Normalized Elution Time (NET) Prediction Utility
The NET Prediction Utility can be used to compute predicted normalized elution time (NET) values for a list of peptide sequences. The elution times are intended for use with reversed phase liquid chromatography (e.g. using C18 coated silica particles) analyses, and are used in our lab for alignment of LC-MS and LC-MS/MS datasets to one another (using the predicted elution times to form a master in-silico dataset to align each dataset to). The predicted elution times are also used by the Protein Digestion Simulator Basic when calculating the number of uniquely identifiable peptides within an input file using both mass and NET. For more information on the utility of predicted elution times, see the References listed below.
The software has now been expanded to include the Kangas / Petritis retention time prediction algorithms for both LC retention time prediction and strong cation exchange (SCX) fraction prediction (using a 0 to 1 scale). For SCX fraction prediction, you have the option of using the SCX Prediction Utility, which is a variant of the NET Prediction Utility and only computes predicted SCX fraction values.
The NET Prediction Utility reads the peptides from a text file containing one peptide sequence on each line. The output file includes the peptide sequence plus the predicted NET value (and/or predicted SCX value) using one or all of the prediction algorithms:
- Kangas/Petritis LC retention time model
- Kangas/Petritis SCX fraction model
- Krokhin hydrophobicity model
- Mant hydrophobicity model
See the References section for the relevant publications that describe these 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) | 647 KB (ZIP) |
| Registration Required | No | File size (Source Code) | 659 KB (ZIP) |
| Developers | Matthew Monroe and Lars Kangas | ||
| Comments | See the complete Revision History for a history of changes | ||
NET Prediction Utility Feature Tour
Screenshot
Example Results
| Peptide | NET (Krokhin) | NET (Kangas) | Average Experimentally Observed NET |
|---|---|---|---|
| ISQAVHAAHA | 0.102 | 0.115 | 0.155 |
| KIDALNENK | 0.125 | 0.157 | 0.188 |
| TGQNSGDVNVEINVAPGKDLTK | 0.250 | 0.291 | 0.207 |
| GPLTGTYR | 0.135 | 0.201 | 0.226 |
| PDPQESIQR | 0.081 | 0.152 | 0.244 |
| GGDFGDTPNDR | 0.081 | 0.164 | 0.256 |
| HHWGYGKHNGPEHWHKDFPIANGER | 0.288 | 0.297 | 0.270 |
| EVDDEALEKFDK | 0.232 | 0.288 | 0.294 |
| GLEPINFQTAADQAR | 0.268 | 0.320 | 0.317 |
| KGEREDLIAYLKK | 0.280 | 0.299 | 0.337 |
| HNIDVLEGNEQFINAAK | 0.376 | 0.356 | 0.357 |
| ALAMVYLGAK | 0.316 | 0.364 | 0.369 |
| DGGYLYIAGK | 0.274 | 0.306 | 0.379 |
| AKVFEHIGKRTPIAVRFSTVAG | 0.437 | 0.375 | 0.399 |
| WGDAGAEYVVESTGVF | 0.391 | 0.414 | 0.406 |
| YAAELHLVHW | 0.374 | 0.429 | 0.416 |
| MIFAGIKKKGEREDLIAYLKKATNE | 0.442 | 0.419 | 0.438 |
| RHPYFYAPELLYYANKYNGVFQDCC | 0.523 | 0.538 | 0.450 |
| PELLMLANWRPAQPLKNR | 0.492 | 0.515 | 0.491 |
| VLQPSSVDSQTAMVLVNAIVFK | 0.528 | 0.608 | 0.558 |
| VATGGTTTTATPTGSGSVTSTSKTTATASK | 0.038 | 0.166 | 0.592 |
| DTLADAVLITTAHAWQHQGK | 0.434 | 0.519 | 0.623 |
| PPLLESVTWIVLK | 0.536 | 0.682 | 0.788 |
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
An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its
application to protein peptide mapping by off-line HPLC-MALDI MS. O.V. Krokhin, R. Craig, V. Spicer, W. Ens,
K.G. Standing, R.C. Beavis, J.A. Wilkins. Mol Cell Proteomics, (2004), 3 (9):909-919.
Abstract on PubMed
The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes. A.D.
Norbeck, M.E. Monroe, J.N. Adkins, and R.D. Smith, Journal of the American Society for Mass
Spectrometry ; (2005) 16, 1239-1249.
Abstract on PubMed
Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach. J.S. Zimmer,
M.E. Monroe, W. Qian, and R.D. Smith. Mass Spectrometry Reviews, (2006), 25
(3):450-482.
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.