using fragmentation spectral libraries which has opened up a new area of research and core service in our lab. We typically lean towards targeted metabolomics by SRM since untargeted metabolomics has been a challenge because intact mass data alone is never enough for confident metabolite ID.
John Asara, Harvard Medical School
Our group produces large amounts of data that is difficult to control, catalogue and analyse. To carry out shotgun proteomics techniques we had to load the MS/MS data manually, which proved both labour intensive and error prone. We tested Scaffold and found that making comparisons between our samples was simple and fast. The most impressive part was that we didn't need to access the help function once, as the software was so intuitive.
Kelvin Cain, MRC Toxicology Unit
I can certainly see the utility of Scaffold for people who wish to compare results between different search engines. Good collection of info under the links section, by the way.
John Cottrell, Matrix Science
Scaffold has proven invaluable in helping explain experimental results to our clients from large proteomics experiments. The visualization tools make it easy for our clients to understand complex MS/MS comparative analyses. Additionally, because Scaffold is so easy to use, it has greatly decreased the amount of time that it takes our lab to prepare experiment reports. Scaffold has quickly become our standard method to visualize, validate, and share MS/MS proteomics data with our clients.
Dave Allen, Proteomic Research Services
Scaffold, along with its statistical evaluation, has given us a way to confidently filter our SEQUEST results. Definitely if you use SEQUEST we would recommend Scaffold to display and organize your results.
Andrew Guzzetta, IonSource
I have to say that [Scaffold] is the best software package I have ever used. Finally, I can get rid of all the excel spreadsheets and look at a nice overview of my data.
Manuel Mayr, University of London
I must say that I am impressed. I had a set of data to be analyzed for publication and I obtained what I wanted out of Scaffold in just a few minutes.
Michael Rosenblatt, Children's Hospital of Philadelphia
Compiling individual data sets to build a proteome database and add statistical analysis to compiled data sets required months of tedium using current free-ware and add-on utilities. We recently duplicated these efforts using Scaffold and were able to compile our database with statistical analysis within hours. Further, the data loading structure of Scaffold is dynamic, thus as we gain information on expression profiles we can update our proteome database. File export functions then allow us to rapidly annotate this proteome database with descriptors (such as structural and functional annotations) of the proteins in the database. In summary, Scaffold has become a significant asset to our research and reagent discovery program.
Karen Dobos, Colorado State University
Scaffold has been a great investment for my facility. It ... allows clients that may not have a deep understanding of mass spectrometry ... to understand our results, [and] it has contributed greatly to ongoing research in the facility. Scaffold is a bargain for what it does, and the people at Proteome Software have been very helpful and supportive of our needs.
Brett Phinney, University of California, Davis
I tried really hard to be as conservative as possible [using Scaffold], but I still could not stop Scaffold from improving my results!
Phil Wilmarth, Oregon Health Sciences University
After using Scaffold for several months now, I have to say that I have been very impressed with its ease of use, robust features, and stability. Since I am doing several replicate experiments using LC/MS/MS, I generate a substantial amount of spectra, and I especially appreciate Scaffold's ability to easily compare proteins/peptides across multiple samples. Also, since I prefer to inspect and evaluate as many MS/MS spectra as possible, Scaffold's "Spectrum" view makes it easy to quickly evaluate the quality of the spectra, while at the same time providing detailed peak labeling if more careful inspection is required.
Todd Greco, Princeton University
I can already see that Scaffold is really going to be a help in organizing and reviewing our data.
Valerie Cavett, Scripps Institute, Florida
We [use] Scaffold to assemble Sequest, Mascot, and GPM results ... of human plasma ... Scaffold has really been useful to pool search results and discriminate between false and true positives.
Pierre Gagne, CHUL Research Center
Not just the software itself is super, but also the support is great!
Bas van Breukelen, Utrecht University
Managing a core facility or shared resource department? Need help with gaps in your software pipeline? Want to try new methods like DIA proteomics? Do you need a free and easy way to share results with your customers?
Need an elegant yet easy to use solution for data processing? Not sure where to begin when starting up a new lab. Let us help take the pressure off setting up a software pipeline so you can focus on the science.
Tutorials & Videos
Check out our YouTube channel for Scaffold tutorials, from getting started to advanced use. We have videos for all our Scaffold products, as well as videos from previous conferences and special events.