Retention Characteristics of Peptides in RP-LC: Peptide Retention Prediction

• Published in: Chromatographia 2010-11, Vol.72 (9-10), p.781-797
• Main Authors: Babushok, Valeri I, Zenkevich, Igor G
• Format: Article
• Language: English
• Subjects: Analytical Chemistry; Chemistry; Chemistry and Materials Science; Chromatography; Laboratory Medicine; peptides; Pharmacy; Proteomics; Retention indices; Retention prediction; Reversed phase-liquid chromatography; Review
• ISSN: 0009-5893; 1612-1112
• DOI: 10.1365/s10337-010-1721-8

A review of recent results of the use of chromatographic retention data in peptide identification and in the development of procedures for peptide retention prediction is presented. In recent years, reversed phase LC (RP-LC) has become an important tool in the separation of peptides in MS analysis. A challenging problem in a further expansion of RP-LC applications is the use of already available retention information for the identification purposes simultaneously with MS-MS identification. This overview focuses on the retention characteristics suggested in LC. We will discuss the application of the retention index concept in LC, which is widely used in GC to characterize retention of organic compounds. The use of retention indices as retention characteristics of analytes in LC was first suggested at the end of 1970s, however the application of retention indices is still somewhat rare today. There are several reasons for this. One is the relatively high sensitivity and variability of retention indices to the change of parameters of chromatographic systems. Another is the chemical restrictions in the search of the universal set of reference compounds suitable for retention scaling. Several methods were suggested for the prediction of the retention times of peptides. A frequently used approach is based on the additivity scheme and calculation of the elution time through the summation of retention coefficients of amino acids constituting the peptide. Such an approach allows fairly accurate predictions of the retention time of peptides made up of not more then 15-20 amino acid residues. Additional correction factors were suggested to improve predictions including corrections for the peptide length, peptide hydrophobicity, sequence of amino acids, etc. Suggested procedures are discussed in detail. Application of predicted retention times in the identification of peptides is considered. Current status of LC retention data collections is presented.