title: AnchorMS: a bioinformatics tool to derive structural information from the mass spectra of cross-linked protein complexes.
abstract: CONCLUSIONS
  Mass spectrometry is being increasingly used in the structural elucidation of mega-Dalton protein complexes in an approach termed MS3D, referring to the application of MS to the study of macromolecular structures. This involves the identification of cross-linked residues in the constituent proteins of chemically cross-linked multi-subunit complexes. AnchorMS was developed to simplify MS3D studies by identifying cross-linked peptides in complex peptide mixtures, and to determine the specific residues involved in each cross-link. When identifying cross-linked peptide pairs (CLPP), AnchorMS implements a mathematical model to exclude false positives by using a dynamic score threshold to estimate the number of false-positive peak matches expected in an MS/MS spectrum. This model was derived from CLPPs with randomly generated sequences. AnchorMS does not require specific sample labeling or pre-treatment, and AnchorMS is especially suited for discriminating between CLPPs that differ only in the cross-linked residue pairs.
  
  
  BACKGROUND
  AnchorMS was coded in Python, and is available as a free web service at cbio.ufs.ac.za/AnchorMS.
authors.affiliation: Advanced Biomolecular Research Cluster, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa.
authors.forename: Shannon L N
authors.initials: SL
authors.lastname: Mayne
authors.forename: Hugh-G
authors.initials: HG
authors.lastname: Patterton
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005189:False Positive Reactions; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D010455:Peptides; D011506:Proteins