samMass

samMass is a software tool used for the analysis of mass spectrometry data. It is primarily designed for the quantification of peptides and proteins from complex biological samples. The software facilitates the identification of peptides through the comparison of experimental mass spectra with theoretical spectra generated from protein sequence databases.

Key functionalities of samMass include spectral library searching, which allows for the rapid identification of known peptides. It also supports de novo sequencing, enabling the identification of peptides without relying on a prior database. For quantitative analysis, samMass utilizes peak intensity measurements from chromatographic separation to determine the relative abundance of different peptides and, by extension, proteins. This allows researchers to compare protein expression levels across different experimental conditions.

The development of samMass is focused on providing an open-source and accessible platform for mass spectrometry data processing. It is often used in proteomics research to identify and quantify proteins in various biological contexts, such as disease biomarker discovery and understanding cellular pathways. The software aims to streamline the workflow from raw data to quantitative results, making it a valuable tool for researchers in the life sciences.