tailieunhanh - Báo cáo khoa học: Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes

A versatile software tool,virtualmslab, is presented that can perform advanced complex virtual proteomic experiments with mass spectrometric analyses to assist in the characterization of proteins. The virtual experimen-tal results allow rapid, flexible and convenient exploration of sample prepar-ation strategies and are used to generate MS reference databases that can be matched with the real MS data obtained from the equivalent real experi-ments. | ềFEBS Journal Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes Leo J. de Koning1 Piotr T. Kasper1 Jaap Willem Back1 Merel A. Nessen1 Frank Vanrobaeys2 Jozef Van Beeumen2 Ermanno Gherardi3 Chris G de Koster1 and Luitzen de Jong1 1 Biomolecular Mass Spectrometry group Swammerdam Institute for Life Sciences University of Amsterdam the Netherlands 2 Laboratory of Protein Biochemistry and Protein Engineering University of Gent Belgium 3 MRC Centre Cambridge UK Keywords cross-linking data analysis protein structure mass spectrometry NK1 Correspondence L. de Jong Swammerdam Institute for Life Sciences Mass spectometry group University of Amsterdam Nieuwe Achtergracht 166 Amsterdam 1018 WV the Netherlands Fax 31 20 525 6971 Tel 31 20 525 5691 E-mail Received 23 September 2005 revised 28 October 2005 accepted 7 November 2005 doi A versatile software tool VIRTUALMSLAB is presented that can perform advanced complex virtual proteomic experiments with mass spectrometric analyses to assist in the characterization of proteins. The virtual experimental results allow rapid flexible and convenient exploration of sample preparation strategies and are used to generate MS reference databases that can be matched with the real MS data obtained from the equivalent real experiments. Matches between virtual and acquired data reveal the identity and nature of reaction products that may lead to characterization of post-translational modification patterns disulfide bond structures and cross-linking in proteins or protein complexes. The most important unique feature of this program is the ability to perform multistage experiments in any user-defined order thus allowing the researcher to vary experimental approaches that can be conducted in the laboratory. Several features of VIRTUALMSLAB are demonstrated by mapping both disulfide bonds and .