SSRCalc (Sequence-Specific Retention Calculator), SSRCalcQ (see links below) are a tools to predict peptides’ behavior in reversed-phase HPLC data, such as prediction of retention filtering, method development for targeted (SRM) and data-independent (SWATH, MSE) in LC-MS, and analytical applications of peptide RP-HPLC.
The SSRCalc algorithm uses retention coefficients summation of the individual amino acids and computes retention coefficients for amino acids at the N-terminal of the peptide, at the C-terminal of the peptide, peptide lengths, hydrophobicity, the nearest-neighbor effect for charged residues, and peptide propensity to form amphipathic helical structures. And, can predict retention for the following chemical modifications: N-terminal cyclization for Gln and Cys alkylated with Iodoacetamide, Methionine oxidation, six types of alkylation chemistries for Cys, TMT, and iTRAQ labels.
The model organisms include Human, E. Coli, Saccharomyces cerevisiae, Bos taurus, Mus musculus, Neurospora crassa, Canis lupus familiaris, Gallus gallus, Caldicelluosiruptor kristjanssonii, Thermotoga petrophilia, Clostridium termitidis, Pseudomonas aeruginosa, Caldicellulosiruptor saccharoylticus, Acinetobacter baumannii, Thermoanaerobacter thermohydrosulfuricus, Ralstonia eutropha, Clostridium butryricum, Pseudomonas putida, Thermobifida fusca, Yarrowia lioplytica, and Clostridium thermocellum.
Proteomics; Proteomics experiment
Krokhin OV, Craig R, Spicer V, Ens W, Standing KG, Beavis RC, Wilkins JA "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." Mol. Cell Proteomics 2004; 3(9):908-19 https://doi.org/10.1074/mcp.M400031-MCP200
PMID: 15238601
Krokhin OV, Spicer V "Predicting peptide retention times for proteomics." Curr Protoc Bioinformatics, 2010 https://doi.org/10.1002/0471250953.bi1314s31
PMID: 20836075
Vu H, Spicer V, Gotfrid A, Krokhin OV "A model for predicting slopes S in the basic equation for the linear-solvent-strength theory of peptide separation by reversed-phase high-performance liquid chromatography." J Chromatogr A, 2010 https://doi.org/10.1016/j.chroma.2009.11.065
PMID: 20004401
Krokhin OV, Ying S, Cortens JP, Ghosh D, Spicer V, Ens W, Standing KG, Beavis RC, Wilkins JA "Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS." Anal Chem, 2006 https://doi.org/10.1021/ac060251b
PMID: 16944911
Vic Spicer, Andriy Yamchuk, John Cortens, Sandra Sousa, Werner Ens, Kenneth G. Standing, John A. Wilkins, and Oleg V. Krokhin "Sequence-Specific Retention Calculator. A Family of Peptide Retention Time Prediction Algorithms in Reversed-Phase HPLC: Applicability to Various Chromatographic Conditions and Columns" Anal. Chem. 2007, 79, 22, 8762–8768 Publication Date:October 16, 2007 https://doi.org/10.1021/ac071474k
Spicer V, Grigoryan M, Gotfrid A, Standing KG, Krokhin OV "Predicting retention time shifts associated with variation of the gradient slope in peptide RP-HPLC." Anal Chem, 2010 https://doi.org/10.1021/ac102228a
PMID: 21049933
Dwivedi RC, Spicer V, Harder M, Antonovici M, Ens W, Standing KG, Wilkins JA, Krokhin OV "Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics." Anal Chem, 2008 https://doi.org/10.1021/ac800984n
PMID: 18686972
Oleg V. Krokhin, Vic Spicer "Peptide Retention Standards and Hydrophobicity Indexes in Reversed-Phase High-Performance Liquid Chromatography of Peptides" Anal. Chem. 2009, 81, 22, 9522–9530 Publication Date:October 22, 2009 https://doi.org/10.1021/ac9016693
If you find errors, please report here.
SECTIONS
TutorialsFind thousands of Bioinformatics and Life Science software tools and databases in the newly launched
Ads