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In proteomics, GPM stands for "Global Proteome Machine".It is a web-based, open source user interface for analyzing and displaying protein identification data. It was originally designed by Rob Craig and Ron Beavis and first released in 2003. [1]
A fingerprint is a group of conserved motifs taken from a multiple sequence alignment - together, the motifs form a characteristic signature for the aligned protein family. The motifs themselves are not necessarily contiguous in sequence, but may come together in 3D space to define molecular binding sites or interaction surfaces.
Label-free quantification is a method in mass spectrometry that aims to determine the relative amount of proteins in two or more biological samples. Unlike other methods for protein quantification , label-free quantification does not use a stable isotope containing compound to chemically bind to and thus label the protein.
UniProt Archive (UniParc) is a comprehensive and non-redundant database, which contains all the protein sequences from the main, publicly available protein sequence databases. [17] Proteins may exist in several different source databases, and in multiple copies in the same database.
MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is a computer software for multiple sequence alignment of protein and nucleotide sequences. It is licensed as public domain . The method was published by Robert C. Edgar in two papers in 2004.
A typical workflow of a peptide mass fingerprinting experiment. Peptide mass fingerprinting (PMF), also known as protein fingerprinting, is an analytical technique for protein identification in which the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer such as MALDI-TOF or ESI-TOF. [1]
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The Human Protein Reference Database (HPRD) is a protein database accessible through the Internet. [1] It is closely associated with the premier Indian Non-Profit research organisation Institute of Bioinformatics (IOB), Bangalore, India. This database is a collaborative output of IOB and the Pandey Lab of Johns Hopkins University.