Strong Cation Exchange Elution Time Prediction Utility
The SCX Prediction Utility can be used to compute the predicted strong cation exchange (SCX) fraction (on a 0 to 1 scale) in which a given peptide will appear. The software reads the peptides from a text file containing one peptide sequence on each line. The output file includes the peptide sequence plus the predicted SCX elution time value, using a normalized elution time scale of 0 to 1.
Note that the NET Prediction Utility includes the ability to compute predicted SCX fraction values, while also supporting several other prediction algorithms. See the References section for the relevant publications that describe this algorithms.
The methods embodied in this software to derive the Kangas/Petritis retention time prediction values are covered by U.S. patent 7,136,759 and pending patent 2005-0267688A1. The software is made available solely for non-commercial research purposes on an "as is" basis by Battelle Memorial Institute. If rights to deploy and distribute the code for commercial purposes are of interest, please e-mail Bruce Harrer.
| Download Software Tool | Download Source Code |
| Version | v2.2.3378 | Requirements | Microsoft .NET Framework 3.5 SP1 |
| Date Updated | April 1, 2009 | File Size (Software Tool) | 477 KB (ZIP) |
| Registration Required | No | File size (Source Code) | 327 KB (ZIP) |
| Developers | Matthew Monroe and Lars Kangas | ||
| Comments | See the complete Revision History for a history of changes | ||
SCX Prediction Utility Feature Tour
Screenshot
Example Results
| Peptide | SCX NET |
|---|---|
| ISQAVHAAHA | 0.6036783 |
| KIDALNENK | 0.5420395 |
| TGQNSGDVNVEINVAPGKDLTK | 0.3459526 |
| GPLTGTYR | 0.3519143 |
| PDPQESIQR | 0.2050209 |
| GGDFGDTPNDR | 0.2108589 |
| HHWGYGKHNGPEHWHKDFPIANGER | 0.9450155 |
| EVDDEALEKFDK | 0.3186882 |
| GLEPINFQTAADQAR | 0.2302728 |
| KGEREDLIAYLKK | 0.8365291 |
| HNIDVLEGNEQFINAAK | 0.4564978 |
| ALAMVYLGAK | 0.2918172 |
| DGGYLYIAGK | 0.1927337 |
| AKVFEHIGKRTPIAVRFSTVAG | 0.9373038 |
| WGDAGAEYVVESTGVF | 0.1135892 |
| YAAELHLVHW | 0.4923325 |
| MIFAGIKKKGEREDLIAYLKKATNE | 0.9267704 |
| RHPYFYAPELLYYANKYNGVFQDCC | 0.7586159 |
| PELLMLANWRPAQPLKNR | 0.5436206 |
| VLQPSSVDSQTAMVLVNAIVFK | 0.2265835 |
| VATGGTTTTATPTGSGSVTSTSKTTATASK | 0.3338929 |
| DTLADAVLITTAHAWQHQGK | 0.416669 |
| PPLLESVTWIVLK | 0.2397025 |
References
Peptide retention time prediction in strong cation exchange chromatography using artificial neural networks. K. Petritis, L.J. Kangas, D. Lopez-Ferrer, M.E. Monroe, N. Jaitly, B.O. Petritis, H.M Mottaz, A.M. Mayampurath, R.A. Maxwell, J.N. Adkins, G.A. Anderson, M.E. Belov, M.S. Lipton, D.G. Camp, and R.D. Smith, Analytical Chemistry, (2009), submitted.
Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating
peptide sequence information. K. Petritis, L.J. Kangas, B. Yan, M.E. Monroe, E.F. Strittmatter, W. Qian, J.N.
Adkins, R.J. Moore, Y. Xu, M.S. Lipton, D.G. Camp, II, and R.D. Smith, Analytical Chemistry, (2006),
78(14):5026-5039.
Abstract on PubMed
Acknowledgment
All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, using this text or a similar variant:
Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.