## Crux glossary

### Mass spectrometry terminology

- c-term peptide: The last peptide in the protein, occurring at the c-terminal end of the protein.
- decoy peptide: A shuffled, reversed or randomly generated peptide sequence. Matches to decoy peptides are used for two purposes: to estimate statistical confidence measures such as the false discovery rate, and to train machine learning methods to recognize correctly identified spectra.
- modification: A chemical modification of a single amino acid, typically corresponding to the addition of a molecular group to the amino acid side chain.
- n-term peptide: The first peptide in the protein, occurring at the n-terminal end of the protein.
- peptide: A subsequence of a protein.
- peptide-spectrum match (PSM): An observed spectrum paired with a peptide sequence, along with a score quantifying the quality of the match.
- static modification: A chemical modification of a single amino that is expected to occur on every instance of that amino acid. A common example is carbamidomethylation of cysteine, which adds 57.02146 Da to the mass of every cysteine.
- target peptide: A real peptide, usually drawn from a protein database.
- trypsin: An enzyme used to cleave a protein into peptides.
- variable modification: A chemical modification of a single amino that is expected to occur on some instances of that amino acid but not others. A common example is phosphorylation of serine, threonine or tyrosine, which adds a mass of 79.966331 Da to each of those amino acids.

### Analysis terminology

- false discovery rate (FDR): Estimated proportion of incorrectly identifications among a set of PSMs, peptides or proteins.
- support vector machine (SVM): A machine learning method that learns to classify data objects into two groups.