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Swiss Mass Abacus is a calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations. TOF-DS Proprietary: Software by Markes International used with BenchTOF time-of-flight mass spectrometers. TopFD Open source
Mascot is a software search engine that uses mass spectrometry data to identify proteins from peptide sequence databases. [1] [2] Mascot is widely used by research facilities around the world.
In computational biology, protein pK a calculations are used to estimate the pK a values of amino acids as they exist within proteins.These calculations complement the pK a values reported for amino acids in their free state, and are used frequently within the fields of molecular modeling, structural bioinformatics, and computational biology.
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
Peptide-Antigen Finder - Peptide Finder for Antibodies and Drugs Peptide Library Design Tools - Can screen highly active compounds such as antigenic peptides, receptor ligands, antimicrobial compounds, and enzyme inhibitors. Oligo Design and Analysis Tools - Oligo calculator and analyzer, antisense design, dilution, resuspension.
The possible peptide that has the most similar spectrum will have the highest chance to be the right sequence. However, the number of possible peptides may be large. For example, a precursor peptide with a molecular weight of 774 has 21,909,046 possible peptides. Even though it is done in the computer, it takes a long time. [17] [18]
PeptideAtlas is a proteomics data resource that gathers tandem mass spectrometry datasets from around the world, reprocesses them with the Trans-Proteomic Pipeline, and makes the combined result freely available to the community.
In this updated version it is possible to determine insulin sensitivity and β-cell function from paired fasting plasma glucose and radioimmunoassay insulin, specific insulin, or C-peptide concentrations. The authors recommend the computer software be used wherever possible. [4] [5]