What is PEAKS?
PEAKS is a complete software package for proteomics mass spectrometry data analysis. Starting from the raw mass spectrometry data, PEAKS effectively performs peptide and protein identification, PTM and mutation characterization, quantification (label and label free) as well as result validation, visualization and reporting.
Different from many software tools that rely solely on database search, PEAKS provides a complete analysis of your data. 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 accuracy and sensitivity. The top benefits of PEAKS reviews some of these distinct features in more detail.
"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."
Workflows 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 allow viewing on a protein, peptide, and even amino acid level. PEAKS' protein coverage view allows users to find a peptide of interest as well as pull up the associated spectra.