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

In Vitro and In Silico Approaches to Generating and Identifying Angiotensin-Converting Enzyme I Inhibitory Peptides from Green Macroalga Ulva lactuca

A protein extract was generated from the macroalga Ulva lactuca, which was subsequently hydrolysed using the food-grade enzyme papain and angiotensin-converting Enzyme I and renin inhibitory peptides identified using a combination of enrichment strategies employing molecular weight cutoff filtration and mass spectrometry analysis. The generated hydrolysates with the most promising in vitro activity were further purified using preparative RP-HPLC and characterised. The 1 kDa hydrolysate (1 kDa-UFH), purified and collected by preparative RP-HPLC at minutes 41‒44 (Fr41‒44), displayed statistically higher ACE-I inhibitory activities ranging from 96.91% to 98.06%. A total of 48 novel peptides were identified from these four fractions by LC-MS/MS. A simulated gastrointestinal digestion of the identified peptide sequences was carried out using in silico enzyme cleavage simulation tools, resulting in 86 peptide sequences that were further assessed for their potential activity, toxicity and allergenicity using multiple predictive approaches. All the peptides obtained in this study were predicted to be non-toxic. However, 28 out of the 86 novel peptides released after the in silico gastrointestinal digestion were identified as potential allergens. The potential allergenicity of these peptides should be further explored to comply with the current labelling regulations in formulated food products containing U. lactuca protein hydrolysates.

High resolution fingerprinting of single and double-stranded RNA using ion-pair reverse-phase chromatography

The emergence of new sustainable approaches for insect management using RNA interference (RNAi) based insecticides has created the demand for high throughput analytical techniques to fully characterise and accurately quantify double stranded RNA (dsRNA) prior to downstream RNAi applications. In this study we have developed a method for the rapid characterisation of single stranded and double stranded RNA using high resolution RNase mapping in conjunction with ion-pair reverse-phase chromatography utilising a column with superficially porous particles. The high resolution oligoribonucleotide map provides an important 'fingerprint' for identity testing and bioprocess monitoring. Reproducible RNA mapping chromatograms were generated from replicate analyses. Moreover, this approach was used to provide a method to rapidly distinguish different RNA sequences of the same size, based on differences in the resulting chromatograms. Principal components analysis of the high resolution RNA mapping data enabled us to rapidly compare multiple HPLC chromatograms and distinguish two dsRNA sequences of different size which share 72% sequence homology. We used the high resolution RNase mapping method to rapidly fingerprint biomanufactured dsRNA across a number of different batches. The resulting chromatograms in conjunction with principal components analysis demonstrated high similarity in the dsRNA produced across the different batches highlighting the potential ability of this method to provide information for batch release in a high throughput manner.

A review of analytical methods for the identification and characterization of nano delivery systems in food

Detection and characterization of nano delivery systems is an essential part of understanding the benefits as well as the potential toxicity of these systems in food. This review gives a detailed description of food nano delivery systems based on lipids, proteins, and/or polysaccharides and investigates the current analytical techniques that can be used for the identification and characterization of these delivery systems in food products. The analytical approaches have been subdivided into three groups; separation techniques, imaging techniques, and characterization techniques. The principles of the techniques together with their advantages and drawbacks, and reported applications concerning nano delivery systems, or otherwise related compounds are discussed. The review shows that for a sufficient characterization, the nano delivery systems need to be separated from the food matrix, for which high-performance liquid chromatography or field flow fractionation are the most promising techniques. Subsequently, online photon correlation spectroscopy and mass spectrometry seem to be a convenient combination of techniques to characterize a wide variety of nano delivery systems.

Effects of column length, particle size, gradient length and flow rate on peak capacity of nano-scale liquid chromatography for peptide separations

The effects of the column length, the particle size, the gradient length and the flow rate of a nanoLC system on peptide peak capacity were investigated and compared. Columns packed with 1.7 microm and 3 microm C(18) materials into pieces of 75 microm capillary tubing of various lengths were tested with different gradient lengths and flow rates. While increasing the length of a column packed with the 1.7 microm material helped improve peptide peak capacity at the whole range of the tested gradient lengths (24-432 min), little improvement in peak capacity was observed with the increase of the length of a column packed with the 3 microm material unless a gradient longer than 50 min was carried out. Up to 30% of peak capacity increase was observed when a column's length is doubled, with little reduction in the throughput. In most cases, more than 50% of the increase in peak capacity was obtained with the reduction in the particle size from 3 microm to 1.7 microm. With the same backpressure generated, a shorter 1.7-microm-particle column outperformed a longer column packed with the 3 microm material. In a flow rate range of 100-700 nl/min, increasing the flow rate improved peak capacity for columns packed with 1.7 microm and 3 microm materials.

Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions

Two-dimensional high performance liquid chromatography is a useful tool for proteome analysis, providing a greater peak capacity than single-dimensional LC. The most popular 2D-HPLC approach used today for proteomic research combines strong cation exchange and reversed-phase HPLC. We have evaluated an alternative mode for 2D-HPLC of peptides, employing reversed-phase columns in both separation dimensions. The orthogonality of 2D separation was investigated for selected types of RP stationary phases, ion-pairing agents and mobile phase pH. The pH appears to have the most significant impact on the RP-LC separation selectivity; the greatest orthogonality was achieved for the system with C18 columns using pH 10 in the first and pH 2.6 in the second LC dimension. Separation was performed in off-line mode with partial fraction evaporation. The achievable peak capacity in RP-RP-HPLC and overall performance compares favorably to SCX-RP-HPLC and holds promise for proteomic analysis.

Multiplexed on-column protein digestion and capillary electrophoresis for high-throughput comprehensive peptide mapping

A novel scheme based on multiplexed capillary electrophoresis (CE) has been developed for high-throughput, low-cost and comprehensive peptide mapping. Orthogonal peptide maps of the protein of interest were obtained by using multiple reaction conditions with three different enzymes (trypsin, pepsin, and chymotrypsin), and multiple separation conditions with six zone electrophoresis buffers and two micellar electrokinetic chromatography (MEKC) buffers. Fifteen nanoliters of two protein samples (beta-lactoglobulin A and beta-lactoglobulin B) were separately mixed on-column and digested independently at 37 degrees C for 10 min to produce peptides in a 20-capillary system. The resulting peptides were detected simultaneously at 214 nm by a photodiode array detector. The overall analysis time from reaction to detection was about 40 min.

Fast separation of UV absorbing anions using ion-interaction chromatography

Ion-interaction chromatography on a short (30 x 4.6 mm) 3 microm ODS column has been investigated with the aim of developing fast chromatographic separations of selected inorganic anions. Tetrabutylammonium chloride (TBA-Cl) was used as the ion-interaction reagent in mobile phases that also contained up to 20% methanol. Separations of simple test mixtures of up to eight UV absorbing anions illustrated how excellent efficiencies (>50,000 plates/m) could be obtained under optimized conditions. The use of an optimised mobile phase containing 20 mM TBA-Cl and 20% methanol resulted in the baseline separation of five important anions (iodate, bromate, nitrite, bromide and nitrate) in a separation window of just 28 s, with a shortest total analysis time of 50 s. The method was briefly applied to the rapid analysis of nitrite and nitrate in both a drinking water and a river water sample with a view to future on-line monitoring.

Ruggedness study of HPLC peptide mapping for the identity of a drug compound: a chemometrics approach

A statistically more reliable approach than the traditional visual inspection of peptide maps to identify a drug compound is to generate a set of reference standards from a designed experiment that incorporates many possible factors that affect variation of peptide mapping. In fact, the experiment can be done for a ruggedness study as part of a high-performance liquid chromatography (HPLC) method validation. Once the ruggedness is proved with the study, those articles in the experiment may form a set of reference standards, and future articles can be compared to the set later to prove identity. A quantitative analysis of the ruggedness study can be done using a chemometrics approach, principal component analysis (PCA). The analysis is used to reduce the many channels of peptide maps to a few manageable dimensions. The scores projected onto the reduced dimensions are used to test factor effects of the ruggedness study. As a by-product, the analysis provides visual inspection of the set of articles in the experiment for any outliers and anomalies.

Validation of a peptide mapping method for a therapeutic monoclonal antibody: what could we possibly learn about a method we have run 100 times?

Peptide mapping is a key analytical method for studying the primary structure of proteins. The sensitivity of the peptide map to even the smallest change in the covalent structure of the protein makes it a valuable 'finger-print' for identity testing and process monitoring. We recently conducted a full method validation study of an optimised reverse-phase high-performance liquid chromatography (RP-HPLC) tryptic map of a therapeutic anti-CD4 IgG1 monoclonal antibody. We have used this method routinely for over 1 year to support bioprocess development and test production lots for clinical trials. Herein we summarize the precision and ruggedness of the testing procedure and the main findings with respect to 'coverage of amino acid sequence' and limits-of-detection for various hypothetical structural variants. We also describe, in more detail, two unanticipated insights into the method gained from the validation study. The first of these is a potentially troublesome side-product arising during the reduction/alkylation step. Once the cause of this side-product was identified, it was easily prevented. We also report on subtle changes to the peptide map upon extended storage of the digest in the autosampler. These findings helped us to develop a 'robust' method for implementation in a quality control laboratory.

Cyclohexylamine additives for enhanced peptide separations in reversed phase liquid chromatography

While the choice of stationary phase, organic modifier, and gradient strength can have significant effects on biomolecule separations, mobile phase additives can also have a significant effect on the chromatographic selectivity, recovery, efficiency and resolution. Given the importance of stationary phase coverage, the beneficial, silanol-masking properties of amines, and the potential for selectivity modification through ion-pair interactions, cyclohexylamine was examined as a mobile phase additive and compared with triethylamine and trifluoroacetic acid. Greatly improved separation was possible when cyclohexylamine was used as compared with phosphate buffer, and cyclohexylamine did not require purification before use, while triethylamine required distillation before 'clean' chromatograms were obtained.

Peptide mapping of bovine and chicken cytochrome c by capillary isoelectric focusing with universal concentration gradient imaging

Capillary isoelectric focusing with universal concentration gradient imaging detection was used to separate and detect tryptic peptides from bovine and chicken cytochrome c. For a desalted sample of peptide angiotensin 2, the isoelectric point (pI) measured by the instrument agreed well with the pI calculated from amino acid pK values. For the cytochrome digests, correlations between measured and calculated pI values were imprecise because peak positions shifted slightly from test to test. This problem is thought to be caused by the inefficient desalting process used on the samples, leaving salt residues which caused distortion in the pH gradient during the focusing process. However, this system differentiated between the two cytochrome c's. The concentration gradient imaging detected peptides which contain no tyrosine and no tryptophan amino acids, which a UV absorption detector operating at 280 nm could not. The separation and detection steps took only 5-7 min because no mobilization was necessary after the focusing process.

Reversed-phase high-performance liquid chromatographic tryptic digest peptide map comparisons of monoclonal antibodies to human tumor necrosis factor

An automatic computer technique was used to compare the retention times and ultraviolet spectra of sixty-two peaks in peptide maps of three monoclonal antibodies against human tumor necrosis factor (TNF) and one monoclonal antibody against recombinant factor VIII. The anti-TNF monoclonal, B6, which has an overlapping epitope with the anti-TNF monoclonal, A10G10, had a 90% peak match with A10G10. The anti-TNF monoclonal, A6, with a different epitope to TNF than A10G10, had only a 60% peak match. The A6 match to A10G10 was similar to the 50% peak match of the anti-factor VIII monoclonal with A10G10. The results of this study suggest that peptide mapping can be used as a quantitative characterization technique for comparing monoclonal antibodies.