Computer simulation of high-performance liquid chromatographic separations of peptide and protein digests for development of size-exclusion, ion-exchange and reversed-phase chromatographic methods

Retention Time Prediction and Protein Identification

In bottom-up proteomics, proteins are typically identified by enzymatic digestion into peptides, tandem mass spectrometry and comparison of the tandem mass spectra with those predicted from a sequence database for peptides within measurement uncertainty from the experimentally obtained mass. Although now decreasingly common, isolated proteins or simple protein mixtures can also be identified by measuring only the masses of the peptides resulting from the enzymatic digest, without any further fragmentation. Separation methods such as liquid chromatography and electrophoresis are often used to fractionate complex protein or peptide mixtures prior to analysis by mass spectrometry. Although the primary reason for this is to avoid ion suppression and improve data quality, these separations are based on physical and chemical properties of the peptides or proteins and therefore also provide information about them. Depending on the separation method, this could be protein molecular weight (SDS-PAGE), isoelectric point (IEF), charge at a known pH (ion exchange chromatography), or hydrophobicity (reversed phase chromatography). These separations produce approximate measurements on properties that to some extent can be predicted from amino acid sequences. In the case of molecular weight of proteins without posttranslational modifications this is straightforward: simply add the molecular weights of the amino acid residues in the protein. For IEF, charge and hydrophobicity, the order of the amino acids, and folding state of the peptide or protein also matter, but it is nevertheless possible to predict the behavior of peptides and proteins in these separation methods to a degree which renders such predictions useful. This chapter reviews the topic of using data from separation methods for identification and validation in proteomics, with special emphasis on predicting retention times of tryptic peptides in reversed-phase chromatography under acidic conditions, as this is one of the most commonly used separation methods in bottom-up proteomics.

Sequence-Specific Model for Peptide Retention Time Prediction in Strong Cation Exchange Chromatography

The development of a peptide retention prediction model for strong cation exchange (SCX) separation on a Polysulfoethyl A column is reported. Off-line 2D LC-MS/MS analysis (SCX-RPLC) of S. cerevisiae whole cell lysate was used to generate a retention dataset of ∼30 000 peptides, sufficient for identifying the major sequence-specific features of peptide retention mechanisms in SCX. In contrast to RPLC/hydrophilic interaction liquid chromatography (HILIC) separation modes, where retention is driven by hydrophobic/hydrophilic contributions of all individual residues, SCX interactions depend mainly on peptide charge (number of basic residues at acidic pH) and size. An additive model (incorporating the contributions of all 20 residues into the peptide retention) combined with a peptide length correction produces a 0.976 R² value prediction accuracy, significantly higher than the additive models for either HILIC or RPLC. Position-dependent effects on peptide retention for different residues were driven by the spatial orientation of tryptic peptides upon interaction with the negatively charged surface functional groups. The positively charged N-termini serve as a primary point of interaction. For example, basic residues (Arg, His, Lys) increase peptide retention when located closer to the N-terminus. We also found that hydrophobic interactions, which could lead to a mixed-mode separation mechanism, are largely suppressed at 20-30% of acetonitrile in the eluent. The accuracy of the final Sequence-Specific Retention Calculator (SSRCalc) SCX model (∼0.99 R² value) exceeds all previously reported predictors for peptide LC separations. This also provides a solid platform for method development in 2D LC-MS protocols in proteomics and peptide retention prediction filtering of false positive identifications.

Retention time prediction and protein identification

In bottom-up proteomics, proteins are typically identified by enzymatic digestion into peptides, tandem mass spectrometry and comparison of the tandem mass spectra with those predicted from a sequence database for peptides within measurement uncertainty from the experimentally obtained mass. Although now decreasingly common, isolated proteins or simple protein mixtures can also be identified by measuring only the masses of the peptides resulting from the enzymatic digest, without any further fragmentation. Separation methods such as liquid chromatography and electrophoresis are often used to fractionate complex protein or peptide mixtures prior to analysis by mass spectrometry. Although the primary reason for this is to avoid ion suppression and improve data quality, these separations are based on physical and chemical properties of the peptides or proteins and therefore also provide information about them. Depending on the separation method, this could be protein molecular weight (SDS-PAGE), isoelectric point (IEF), charge at a known pH (ion exchange chromatography), or hydrophobicity (reversed phase chromatography). These separations produce approximate measurements on properties that to some extent can be predicted from amino acid sequences. In the case of molecular weight of proteins without posttranslational modifications this is straightforward: simply add the molecular weights of the amino acid residues in the protein. For IEF, charge and hydrophobicity, the order of the amino acids, and folding state of the peptide or protein also matter, but it is nevertheless possible to predict the behavior of peptides and proteins in these separation methods to a degree which renders such predictions useful. This chapter reviews the topic of using data from separation methods for identification and validation in proteomics, with special emphasis on predicting retention times of tryptic peptides in reversed-phase chromatography under acidic conditions, as this is one of the most commonly used separation methods in proteomics.

Design of peptide standards with the same composition and minimal sequence variation to monitor performance/selectivity of reversed-phase matrices

The present manuscript extends our de novo peptide design approach to the synthesis and evaluation of a new generation of reversed-phase HPLC peptide standards with the same composition and minimal sequence variation (SCMSV). Thus, we have designed and synthesized four series of peptide standards with the sequences Gly-X-Leu-Gly-Leu-Ala-Leu-Gly-Gly-Leu-Lys-Lys-amide, where the N-terminal is either N(α)-acetylated (Series 1) or contains a free α-amino group (Series 3); and Gly-Gly-Leu-Gly-Gly-Ala-Leu-Gly-X-Leu-Lys-Lys-amide, where the N-terminal is either N(α)-acetylated (Series 2) or contains a free α-amino group (Series 4). In this initial study, the single substitution position, X, was substituted with alkyl side-chains (Ala Collapse

Key Words Collapse

MESH Headings

• Amino Acid Sequence
• Chromatography, High Pressure Liquid/standards
• Chromatography, Reverse-Phase/standards
• Peptides/chemistry
• Reference Standards

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Grants

• R01 GM061855 NIGMS NIH HHS
• R01 GM061855-10 NIGMS NIH HHS
• R01 GM61855 NIGMS NIH HHS

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Affiliation(s)

Colin T. Mant Department of Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
Robert S. Hodges Department of Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA

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New practical algorithm for modelling retention times in gradient reversed-phase high-performance liquid chromatography

Computer models have been widely used to predict the chromatographic behaviour of liquid chromatography systems. With the introduction of mass spectrometric detection and the use of lower mobile phase flow rates with conventional LC equipment, the influence of the dwell volume on the shape of the gradient curve becomes an issue in predicting the retention times. A new straight forward algorithm is proposed for the modelling of retention times in reversed-phase LC, taking the effect of the dwell volume on the gradient shape into account. The results show that the dwell volume has a large effect at lower flow rates and on the retention times of the analytes eluting at the end of fast gradient curves. The proposed model is able to make reliable predictions and can be helpful in LC-MS method development.

Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses

The use of artificial neural networks (ANNs) is described for predicting the reversed-phase liquid chromatography retention times of peptides enzymatically digested from proteome-wide proteins. To enable the accurate comparison of the numerous LC/MS data sets, a genetic algorithm was developed to normalize the peptide retention data into a range (from 0 to 1), improving the peptide elution time reproducibility to approximately 1%. The network developed in this study was based on amino acid residue composition and consists of 20 input nodes, 2 hidden nodes, and 1 output node. A data set of approximately 7000 confidently identified peptides from the microorganism Deinococcus radiodurans was used for the training of the ANN. The ANN was then used to predict the elution times for another set of 5200 peptides tentatively identified by MS/MS from a different microorganism (Shewanella oneidensis). The model was found to predict the elution times of peptides with up to 54 amino acid residues (the longest peptide identified after tryptic digestion of S. oneidensis) with an average accuracy of approximately 3%. This predictive capability was then used to distinguish with high confidence isobar peptides otherwise indistinguishable by accurate mass measurements as well as to uncover peptide misidentifications. Thus, integration of ANN peptide elution time prediction in the proteomic research will increase both the number of protein identifications and their confidence.

Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry

Liquid chromatography coupled on- or off-line with mass spectrometry is rapidly advancing as a tool in proteomics capable of dealing with the inherent complexity in biology and complementing conventional approaches based on two-dimensional gel electrophoresis. Proteins can be identified by proteolytic digestion and peptide mass fingerprinting or by searching databases using short-sequence tags generated by tandem mass spectrometry. This paper shows that information on the chromatographic behavior of peptides can assist protein identification by peptide mass fingerprinting in liquid chromatography/mass spectrometry. This additional information is significant and already available at no extra experimental cost.

Theoretical studies on the mobility-shift assay of protein-DNA complexes

The theory of mass transport coupled to reversible macromolecular interactions under chemical kinetic control forms the basis for computer simulation of the electrophoretic mobility-shift behavior of protein-DNA complexes. Model systems include (i) specific binding of a univalent protein molecule to a single site on the DNA molecule; (ii) the putative cage effect; (iii) cooperative binding to multiple sites; (iv) formation of looped complexes of 1:1 and 2:1 stoichiometry; (v) noncooperative and cooperative, nonspecific binding modes; and (vi) binding of dimerizing transcriptional factors to response elements of target genes. Favorable comparison of simulated with experimental mobility-shift behavior indicates that the phenomenological mechanisms, whereby observed mobility-shift patterns are generated during electrophoresis, are embodied in the theory. These studies have provided guidelines for definitive interpretation of mobility-shift assays and for the design of experiments to develop a detailed understanding of the particular system under investigation.

Selectivity due to conformational differences between helical and non-helical peptides in reversed-phase chromatography

The reversed-phase retention behaviour of two series of peptides, one non-helical and the other alpha-helical, was studied under various linear AB gradients in order to determine the effect of peptide conformation on selectivity of the separation. The non-helical series, designated X1, with the sequence Ac-XLGAKGAGVG-amide, exhibited negligible alpha-helical content in a hydrophobic medium; whereas, the amphipathic alpha-helical series, designated AX9, with the sequence Ac-EAEKAAKEXEKAAKEAEK-amide, exhibited high alpha-helical content in a hydrophobic medium. We have shown that plots of log k vs. phi (where k is the median capacity factor and phi is the median volume fraction of organic solvent) are very similar for any one peptide conformation, i.e., peptides from either the non-helical or amphipathic alpha-helical series exhibit similar S (solute parameter) values and the b (gradient steepness parameter) values are also similar for 17 different amino acid substitutions within each series of peptides. If mixtures of peptides from the two different series are separated using either increasing or decreasing gradient rates, large increases in resolution occur due to selectivity, which may be attributed to the difference in the log k vs. phi plots for each series of peptides. In addition, by using a polymer of an X1 peptide, which is 20 residues in length, it has been shown that the molecular mass difference between the X1 and the AX9 series of peptides is not sufficient to account for the selectivity difference. The S value of a non-amphipathic alpha-helical peptide further suggested that the difference in selectivity between the two series of peptides was due to differences in conformation. We believe that the peptide mixtures presented here provide a good model for studying selectivity effects due to conformational differences between peptides, an important concern when attempting to develop rational approaches to the prediction and optimization of peptide separation protocols from primary sequence information alone.

Reversed-phase HPLC analysis of peptides in standard and dairy samples using on-line absorbance and post-column OPA-fluorescence detection

Absorbance and post-column o-phthalaldehyde (OPA)-fluorescent detection were used to analyse standard and dairy peptides following reverse-phase HPLC. Using both detection systems on-line provides additional information on the presence of peptides in dairy products. The detection response depends on the amino acid composition of the peptide involved. Among the peptides used, glutathione, lysine-containing peptides and peptides with glycine as the N-terminal residue give the highest fluorescence after the OPA post-column reaction. Absorbance is more sensitive than fluorescence for peptides with aromatic amino acids. Different parameters, such as the flow rate of OPA, the amount of mercaptoethanol in the OPA reagent and the temperature of reaction, substantially influence the fluorescent response of peptides. The interest of using on-line absorbance and fluorescence detection is highlighted by analysing peptides from skim milk and from a tryptic hydrolysate.

Effect of the alpha-amino group on peptide retention behaviour in reversed-phase chromatography. Determination of the pK(a) values of the alpha-amino group of 19 different N-terminal amino acid residues

We have examined the contribution of the alpha-amino group to retention behaviour for peptides in reversed-phase chromatography using two series of peptide analogues, one containing an N alpha-acetylated terminal and the other containing an alpha-amino group (non-acetylated). The effect of the alpha-amino group, at pH 2, on the hydrophobicity of the side-chain of the N-terminal residue was obtained by referencing the retention time of the acetylated or non-acetylated peptide to the retention time of a glycine analogue. It was shown that the presence of an alpha-amino group could decrease or increase the hydrophobicity of the side-chain of the N-terminal residue with respect to the hydrophobicity of the side-chain in the absence of an alpha-amino group. The effect was also shown to be sequence dependent, with respect to the N-terminal residue. Increasing pH was shown to increase retention time dramatically for the non-acetylated analogues, through the deprotonation of the alpha-amino group. By separating pairs of acetylated/non-acetylated analogues over the pH range 2-9, it was possible to determine the pK(a) of the alpha-amino group, where it was shown that the pK(a) was dependent on two probable factors: (1) the inherent hydrophobicity of the stationary phase; and (2) the amino acid substituted in the N-terminal position. Interestingly, the pK(a) values determined were very similar to that found in proteins. It was also possible to determine the pK(a) values of some of the substituted amino acids containing ionizable side-chains. This study shows that, in order to understand fully the retention behaviour of peptides containing an alpha-amino group in reversed-phase chromatography, one must incorporate an alpha-amino group contribution and its effect on the hydrophobicity of the side-chain of the N-terminal residue.

Factors influencing the performance of peptide mapping by reversed-phase high-performance liquid chromatography

Factors controlling the performance of peptide mapping on reversed-phase columns were systematically evaluated. Performance criteria included resolution (peak capacity and selectivity), system reproducibility, sensitivity and analysis speed. Column configuration, characteristics of packing materials, mobile phase composition, operating variables and instrumental designs were found to influence the performance of peptide mapping. Considerations for peptide identification techniques are discussed.

Reversed-phase chromatographic method development for peptide separations using the computer simulation program ProDigest-LC

A computer program, ProDigest-LC, has been developed that assists scientists in devising methods of size-exclusion, cation-exchange and reversed-phase high-performance liquid chromatography for the analytical separation and purification of biologically active peptides and peptide fragments from enzymatic and chemical digests of proteins. ProDigest-LC accurately predicts the retention behaviour of peptides of known composition, containing 2-50 amino acid residues, and simulates the elution profiles in all three modes of chromatography. In addition, ProDigest-LC is a user-friendly program, designed as a teaching aid for both students and researchers in selecting the correct conditions for chromatography, that is, the mode of chromatography, column selection and mobile-phase selection, and has the ability to examine the effects of gradient-rate, flow-rate and sample size on the separation. The simulation capabilities of ProDigest-LC as they apply to the reversed-phase chromatography of peptides were examined. The development of the reversed-phase simulation features of the program is described, stressing the importance of peptide standards in the development, testing and practical use of ProDigest-LC. The ease of use of the program is clearly demonstrated by presenting a step-by-step procedure to produce several of the simulations illustrated in the paper. The predictive accuracy of the program was rigorously tested by its application to retention time prediction, at different gradient-rates and flow-rates, for a sample mixture containing peptides exhibiting a wide range of size (11-50 residues), charge (+1 to +8 net charge), hydrophobicity and conformation (random coil to considerable alpha-helical structure). The excellent accuracy of these peptide retention time predictions complemented the successful simulation (in terms of peptide retention times, peptide resolution, peak heights and peak widths) of the effects of gradient-rate and flow-rate on the elution profile of a mixture of closely related peptide analogues.

Strong cation-exchange high-performance liquid chromatography of peptides. Effect of non-specific hydrophobic interactions and linearization of peptide retention behaviour

Strong cation-exchange chromatography (strong CEX) is probably the most useful mode of high-performance ion-exchange chromatography (IEC) for peptide separations. Although the hydrophobic character of high-performance ion-exchange packings, often giving rise to mixed-mode contributions to solute separations, has long been recognized, a systematic approach to examining the effect and magnitude of the hydrophobicity of these packings during IEC of peptides has so far been lacking. In the present study, we report the synthesis of three series of positively charged peptide polymers which vary significantly in overall hydrophobicity and polypeptide chain length (5-50 amino acid residues): Ac-(Gly-Lys-Gly-Leu-Gly)n-amide, Ac-(Leu-Gly-Leu-Lys-Ala)n-amide and Ac-(Leu-Gly-Leu-Lys-Leu)n-amide (n = 1, 2, 4 6, 8, 10). We have examined non-specific hydrophobic interactions of these peptides with both silica-and polymer-based ion-exchange packings, demonstrating how these interactions are overcome by the addition of acetonitrile to the mobile phase. It was also shown that removal of non-specific hydrophobic interactions may be necessary just to elute peptides from the ion-exchange matrix. In addition, from the observed retention times of these three peptide polymer series and other peptides which vary substantially in charge density, net charge, polypeptide chain length and hydrophobicity, we have established a simple approach to linearization and, thus, prediction of peptide retention behaviour in CEX.