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.

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.

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.

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.

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.

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.