Microcapillary liquid chromatography/tandem mass spectrometry using alkaline pH mobile phases and positive ion detection

Extending the dynamic range of microcapillary liquid chromatography/tandem mass spectrometry (LC/MS/MS) peptide sequencing methods is essential for extracting new discoveries from proteomic studies. The complexity of global protein digests and in vivo processed peptide repertoires (as isolated from immunologically important HLA complexes) have led to the development of novel separation methods to increase the number of peptides identified by a single analysis. Separation of complex mixtures by multidimensional high-performance liquid chromatography (HPLC) decreases the number of isolated peptides contained in each fraction and increases the likelihood of detecting low abundant peptides in a background of dominant signals. In this study, we have evaluated the use of two dimensions of reversed-phase chromatography for resolving and sequencing naturally processed HLA-A2 presented peptide repertoires. The first dimension of separation was reversed-phase chromatography using the strong ion pairing reagent trifluoroacetic acid (TFA) to ensure the highest efficiency of peptide fractionation. The second dimension of reversed-phase chromatography was online with an electrospray ionization (ESI) ion trap mass spectrometer. Mobile phases used for the second dimension of chromatography were modified with volatile reagents including a contemporary acetate-modified acidic solvent, which was compared with mobile phases prepared with ammonium hydroxide at an alkaline pH. As expected, we demonstrate improved separation of the HLA-A2 presented fractions using the alkaline pH conditions. However, less obvious was the improved peptide signal-to-noise detected for peptide signals by positive ion ESI ion trap mass spectrometric detection, which was attributed to a reduced chemical background when using the alkaline pH mobile phases that allowed the ion trap to fill with the peptide ions until the automatic gain control detected a full trap. The term 'wrong-way-round ionization' has been used to describe intense [M+H](+) ions generated during ESI under strongly basic solutions. Ultimately, a larger number of the HLA-A2 peptide repertoire was sequenced by coupling TFA-modified reversed-phase fractionation with alkaline-modified microcapillary LC/MS/MS analysis of each fraction. In the present report, we compare the two second-dimension approaches and demonstrate the quality of data that was acquired using alkaline pH reversed-phase conditions.     

LC-MS of enzymatic peptic haemoglobin hydrolysate produced at the pilot-plant level

Summary A method is described for the ready identification of any peptide isolated from a complex peptic haemoglobin hydrolysate produced on the pilot-plant scale. A combination of size exclusion and reversed-phase, high-performance liquid chromatography have proved to be a useful strategy for fractionation of such a mixture. This technique enabled pure peptides from the total hydrolysate to be obtained. Amino acid analysis and fast atom bombardment mass spectrometry provided the accurate composition and molecular weight of any isolated peptide. Molecular weights are compared with those deduced from size-exclusion chromatography (SEC) and the usefulness of SEC is discussed. The procedure described in this study will be useful for acquiring a better knowledge of such an hydrolysate and could be extended to other crude protein digests.Presented in part at the 8th International Biotechnology Symposium, July 17–22, 1988, Paris, France.     

Characterization of an apolipoprotein C-III mutant by high-performance liquid chromatography and time-of-flight secondary ion mass spectrometry

Apolipoprotein (apo) C-III isoforms from a patient with a mutant apo C-III and from controls were isolated to homogeneity by isoelectric focusing and subjected to proteolytic digestion. The peptides obtained were separated by reversed-phase high-performance liquid chromatography, and their molecular masses were determined by time-of-flight secondary ion mass spectrometry. Molecular masses of peptides derived from apo C-III0, C-III1 and C-III2 were indistinguishable from control preparations, whereas the mutant apo C-III contained a COOH-terminal, carbohydrate-containing peptide with an abnormal retention time in high-performance liquid chromatography and a molecular mass higher by 291 daltons owing to oversialation at position 74 of the amino acid sequence (apo C-III3).     

Comparative study of capillary electroendosmotic chromatography and electrically assisted gradient nano-liquid chromatography for the separation of peptides

Capillary electroendoendosmotic chromatography (CEC), being a hybrid of high-performance liquid chromatography (HPLC) and capillary electrophoresis, offers considerable changes to enhance column efficiency, speed of analysis and additional selectivity as compared to the parent methods. The analytes are driven by the electroendosmotic flow (EOF) and separated by surface-solute interactions as well as by differences in electromigration. In this paper on the separation of peptides on C18 reversed-phase and mixed-mode (sulphonic acid-n-alkyl) packings in CEC and electrically assisted reversed-phase gradient nano-LC are investigated. It is shown that mixed mode packings generate a higher EOF than reversed-phase packings that is scarcely dependent on the pH of the eluent. Applying a potential in gradient elution reversed-phase nano-LC of peptides shortens the analysis time as compared to separations without a potential. Electrically assisted reversed-phase gradient elution nano-LC is a powerful separation tool for analysis of tryptic digests. Peptides can be successfully resolved in acidic organic mobile phase at pH 2-3 with and without trifluoroacid as ion pairing reagent under isocratic conditions. It is demonstrated that CEC with mixed mode packing and an eluent of pH 2.3 with varying acetonitrile content can be applied to monitor impurities in a synthetic peptide.     

Solution syntheses of two enkephalin-containing peptides, peptide E and dynorphin(1-24), using Nin-(2,4,6-triisopropylphenylsulfonyl)tryptophan

Two enkephalin-containing peptides, peptide E and dynorphin(1-24), were synthesized by conventional solution methods employing a new Trp derivative, Nin-(2,4,6-triisopropylphenylsulfonyl)tryptophan [Trp(Tps)]. All protecting groups employed including the Tps group were removed by treatment with 1 M trifluoromethanesulfonic acid (TFMSA)-thioanisole in trifluoroacetic acid (TFA) at the final steps of these syntheses. Subsequent purifications by Sephadex G-25 chromatography, CM-Biogel A ion exchange chromatography, and reversed-phase high-performance liquid chromatography afforded highly purified samples. Both synthetic peptide E and dynorphin(1-24) exhibited high in vitro opioid activity. The usefulness of this new tryptophan derivative for practical peptide synthesis was established through these syntheses of complex Trp-containing peptides.     

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.     

Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates

This paper describes a procedure for quantitative proteomics that selects peptides containing both cysteine and histidine residues from tryptic digests of cell lysates. Cysteine-containing peptides were selected first by covalent chromatography using thiol disulfide exchange. Following the release of cysteine-containing peptides from the covalent chromatography column with reductive cleavage, histidine-containing peptides were captured by passage through an immobilized metal affinity chromatography column loaded with copper. Quantification was achieved in a four-step process involving (i) differential labeling of control and experimental samples with isotopically differing forms of succinic anhydride, (ii) mixing the two globally labeled samples, (iii) fractionating the labeled peptides by reversed-phase liquid chromatography, and (iv) determining the isotope ratio in individual peptides by mass spectrometry. The results of these studies indicate that by selecting peptides containing both cysteine and histidine, the complexity of protein digests could be substantially reduced. Up-regulated proteins from plasmid bearing Escherichia coli that had been induced with isopropyl beta-thiogalacto-pyranoside were identified and quantified by the global internal standard technology (GIST) described above. Database searches were greatly simplified because the number of possible peptide candidates was reduced more than 95%.     

Reversed-phase high-performance liquid chromatography peptide mapping of bovine somatotropin

Reversed-phase high-performance liquid chromatography peptide mapping techniques have been used to examine the primary structure of bovine somatotropin (bSt) isolated from Escherichia coli modified by recombinant DNA techniques (rbSt) and from bovine pituitary (pbSt). Peptide fragments arising from tryptic digestion of bSt were separated on Baker wide pore C4 or C8 columns with linear gradients (acetonitrile-water with 0.1% trifluoroacetic acid). Major peaks eluted in a consistent order, but significant day-to-day variation in retention times was observed. Isolated peptide fragments were analyzed via acid hydrolysis followed by formation and separation of the phenylthiocarbamyl amino acids. These correspond to expected tryptic fragments.     

Peptide mapping with mobile phases of intermediate pH value using capillary reversed-phase high-performance liquid chromatography/electrospray ionisation tandem mass spectrometry

This investigation describes the separation of tryptic peptides by capillary reversed-phase high-performance liquid chromatography (RP-HPLC) with eluents in the intermediate pH range, followed by in-line electrospray ionisation tandem mass spectrometry (ESI-MS/MS) analysis. For these purposes, gradient elution procedures with an aqueous eluent containing 20 mM ammonium formate, and an increasing content of acetonitrile or methanol, were employed. Compared to the analysis of the same tryptic peptides under low-pH conditions with an ion-pairing reagent, the increase in the pH with the 20 mM ammonium formate mobile phase led to significant changes in both peptide retention to the reversed-phase column and the collision-induced dissociation at the MS/MS stage as a consequence of the changes in the physico-chemical properties of these peptides, such as their overall charge, polarity and relative hydrophobicity. Thus, improved selectivity for the peptide separation and favourable tandem mass spectrometry analysis could be obtained with eluents in this intermediate pH range. The number of tryptic peptides identified by the new approach for the proteins investigated were significantly higher than that obtained by the conventional low-pH methods. Moreover, analysis of protein digests at very low concentrations was also performed under both acidic and intermediate pH conditions and similar improvements in selectivity and MS/MS detection limits were observed, i.e. identification of more distinct peptides and higher sequence coverage of the protein was obtained when eluents of intermediate pH were employed. This study therefore highlights the potential of conducting peptide mapping in the intermediate pH range to achieve more reliable and sensitive protein identifications with capillary RP-HPLC–ESI-MS/MS.     

Identification of food-derived bioactive peptides in blood and other biological samples

Recent studies have demonstrated the presence of food-derived peptides in human blood after ingestion of enzymatic hydrolysates of food proteins, while most peptides in food are degraded into amino acids during digestion and absorption. To capture and clarify the food-derived peptides in blood, solid-phase extraction (SPE) using a mini-spin column packed with a strong cation exchanger was developed. This technique allows the use of a nonvolatile acid such as trichloroacetic acid, a strong protein denaturant, for the deproteinizing procedure. To improve resolution of hydrophilic peptide and increase specificity and sensitivity in the detection of peptide by reversed-phase high-performance liquid chromatography (RP-HPLC) after subfractionation by size-exclusion chromatography (SEC), peptides are derivatized with phenyl isothiocyanate. The resultant phenyl thiocarbamyl (PTC)-peptides can be resolved with high resolution and sensitivity by RP-HPLC. By comparing chromatograms of PTC derivatives from blood before and after ingestion of a peptide sample, food-derived peptide can be detected. The isolated PTC-peptide can be applied to a peptide sequencer based on the Edman degradation reaction.     

Protein proteolysis and the multi-dimensional electrochromatographic separation of histidine-containing peptide fragments on a chip

This paper reports a system for three-dimensional electrochromatography in a chip format. The steps involved included trypsin digestion, copper(II)-immobilized metal affinity chromatography [Cu(II)-IMAC] selection of histidine-containing peptides, and reversed-phase capillary electrochromatography of the selected peptides. Trypsin digestion and affinity chromatography were achieved in particle-based columns with a microfabricated frit whereas reversed-phase separations were executed on a column of collocated monolithic support structures. Column frits were designed to maintain constant cross sectional area and path length in all channels and to retain particles down to a size of 3 microm. Cu(II)-IMAC selection of histidine-containing peptides from standard peptide mixtures and protein digests followed by reversed-phase chromatography of the selected peptides was demonstrated in the electrochromatography mode. The possibility to run a comprehensive proteomic analysis by combining trypsin digestion, affinity selection, and a reversed-phase separation on chips was shown using fluorescein isothiocyanate-labeled bovine serum albumin as an example.     

Comparison of reversed-phase and weak anion-exchange high-performance liquid chromatographic methods for peptide separations

Weak anion-exchange and reversed-phase high-performance liquid chromatographic methods for peptide separations were compared using a tryptic digest of "rat small myelin basic protein". In these experiments, a number of tryptic peptides that were not resolved on the reversed-phase column could be separated on the weak anion-exchange column, and in other instances, as might be expected, reversed-phase chromatography provided better resolution of certain peptides than did the weak anion-exchange method. The results obtained strongly suggest that the combined use of these two methods of separation, which utilize different selectivities, can provide an excellent improvement in resolving power for a number of peptide separations.     

高活性燕麦蛋白源ACE抑制肽的制备、纯化及结构鉴定

利用胰蛋白酶水解燕麦蛋白制备了高血管紧张素转化酶(Angiotensin I-Converting Enzyme, ACE)抑制活性的燕麦蛋白酶解物, 分别采用离子交换色谱、凝胶过滤色谱和反相高效液相色谱等分离手段从酶解物中分离出一种新的强活性ACE抑制肽, 其IC50值为77.3 μmol/L; 通过基质辅助激光解析电离飞行时间串联质谱对其进行结构鉴定, 其氨基酸序列为Glu-Gly-Gly-Tyr-Arg.     

Isolation from fetal bovine serum of a peptide similar to the alpha chain of thrombin by reversed-phase high-performance liquid chromatography

During the preparation of erythrotropin from fetal bovine serum, a group of peptides co-eluted with this erythroid cell stimulating factor on semi-preparative reversed-phase high-performance liquid chromatography. They could be subsequently separated by a combination of reversed-phase high-performance liquid chromatography in the presence of heptafluorobutyric acid as ion-pairing reagent and gel permeation high-performance liquid chromatography. One of these peptides has been extensively purified. Partial amino acid sequence analysis indicated that fourteen of the seventeen N-terminal amino acids are identical with the N-terminal sequence of the alpha chain of bovine thrombin. The same isolation procedure could be useful for the identification of other major peptides of fetal bovine serum.     

Protein identification by in-gel digestion, high-performance liquid chromatography, and mass spectrometry: Peptide analysis by complementary ionization techniques

A biologically active protein fraction was isolated from rabbit intestine, purified by one-dimensional SDS-PAGE and stained with Coomassie Brilliant Blue. A predominant band of approximately 110-130 kDa was excised and digested in-gel with trypsin. The resulting peptides were extracted then separated by microbore reversed-phase high-performance liquid chromatography (HPLC). Mass spectrometric data from one HPLC fraction obtained by two different ionization techniques proved to be complementary. Matrix-assisted laser desorption/ionization (MALDI) showed nine peptide masses, which by post source decay analysis and database searching were attributed to two proteins. Nanoflow electrospray analysis performed on a hybrid tandem mass spectrometer of quadrupole-quadrupole-orthogonal acceleration time-of-flight (QqTOF) geometry detected six additional peptide components. On the basis of the additional peptides and superior quality collision-induced dissociation spectra typical of this instrument type, two further proteins were identified. The resolution afforded by the QqTOF instrument permitted charge state determination for the fragment ions while preserving the high detection sensitivity that was essential in obtaining the composition of this mixture of proteins.     

用2D Micro-HPLC/MS分析六种蛋白质混合物的胰蛋白酶解多肽产物

采用2D Micro-HPLC系统,用MS对六种蛋白质的胰蛋白酶解多肽产物进行了分析,实现了蛋白质的高灵敏度、高分离度的检测。结合离子交换色谱法和反相毛细管色谱法,利用六个捕集柱和脱盐系统,可对各种分离条件进行优化。因此,可以实现对多种痕量酶解多肽的分离检测。该系统是痕量蛋白质和未知蛋白质检测的有力工具,结合高性能质谱仪,可以达到非常高的灵敏度。     

Evaluation of charge derivatization of a proteolytic protein digest for improved mass spectrometric analysis: de novo sequencing by matrix-assisted laser desorption/ionization post-source decay mass spectrometry.

A simple mass spectrometric method to sequence a recombinant phosphoenolpyruvate carboxykinase of known structure and a novel variant of unknown structure isolated from Anaerobiospirillum succiniciproducens and Actinobacillus succinogenes 130Z, respectively, was evaluated. The proteolytic digests of the proteins were each chemically derivatized at the N-terminus by addition of a tris(trimethoxyphenyl)phosphoniumacetyl (TMPP(+)-Ac) group to produce peptides with a fixed positive charge. The derivatized digests were then partially separated by reversed-phase high-performance liquid chromatography. The fractions collected were subjected to matrix-assisted laser desorption/ionization post-source decay (MALDI/PSD) mass spectrometric analysis. The resulting spectra are sufficiently simple to allow the sequence to be read directly without extensive interpretation. This is in contrast to spectra of underivatized peptides obtained by MALDI/PSD or conventional tandem mass spectrometry, where full sequence interpretation can be challenging. Aided with a set of very simple established rules, it was shown that the sequence of TMPP(+)-Ac derivatives can be derived strictly from predictable fragment ion series. In most cases, this is sufficient to determine extensive, unambiguous, peptide sequences de novo. The partial sequence (35%) of the unknown phosphoenolpyruvate carboxykinase from Actinobacillus succinogenes 130Z was obtained entirely by the mass spectrometric method evaluated here, which provided the basis for evaluating homology and for the design of oligonucleotide probes for cloning the corresponding gene.     

Identification and assay of phosphoserine and tyrosine-O-sulphate in fibrinopeptides by reversed-phase high-performance liquid chromatography

A procedure utilizing reversed-phase high-performance liquid chromatography (HPLC) is described for the identification and quantitation of individual phosphorylated and sulphated fibrinopeptides present in fibrin clot supernatants. Fibrinopeptides from human, rabbit and canine fibrinogens, which have different structures and degrees of phosphorylation and sulphation, were used to demonstrate the applicability of these methods. The procedure relies on the increased peptide hydrophobicity following removal of highly charged phosphate or sulphate groups. Dephosphorylated or desulphated peptides are thus more strongly retained on the reversed-phase HPLC column and are eluted later than their corresponding phosphorylated or sulphated peptide counterparts. Dephosphorylation is achieved by treatment of fibrinopeptide-containing clot supernatants with alkaline phosphatase. Phosphorylated peptides are characterized by an increased retention time resulting from loss of phosphate, whereas non-phosphorylated peptides remain unaffected. Similarly, a prolongation of the peptide retention time resulting from desulphation by mild acid hydrolysis serves to verify sulphation of a peptide.     

Piperazines for peptide carboxyl group derivatization: effect of derivatization reagents and properties of peptides on signal enhancement in matrix-assisted laser desorption/ionization mass spectrometry

Piperazine-based derivatives, including 1-(2-pyridyl)piperazine (2-PP), 1-(2-pyrimidyl)piperazine (2-PMP), 1-(4-pyridyl)piperazine (4-PP), and 1-(1-methyl-4-piperidinyl)piperazine (M-PP), were used for the derivatization of carboxyl groups on peptides with 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC) and 1-hydroxy-7-azabenzotriazole (HOAt) as coupling reagents, and trifluoroacetic acid (TFA) as activator. Taking synthetic peptides RVYVHPI (RI-7) and APGDRIYVHPF (AF-11) as samples, the yields of derivatized peptides by 2-PP, 2-PMP and 4-PP were higher than 94%. The effect of piperazine derivatives on the signals of tryptic digests of α-transferrin and bovine serum albumin (BSA) was investigated, and it was found that peptides derivatized by 2-PP and 2-PMP exhibited obviously improved ionization efficiency. Furthermore, comparison of identified peptides before and after derivatization showed that peptides with low molecular weight (MW) and high pI value were preferably detected after derivatization. In addition, after derivatization with 2-PP and 2-PMP, protein myelin basic protein S, 20 kDa protein, and histone H were confidently identified from the tryptic digests of two fractions of rat brain protein separated by reversed-phase high-performance liquid chromatography (HPLC), indicating the potential application of 2-PP and 2-PMP for the highly sensitive determination of peptides in comprehensive proteome analysis.     

Use of narrow-bore high-performance liquid chromatography for microanalysis of protein structure

We report here systematic approaches to microanalysis of protein structures using narrow-bone high-performance liquid chromatography of protein, peptide and derivatized [phenylthiocarbamyl (PTC-) and phenylthiohydantoinyl (PTH-)] amino acids. The utilization of columns with small diameters (2 mm or less) has improved resolution and sensitivity and enabled protein structure analysis at the low pmol level. Preparative isolation of proteins and peptides of pmol quantity is achieved and separation and identification of PTC- and PTH-amino acids can be routinized at the low pmol to subpmol level. The use of diode-array detection enables simultaneous multiple-wavelength monitoring and spectral retreat, which greatly enhances flexibility and usefulness of the present methods. In combination with protein microsequencing techniques, these narrow-bore high-performance liquid chromatographic procedures can facilitate structural analysis of minutely available proteins of biochemical and physiological significance.