Normalized Elution Time (NET) Prediction Utility
The NET Prediction Utility can be used to compute the predicted normalized elution time (NET) value 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 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, using either of the two included NET prediction algorithms (the Krokhin hydrophobicity model or the Mant hydrophobicity model; PNNL-trained model available via GUA).
| Download Software Tool | Download Source Code |
| Version | v2.0.2797 | Requirements | .NET Framework v1.1; |
| Date Updated | August 29, 2007 | File Size (Software Tool) | 160 KB (ZIP) |
| Registration Required | No | File size (Source Code) | 118 KB (ZIP) |
| Developers | Matthew Monroe and Lars Kangas | ||
| Comments | See the complete Revision History for a history of changes | ||
Important Note: The publicly available version of this software does not contain the NET prediction model developed at PNNL (described in the Petritis et. al. paper listed below) because that model is patented. However, a version that does include the PNNL-trained (Kangas) model is freely available to U.S. Government funded research groups located in the United States (e.g. at universities, national laboratories, or other public research institutions). To request a copy of the NET Prediction Utility that includes the Kangas model, you will need to complete this Government Use Agreement (GUA) for the software and both e-mail it to proteomics@pnl.gov and print, sign and mail the document using traditional mail (or UPS/FedEx). Once we have received and approved the signed agreement, we will e-mail you an installer for the NET Prediction Utility with the Kangas model (source code is not available for this version, but you can call the VB.NET DLL from other software for automated computation of predicted elution times).
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
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 result from the use of this software should include this statement:
Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), and 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). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.
