TIMPeket

TIMPeket is a software tool designed to analyze and visualize data from mass spectrometry-based proteomics experiments. It is particularly useful for researchers studying protein expression and post-translational modifications. The tool is developed by the Institute for Systems Biology and is available as open-source software.

TIMPeket operates by processing raw mass spectrometry data files, such as those generated by instruments like the Thermo Fisher Scientific Orbitrap or the Waters Synapt G2. It can handle various data formats, including mzML and mzXML. The software provides a user-friendly interface that allows researchers to easily navigate and analyze their data.

One of the key features of TIMPeket is its ability to perform peptide and protein identification. It uses a database search algorithm to match observed peptide spectra to theoretical spectra, allowing researchers to identify the proteins present in their samples. TIMPeket also supports the use of decoy databases to estimate the false discovery rate, ensuring the reliability of the identification results.

In addition to identification, TIMPeket offers a range of visualization tools. Researchers can generate plots such as peptide spectra, mass error plots, and protein coverage maps to gain insights into their data. The software also supports the generation of quantitative data, allowing researchers to compare protein expression levels between different samples.

TIMPeket is compatible with various operating systems, including Windows, macOS, and Linux. It can be installed and run locally on a researcher's computer, or it can be accessed through a web-based interface. The software is regularly updated to include new features and improvements, ensuring that researchers have access to the latest tools for their proteomics research.