Computational Studies of Mechanisms of Peptide-Ion Fragmentation</ti= tle>  <style>  </style>  </head> <body lang=3DEN-US link=3Dblue vlink=3Dpurple style=3D'tab-interval:.5in'> <div class=3DSection1> Computational Studies of Mechanism= s of Peptide-Ion Fragmentation<o:p></o:p> <o:p> </o:p> Author: &nb= sp; Christopher R. Kinsinger, Karl K. Irikura, Division of Phys= ical and Chemical Properties, CSTL Room: = A157, Bldg 222 Mail: = ; 8380 Phone: = ; x2526 Fax: &= nbsp; 301-869-4020 E-mail: &nbs= p; Christopher.kinsinger@nist.gov Not a member of Sigma Xi Chemistry <o:p>&nb= sp;</o:p> Proteomi= cs is the branch of genetics that studies the full set of proteins encoded by a genome. A primary tool of proteomics is the mass spectrometer, which reports the mass-to-charge ratio= of dissociated fragments of the protein digest under study. Ideally, the fragmentation pattern= of one protein digest can be used as a fingerprint for identification of an individual protein among a mixture of many proteins. However, many mass spectral peaks = remain unidentified due to limited understanding of the chemistry of fragmentation. Additionally, information from peak intensities is not usually incorporated into current protein sequencing algorithms and databases. Peaks comprisi= ng as much as half of the total ion intensity are typically regarded as noise bec= ause of ignorance. Little research has been devoted to the chemistry of dissociation of ionized polypeptides in a vacuum. <o:p>&nb= sp;</o:p> Since th= e basic ab initio calculation assumes a gas-phase vacuum, computational chemistry is well-sui= ted to study gas-phase peptide fragmentation.&= nbsp; Using computational chemistry, we have investigated two hypotheses capable of explaining the mechanism of peptide fragmentation. Specifically, we are seeking insig= ht into the C-terminal or N-terminal bias of fragmentation for some individual residues. The first hypothesi= s is that the peptide site with the highest proton affinity corresponds to the s= ite most likely to undergo fragmentation. The second hypothesis involves comparing the thermodynamic stability= of different sets of products. E= ach set of products results from a different fragmentation pathway. According to the Hammond Postulate= , the most thermodynamically stable set of products should result from the prefer= red fragmentation pathway. Through understanding fragmentation chemistry of individual peptide bonds, we hope = to supply knowledge that will allow protein sequencers to utilize more informa= tion from protein spectra. </div> </body> </html> ------=_NextPart_01C4E2BD.12DDF950 Content-Location: file:///C:/6CC8A912/1.Kinsinger_files/preview.wmf Content-Transfer-Encoding: base64 Content-Type: image/x-wmf AQAJAAADtxQAAAQAlQAAAAAABAAAAAMBCAAFAAAACwIAAAAABQAAAAwCzxnyEwQAAAAuARgAHAAA APsCEAAHAAAAAAC8AgAAAAABAgIiU3lzdGVtABnyEwAAi/CbWKQw7g5wg4I5uCXhAgwCAAAEAAAA LQEAAAQAAAACAQEAHAAAAPsCi/8AAAAAAAC8AgAAAAAEQAASVGltZXMgTmV3IFJvbWFuAAAAAAAA AAAAAAAAAAAAAAAEAAAALQEBAAUAAAAJAgAAAAJQAAAAMgq2AkADLgAEAAAAAADsE8gZQ29tcHV0 YXRpb25hbCBTdHVkaWVzIG9mIE1lY2hhbmlzbXMgb2YgUGVwdGlkZVQAOgBhAEEAQQAnADoAJwAg ADoAQgA6ACAAHQBBACcAQQBCACAANAAtAB0AOgAnAB0AbgA0ADQAQQA6AEEAIQAtAGEALgAdADsA JwAdAEcANABBACcAIABBADQADQAAADIKtgLWDAEABAAAAAAA7BPIGS2/JwAlAAAAMgq2Av0MEQAE AAAAAADsE8gZSW9uIEZyYWdtZW50YXRpb25hLQA6AEEAHQBHADQAOgA6AGIANABBACcAOgAnACAA 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MIME-Version: 1.0 Content-Type: multipart/related; boundary="----=_NextPart_01C4E2BD.12DDF950" This document is a Single File Web Page, also known as a Web Archive file. If you are seeing this message, your browser or editor doesn't support Web Archive files. Please download a browser that supports Web Archive, such as Microsoft Internet Explorer. ------=_NextPart_01C4E2BD.12DDF950 Content-Location: file:///C:/6CC8A912/1.Kinsinger.htm Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="us-ascii" Computational Studies of Mechanisms of Peptide-Ion Fragmentation</ti= tle>  <style>  </style>  </head> <body lang=3DEN-US link=3Dblue vlink=3Dpurple style=3D'tab-interval:.5in'> <div class=3DSection1> Computational Studies of Mechanism= s of Peptide-Ion Fragmentation<o:p></o:p> <o:p> </o:p> Author: &nb= sp; Christopher R. Kinsinger, Karl K. Irikura, Division of Phys= ical and Chemical Properties, CSTL Room: = A157, Bldg 222 Mail: = ; 8380 Phone: = ; x2526 Fax: &= nbsp; 301-869-4020 E-mail: &nbs= p; Christopher.kinsinger@nist.gov Not a member of Sigma Xi Chemistry <o:p>&nb= sp;</o:p> Proteomi= cs is the branch of genetics that studies the full set of proteins encoded by a genome. A primary tool of proteomics is the mass spectrometer, which reports the mass-to-charge ratio= of dissociated fragments of the protein digest under study. Ideally, the fragmentation pattern= of one protein digest can be used as a fingerprint for identification of an individual protein among a mixture of many proteins. However, many mass spectral peaks = remain unidentified due to limited understanding of the chemistry of fragmentation. Additionally, information from peak intensities is not usually incorporated into current protein sequencing algorithms and databases. Peaks comprisi= ng as much as half of the total ion intensity are typically regarded as noise bec= ause of ignorance. Little research has been devoted to the chemistry of dissociation of ionized polypeptides in a vacuum. <o:p>&nb= sp;</o:p> Since th= e basic ab initio calculation assumes a gas-phase vacuum, computational chemistry is well-sui= ted to study gas-phase peptide fragmentation.&= nbsp; Using computational chemistry, we have investigated two hypotheses capable of explaining the mechanism of peptide fragmentation. Specifically, we are seeking insig= ht into the C-terminal or N-terminal bias of fragmentation for some individual residues. The first hypothesi= s is that the peptide site with the highest proton affinity corresponds to the s= ite most likely to undergo fragmentation. The second hypothesis involves comparing the thermodynamic stability= of different sets of products. E= ach set of products results from a different fragmentation pathway. According to the Hammond Postulate= , the most thermodynamically stable set of products should result from the prefer= red fragmentation pathway. Through understanding fragmentation chemistry of individual peptide bonds, we hope = to supply knowledge that will allow protein sequencers to utilize more informa= tion from protein spectra. </div> </body> </html> ------=_NextPart_01C4E2BD.12DDF950 Content-Location: file:///C:/6CC8A912/1.Kinsinger_files/preview.wmf Content-Transfer-Encoding: base64 Content-Type: image/x-wmf AQAJAAADtxQAAAQAlQAAAAAABAAAAAMBCAAFAAAACwIAAAAABQAAAAwCzxnyEwQAAAAuARgAHAAA APsCEAAHAAAAAAC8AgAAAAABAgIiU3lzdGVtABnyEwAAi/CbWKQw7g5wg4I5uCXhAgwCAAAEAAAA LQEAAAQAAAACAQEAHAAAAPsCi/8AAAAAAAC8AgAAAAAEQAASVGltZXMgTmV3IFJvbWFuAAAAAAAA AAAAAAAAAAAAAAAEAAAALQEBAAUAAAAJAgAAAAJQAAAAMgq2AkADLgAEAAAAAADsE8gZQ29tcHV0 YXRpb25hbCBTdHVkaWVzIG9mIE1lY2hhbmlzbXMgb2YgUGVwdGlkZVQAOgBhAEEAQQAnADoAJwAg ADoAQgA6ACAAHQBBACcAQQBCACAANAAtAB0AOgAnAB0AbgA0ADQAQQA6AEEAIQAtAGEALgAdADsA JwAdAEcANABBACcAIABBADQADQAAADIKtgLWDAEABAAAAAAA7BPIGS2/JwAlAAAAMgq2Av0MEQAE AAAAAADsE8gZSW9uIEZyYWdtZW50YXRpb25hLQA6AEEAHQBHADQAOgA6AGIANABBACcAOgAnACAA 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