What is PEAKS
PEAKS is a complete software package for proteomics mass spectrometry data analysis. Starting from the raw mass spectrometry data, PEAKS takes care of every step of data conversion. PEAKS effectively performs peptide and protein identification, PTM and mutation characterization, as well as results validation, visualization and reporting.
Different from many software tools that rely solely on database search, PEAKS provides a complete analysis of your data by employing multiple analytical algorithms. PEAKS is able to identify every peptide in the data, whether it is in a database or not, even if it is modified or mutated. Equipped with superior algorithms and scoring functions, PEAKS maximizes the accuracy and sensitivity of your data analysis. The key benefits of PEAKS reviews some of these distinct features in more details.
“ Our research has always fought a "battle" against traditional MS/MS protein identification programs in that they were not flexible enough for our application. We look for endogenous peptides that are not cleaved at basic residues (necessarily) and they have multiple PTMs including amidation, acetylation, pyroglutamylation, etc. We don't do tryptic digests, we let our cells do the digesting so to speak, and therefore, other algorithms didn't allow us to search with the flexibility that PEAKS allows. Now we can identify our endogenous peptides with ease.”
The user-friendly graphical interface allows even a beginner of PEAKS to easily analyze the data, while the built-in result validation guards the result quality and provides additional confidence. Users have access to several different views of their results that can allow them to view their results on a protein, peptide, and even amino acid level. The new protein coverage view in PEAKS 6 allows users to find a peptide of interest and see which algorithm it was identified by as well as pull up the associated spectra.