File Download
There are no files associated with this item.
Links for fulltext
(May Require Subscription)
- Publisher Website: 10.1002/jms.474
- Scopus: eid_2-s2.0-0037603213
- PMID: 12794879
- WOS: WOS:000183171700012
- Find via
Supplementary
- Citations:
- Appears in Collections:
Article: COMPLX: A computer algorithm for the detection of protein-ligand and other macromolecular complexes in mass spectra
Title | COMPLX: A computer algorithm for the detection of protein-ligand and other macromolecular complexes in mass spectra |
---|---|
Authors | |
Keywords | Mass spectrometry Computer algorithm Protein complex Macromolecule |
Issue Date | 2003 |
Citation | Journal of Mass Spectrometry, 2003, v. 38, n. 5, p. 573-581 How to Cite? |
Abstract | A new algorithm has been designed and tested to identify protein, or any other macromolecular, complexes that have been widely reported in mass spectral data. The program takes advantage of the appearance of multiply charged ions that are common to both electrospray ionization and, to a lesser extent, matrix-assisted laser desorption/ionization (MALDI) mass spectra. The algorithm, known as COMPLX for the COMposition of Protein-Ligand compleXes, is capable of identifying complexes for any protein or macromolecule with a binding partner of molecular mass up to 100 000 Da. It does so by identifying ion pairs present in a mass spectrum that, when they share a common charge, have an m/z value difference that is an integer fraction of a ligand or binding partner molecular mass. Several additional criteria must be met in order for the result to be ranked in the output file including that all m/z values for ions of the protein or complex have progressively lower values as their assigned charge increases, the difference between the m/z values for adjacent charge states (z, z + 1) decrease as the assigned charge state increases, and the ratio of any two m/z values assigned to a protein or complex is equal to the inverse ratio of their charge. The entries that satisfy these criteria are then ranked according to the appearance of ions in the mass spectrum associated with the binding partner, the length of a continuous series of charges across any set of ions for a protein and complex and the lowest error recorded for the molecular mass of the ligand or binding partner. A diverse range of hypothetical and experimental mass spectral data were used to implement and test the program, including those recorded for antibody-peptide, protein-peptide and protein-heme complexes. Spectra of increasing complexity, in terms of the number of ions input, were also successfully analysed in which the number of input m/z values far exceeds the few associated with a macromolecular complex. Thus the program will be of value in a future goal of proteomics, where mass spectrometry already plays a central role, for the direct analysis of protein and other associations within biological extracts. Copyright © 2003 John Wiley & Sons, Ltd. |
Persistent Identifier | http://hdl.handle.net/10722/250841 |
ISSN | 2023 Impact Factor: 1.9 2023 SCImago Journal Rankings: 0.431 |
ISI Accession Number ID |
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Wong, Jason W.H. | - |
dc.contributor.author | Downard, Kevin M. | - |
dc.date.accessioned | 2018-02-01T01:53:52Z | - |
dc.date.available | 2018-02-01T01:53:52Z | - |
dc.date.issued | 2003 | - |
dc.identifier.citation | Journal of Mass Spectrometry, 2003, v. 38, n. 5, p. 573-581 | - |
dc.identifier.issn | 1076-5174 | - |
dc.identifier.uri | http://hdl.handle.net/10722/250841 | - |
dc.description.abstract | A new algorithm has been designed and tested to identify protein, or any other macromolecular, complexes that have been widely reported in mass spectral data. The program takes advantage of the appearance of multiply charged ions that are common to both electrospray ionization and, to a lesser extent, matrix-assisted laser desorption/ionization (MALDI) mass spectra. The algorithm, known as COMPLX for the COMposition of Protein-Ligand compleXes, is capable of identifying complexes for any protein or macromolecule with a binding partner of molecular mass up to 100 000 Da. It does so by identifying ion pairs present in a mass spectrum that, when they share a common charge, have an m/z value difference that is an integer fraction of a ligand or binding partner molecular mass. Several additional criteria must be met in order for the result to be ranked in the output file including that all m/z values for ions of the protein or complex have progressively lower values as their assigned charge increases, the difference between the m/z values for adjacent charge states (z, z + 1) decrease as the assigned charge state increases, and the ratio of any two m/z values assigned to a protein or complex is equal to the inverse ratio of their charge. The entries that satisfy these criteria are then ranked according to the appearance of ions in the mass spectrum associated with the binding partner, the length of a continuous series of charges across any set of ions for a protein and complex and the lowest error recorded for the molecular mass of the ligand or binding partner. A diverse range of hypothetical and experimental mass spectral data were used to implement and test the program, including those recorded for antibody-peptide, protein-peptide and protein-heme complexes. Spectra of increasing complexity, in terms of the number of ions input, were also successfully analysed in which the number of input m/z values far exceeds the few associated with a macromolecular complex. Thus the program will be of value in a future goal of proteomics, where mass spectrometry already plays a central role, for the direct analysis of protein and other associations within biological extracts. Copyright © 2003 John Wiley & Sons, Ltd. | - |
dc.language | eng | - |
dc.relation.ispartof | Journal of Mass Spectrometry | - |
dc.subject | Mass spectrometry | - |
dc.subject | Computer algorithm | - |
dc.subject | Protein complex | - |
dc.subject | Macromolecule | - |
dc.title | COMPLX: A computer algorithm for the detection of protein-ligand and other macromolecular complexes in mass spectra | - |
dc.type | Article | - |
dc.description.nature | link_to_subscribed_fulltext | - |
dc.identifier.doi | 10.1002/jms.474 | - |
dc.identifier.pmid | 12794879 | - |
dc.identifier.scopus | eid_2-s2.0-0037603213 | - |
dc.identifier.volume | 38 | - |
dc.identifier.issue | 5 | - |
dc.identifier.spage | 573 | - |
dc.identifier.epage | 581 | - |
dc.identifier.isi | WOS:000183171700012 | - |
dc.identifier.issnl | 1076-5174 | - |