Prediction of peptide retention time in reversed-phase high-performance liquid chromatography.

Peptide retention in reversed-phase chromatography depends mainly on the amino acid composition of peptides and can therefore be predicted by summing the relative hydrophobic contributions of each constitutive amino acid residue. The prediction is correct for small peptides but overestimates the retention times of peptides larger than 10-15 residues. A new prediction model is proposed in which the contribution to peptide retention of each amino acid residue is not a constant but a decreasing function of peptide length. From the retention times of 104 peptides, the parameters of decreasing functions were estimated by a non-linear multiple regression analysis. The contribution to peptide retention of charged, polar and non-polar residues appears to be differently affected by peptide length. The secondary structure of most peptides during reversed-phase high-performance liquid chromatography could be responsible for this. The high correlation between the predicted and observed retention times of peptides which were not used to establish the model indicates a good predictive accuracy of the new model.     

Hydrophilic properties as a new contribution for computer-aided identification of short peptides in complex mixtures

A new method to predict elementary amino acid (AA) composition of peptides (molar mass <1,000 g/mol) is described. This procedure is based on a computer-aided method using three combined analyses-reversed phase liquid chromatography (RPLC), hydrophilic interaction chromatography (HILIC) and capillary electrophoresis coupled with mass spectrometry-and using a software calculating all possible amino acid combinations from the mass of any given peptide. The complementarity between HILIC and RPLC was demonstrated. Peptide retention prediction in HILIC was successfully modelled, and the achieved prediction accuracy was as high as r2=0.97. This mathematical model, based on amino acid retention contributions and peptide length, provided the information about peptide hydrophilicity that was not redundant with its hydrophobicity. Correlations between respectively the hydrophobicity coefficients and RPLC retention time, hydrophilicity and HILIC retention time, and electrophoretic mobility and migration time were used for ranking all potential AA combinations corresponding to the given mass. The essential contribution of HILIC in this identification strategy and the need to combine the three models to significantly increase identification capabilities were both shown. Applied to an 18-standard peptide mixture, the identification procedure enabled the actual AA combination determination of the 14 di- to pentapeptides, in addition to an over 98 % reduction of possible combination numbers for the four hexapeptides. This procedure was then applied to the identification of 24 unknown peptides in a rapeseed protein hydrolysate. The effective AA composition was found for ten peptides, whereas for the 14 other peptides, the number of possible combinations was reduced by over 95 % thanks to the association of the three analyses. Finally, as a result of the information provided by the analytical techniques about peptides present in the mixture, the proposed method could become a highly valuable tool to recover bioactive peptides from undefined protein hydrolysates.     

Prediction of peptide retention times in normal-phase liquid chromatography with only a single gradient run.

Previous studies of peptide separation by normal-phase liquid chromatography have shown a linear relationship between the logarithm of the capacity factor and the logarithm of the volume fraction of modifier in the mobile phase. This permitted the use of a model to predict isocratic and gradient retention times based on data obtained by two initial gradient runs. In the present study, chromatographic behavior of 25 peptides in normal-phase liquid chromatography with isocratic elution have been studied and a linear relationship between the slope (S) and intercept [log k(0)] was obtained. This relationship was combined with the algorithm of prediction reported in the previous paper. The prediction of peptide retention times with only a single experimental gradient retention data was investigated.     

Requirements for prediction of peptide retention time in reversed-phase high-performance liquid chromatography: hydrophilicity/hydrophobicity of side-chains at the N- and C-termini of peptides are dramatically affected by the end-groups and location

The value of reversed-phase high-performance liquid chromatography (RP-HPLC) and the field of proteomics would be greatly enhanced by accurate prediction of retention times of peptides of known composition. The present study investigates the hydrophilicity/hydrophobicity of amino acid side-chains at the N- and C-termini of peptides while varying the functional end-groups at the termini. We substituted all 20 naturally occurring amino acids at the N- and C-termini of a model peptide sequence, where the functional end-groups were N(alpha)-acetyl-X- and N(alpha)-amino-X- at the N-terminus and -X-C(alpha)-carboxyl and -X-C(alpha)-amide at the C-terminus. Amino acid coefficients were subsequently derived from the RP-HPLC retention behaviour of these peptides and compared to each other as well as to coefficients determined in the centre of the peptide chain (internal coefficients). Coefficients generated from residues substituted at the C-terminus differed most (between the -X-C(alpha)-carboxyl and -X-C(alpha)-amide peptide series) for hydrophobic side-chains. A similar result was seen for the N(alpha)-acetyl-X- and N(alpha)-amino-X- peptide series, where the largest differences in coefficient values were observed for hydrophobic side-chains. Coefficients derived from substitutions at the C-terminus for hydrophobic amino acids were dramatically different compared to internal coefficients for hydrophobic side-chains, ranging from 17.1 min for Trp to 4.8 min for Cys. In contrast, coefficients derived from substitutions at the N-terminus showed relatively small differences from the internal coefficients. Subsequent prediction of peptide retention time, within an error of just 0.4 min, was achieved by a predictive algorithm using a combination of internal coefficients and coefficients for the C-terminal residues. For prediction of peptide retention time, the sum of the coefficients must include internal and terminal coefficients.     

Prediction of peptide retention times in reversed-phases high-performance liquid chromatography during linear gradient elution

The retention behavior of 100 peptides was studied during high-performance liquid chromatography on a C₁₈ column using aqueous trifluoroacetic acid as the mobile phase and acetonitrile as the mobile phase modifier in a linear gradient elution system. Retention times of the peptides were linearly related to the logarithm of the sum of Rekker's constants (R.F. Rekker, The Hydrophobic Fragmental Constant, Elsevier, Amsterdam, 1977, p. 301) for the constituent amino acid. Assuming this relationship, the best fit constants for this system were computed by non-linear multiple regression analysis. Using the new constants, it is possible to predict retention times for a wide variety of peptides at any slope of linear gradient, if the amino acid composition is known. It also enables accurate prediction of the retention time of peptides, whose amino acid composition in not known, after an analytical run with an alternate gradient.     

Prediction of Peptide Retention in RP-LC

The retention of small peptides can be predicted by summing the hydrophobic contribution to retention of each amino acid of peptides. But the retention time of peptides larger than 10–15 residues are less than that predicted by summing the retention coefficients of each constitutive residue. A new prediction model, considering the effects of the peptide length and contact area of each amino acid with the stationary phase for larger peptides was proposed. The model was validated by 136 peptides identified by nano-flow 2-D-LC-ESI-MS-MS platform and other retention data observed from literature. The high degree of correlation between the observed and predicted retention time by using the new model is not only good evidence for the accuracy of our predictive method, but supports the supposition that the peptide length and contact area of each amino acid with stationary phase are important factors affecting peptide retention time for larger peptide. In addition it is found that the range of peptide length is wider, the accuracy of prediction is better. The ratio coefficient of surface area of non-polar, polar and charged amino residues contacting with the stationary phase were all calculated to be less than one. Revised: 30 June and 11 August 2005     

The Use of Perfluorinated Carboxylic Acids in the Reversed-Phase HPLC of Peptides

Abstract

The relative effectiveness of trifluoroacetic acid (TFA), pentafluoropropanoic acid (PFPA), heptafluorobutyric acid (HFBA) and undecafluorocaproic acid (UFCA) as hydrophobic counter-ions in the reversedphase high performance liquid chromatography (RP-HPLC) of peptides was assessed. Four solvent systems were compared each containing 0.01M of a perfluorocarboxylic acid throughout. Twelve standard peptides and proteins were loaded onto the RP-HPLC column which was eluted with a linear gradient of 20-58.4% aqueous acetonitrile over 90 minutes. The retention times of the peptide standards were different in each solvent system. In progressing from TFA to PFPA, HFBA and UFCA all the peptides showed greater retention times. However, the effect was most marked with peptides having the greatest number of basic groups. By exploiting this behaviour a different type of chromatography can be introduced into the RP-HPLC purification of peptides. For instance, column fractions obtained from the use of the TFA solvent system can be re-chromatographed in a solvent system containing HFBA. It is possible by this procedure to purify naturally occurring peptides on the basis of their overall positive charges. At 0.01M each acid solution is sufficiently U.V. transparent to permit monitoring of column effluents at 210 nm. TFA, PFPA, HFBA and UFCA solvent systems are also completely volatile and this property facilitates the bioassay, radioimmunoassay and amino acid analysis of column fractions.     

Separation characteristics of alkylated guanines in high-performance liquid chromatography

The retention behavior of thirteen alkylated guanines on normal-phase silica gel and amino columns and on reversed-phase ODS and phenyl columns was studied. The larger the alkyl substituent at the same position of guanine the weaker was the retention in the normal-phase chromatographic system and the greater the retention during reversed-phase chromatography. O6-Derivatives possess the lowest polarity in each set of isomers. An amino column was found to be of highest efficiency in terms of separation of the set of ethylguanine isomers and of benzylguanines studied. A phenyl column provided the best resolution of methylated guanines.     

Quantitation of the nearest-neighbour effects of amino acid side-chains that restrict conformational freedom of the polypeptide chain using reversed-phase liquid chromatography of synthetic model peptides with L- and D-amino acid substitutions

Side-chain backbone interactions (or "effects") between nearest neighbours may severely restrict the conformations accessible to a polypeptide chain and thus represent the first step in protein folding. We have quantified nearest-neighbour effects (i to i+1) in peptides through reversed-phase liquid chromatography (RP-HPLC) of model synthetic peptides, where L- and D-amino acids were substituted at the N-terminal end of the peptide sequence, adjacent to a L-Leu residue. These nearest-neighbour effects (expressed as the difference in retention times of L- and D-peptide diastereomers at pHs 2 and 7) were frequently dramatic, depending on the type of side-chain adjacent to the L-Leu residue, albeit such effects were independent of mobile phase conditions. No nearest-neighbour effects were observed when residue i is adjacent to a Gly residue. Calculation of minimum energy conformations of selected peptides supported the view that, whether a L- or D-amino acid is substituted adjacent to L-Leu, its orientation relative to this bulky Leu side-chain represents the most energetically favourable configuration. We believe that such energetically favourable, and different, configurations of L- and D-peptide diastereomers affect their respective interactions with a hydrophobic stationary phase, which are thus quantified by different RP-HPLC retention times. Side-chain hydrophilicity/hydrophobicity coefficients were generated in the presence of these nearest-neighbour effects and, despite the relative difference in such coefficients generated from peptides substituted with L- or D-amino acids, the relative difference in hydrophilicity/hydrophobicity between different amino acids in the L- or D-series is maintained. Overall, our results demonstrate that such nearest-neighbour effects can clearly restrict conformational space of an amino acid side-chain in a polypeptide chain.     

Visualization and application of amino acid retention coefficients obtained from modeling of peptide retention

We introduce a method for data inspection in liquid separations of peptides using amino acid retention coefficients and their relative change across experiments. Our method allows for the direct comparison between actual experimental conditions, regardless of sample content and without the use of internal standards. The modeling uses linear regression of peptide retention time as a function of amino acid composition. We demonstrate the pH dependency of the model in a control experiment where the pH of the mobile phase was changed in controlled way. We introduce a score to identify the false discovery rate on peptide spectrum match level that corresponds to the set of most robust models, i.e. to maximize the shared agreement between experiments. We demonstrate the method utility in reversed‐phase liquid chromatography using 24 datasets with minimal peptide overlap. We apply our method on datasets obtained from a public repository representing various separation designs, including one‐dimensional reversed‐phase liquid chromatography followed by tandem mass spectrometry, and two‐dimensional online strong cation exchange coupled to reversed‐phase liquid chromatography followed by tandem mass spectrometry, and highlight new insights. Our method provides a simple yet powerful way to inspect data quality, in particular for multidimensional separations, improving comparability of data at no additional experimental cost.     

Reversed-phase ion-pair liquid chromatography of the angiotensins

The isocratic reversed-phase liquid chromatography of the angiotensins and a number of their synthetic analogues is described. Complete separation of 10 out of 12 peptides was achieved through a solvent optimization strategy with a total analysis time of about 20 min. The retention behavior of the angiotensins studied was described in terms of the hydrophobic contribution of their amino acid residues; there was good correlation between predicted and experimental retention for those peptides that were retained by a common mechanism. However, because ion-pair chromatography was required for good peak symmetry, retention was substantially modulated by the presence of acidic and basic residues. The limit of detection of these peptides was 3-5 pmol by UV absorbance at 214 nm. For those peptides containing a primary amino group the detection limit was improved by two orders of magnitude by fluorogenic derivatization with naphthalene-2,3-dicarboxaldehyde/cyanide to the corresponding N-substituted 1-cyanobenz[f]isoindole (CBI) derivatives. The contribution of the CBI ring system to retention was also investigated.     

Reversed-phase chromatography of phenylthiocarbamyl amino acid derivatives of physiological amino acids: an evaluation and a comparison with analysis by ion-exchange chromatography.

Reversed-phase chromatography of phenylthiocarbamyl (PTC) amino acid derivatives of physiological amino acids was evaluated and compared with the traditional method of ion exchange. The PTC amino acid derivatives were stable for at least 32 h at ambient temperature before injection. The relationship of detector response to concentration for the PTC derivatives was linear from 39 to 1250 pmol. With few exceptions, the within- and between-run precisions of plasma amino acid retention times were less than 0.2 and 0.3%, respectively; the within- and between-run precisions of their concentrations were less than 4.0 and 5.0%, respectively. Twenty-four plasma samples were quantitated by both reversed-phase and ion-exchange chromatography; fifteen of the twenty amino acids determined had correlation coefficients in the range 0.81-1.00. Nine non-standard amino acids and ten therapeutic drugs were added to plasma; D-glucosaminic acid and alpha-amino-beta-guanidinopropionic acid co-eluted with alpha-aminoadipic acid and threonine, respectively. Of the ten drugs added, only metronidazole and theophylline co-eluted with beta-alanine and histidine, respectively. The precision, stability, and sensitivity of the method render it ideal for the quantitation of plasma amino acids.     

Separation and quantitative analysis of some carotenoid fatty acid esters of fruits by liquid chromatography

The adsorption and partition properties of several fatty acid esters of capsanthin, capsorubin, beta-cryptoxanthin, lutein, violaxanthin and beta-citraurin isolated from fruits were studied by normal-phase (silica) and reversed-phase (octadecylsilane) liquid chromatography using Sudan 1 as internal standard. The separation on a normal phase was based on the functional group of the carotenoids and individual esters of the same carotenoid did not resolve. The separation on a reversed phase was more dependent on the number of acyl carbons than the functional group, and individual esters of the same carotenoid differing only two acyl carbons were separated with a resolution of 3. There was a linear relationship between number of acyl carbons and retention times of the same carotenoid on reversed phase. The separation on a normal phase was the reverse of that on a reversed phase, and a combination of normal-phase followed by reversed-phase chromatography was used for the separation of esters with the same or close retention times.     

Applicability of the critical chromatography concept to proteomics problems: Dependence of retention time on the sequence of amino acids

A peptide separation model based on the technique of liquid chromatography of macromolecules at the critical condition was proposed. In terms of this model, the array of experimental data on the separation of peptides is considered. The main phenomenological parameters of the model—effective adsorption energies of amino acid residues—were determined, thus allowing the influence of character of their alternation in the chain on retention times to be predicted. The model is applicable to investigation into the feasibility of separation in different chromatographic modes of not only peptides with the same amino acid composition and different sequences of units in the chain but also peptides containing amino acid isomers and mirror sequences with different terminal groups.     

Characterization of surface-confined ionic liquid stationary phases: impact of cation and anion identity on retention

A series of surface-confined ionic liquid (SCIL) stationary phases for high-performance liquid chromatography were synthesized in-house. The synthesized phases were characterized by the linear solvation energy relationship (LSER) method to determine the effect of residual linking ligands and the role of the cation and the anion on retention. Statistical analysis was utilized to determine whether the system coefficients returned from multiple linear regression analysis of chromatographic retention data for a set of 28 neutral aromatic probe solutes were significantly different. Examination of the energetics of retention via κ−κ plots agrees with the results obtained from the LSER analysis. Residual linking ligands were determined to contribute reversed-phase-type retention character to the chromatographic system. Furthermore, retention on the SCIL phases was observed to be more profoundly affected by the identity of the anion than by that of the cation.     

Reversed-phase high-performance liquid chromatographic behavior of peptide isomers including a D-amino acid

Summary The chromatographic behavior of ten peptide isomers was investigated using isocratic eluting with reversedphase high-performance liquid chromatography. These peptides are growth hormone releasing factor, consisting of 29 amino acid residues and its isomers where on amino acid residue in the sequence was replaced with the corresponding D-amino acid. Linear relationship was observed between the logarithm of the capacity factors of the isomers and the acetonitrile concentration in the mobile phase with correlation coefficients of 0.995–0.998. The regression coefficients were almost the same for all the isomers with a relative standard deviation of 5.3%. These results suggest that the chromatographic behavior of peptide isomers is also predictable from the solvophobic theory. The regression coefficient reflects the molecular weight and the Y-intercept represents the hydrophobicity of the isomer. The peptide isomers can be separated from one another, based on the differences in the hydrophobicity of each isomer.     

OPA柱前衍生反相高效液相色谱法测定氨基酸含量

建立了邻苯二甲醛（ＯＰＡ）手动柱前衍生反相高效液相色谱法测定样品中氨基酸含量的方法。以邻苯二甲醛（ＯＰＡ）／３－巯基丙酸（３－ＭＰＡ）为衍生试剂进行衍生,ＯＤＳ柱分离,３４０ｎｍ检测,在４０ｍｉｎ内１８种氨基酸全部得到基线分离。测定牛血清白蛋白（ＢＳＡ）的氨基酸组成和小鼠血清中的游离氨基酸,取得满意的结果。     

Enantioresolution of basic pharmaceuticals using cellulose tris(4-chloro-3-methylphenylcarbamate) as chiral stationary phase and polar organic mobile phases

A polysaccharide-based chiral stationary phase (Sepapak-4), with cellulose tris(4-chloro-3-methylphenylcarbamate) as chiral selector, has been investigated in liquid chromatography (LC). Its enantioresolution power was evaluated towards 13 basic amino-drugs with widely different structures and polarities, using polar organic mobile phases. After preliminary experiments, acetonitrile was selected as the main mobile phase component, to which a low concentration of diethylamine (0.1%) was systematically added in order to obtain efficient and symmetrical peaks. Different organic solvents were first added in small proportions (5–10%) to acetonitrile to modulate analyte retention. Polar organic modifiers were found to decrease retention and enantioresolution while hexane had the opposite effect, indicating normal-phase behaviour under these conditions. The addition of an organic acid (formic, acetic or trifluoroacetic acid) was found to strongly influence the retention of the basic amino drugs in these nonaqueous systems. The nature and proportion of the acidic additive in the mobile phase had also deep impact on enantioresolution. Therefore, the studied compounds could be subdivided in three groups in respect to the acidic additive used. All analytes could be enantioseparated in relatively short analysis times (10–20 min) using these LC conditions.     

Limitation of predictive 2-D liquid chromatography in reducing the database search space in shotgun proteomics: in silico studies

A two-dimensional (2-D) liquid chromatography (LC) separation of complex peptide mixtures that combines a normal phase utilizing hydrophilic interactions and a reversed phase offers reportedly the highest level of 2-D LC orthogonality by providing an even spread of peptides across multiple LC fractions. Matching experimental peptide retention times to those predicted by empirical models describing chromatographic separation in each LC dimension leads to a significant reduction in a database search space. In this work, we calculated the retention times of tryptic peptides separated in the C18 reversed phase at different separation conditions (pH 2 and pH 10) and in TSK gel Amide-80 normal phase. We show that retention times calculated for different 2-D LC separation schemes utilizing these phases start to correlate once the mass range of peptides under analysis becomes progressively narrow. This effect is explained by high degree of correlation between retention coefficients in the considered phases.