Multidimensional nano-HPLC coupled with tandem mass spectrometry for analyzing biotinylated proteins

Multidimensional high-performance liquid chromatography (HPLC) is a key method in shotgun proteomics approaches for analyzing highly complex protein mixtures by complementary chromatographic separation principles. Here, we describe an integrated 3D-nano-HPLC/nano-electrospray ionization quadrupole time-of-flight mass spectrometry system that allows an enzymatic digestion of proteins followed by an enrichment and subsequent separation of the created peptide mixtures. The online 3D-nano-HPLC system is composed of a monolithic trypsin reactor in the first dimension, a monolithic affinity column with immobilized monomeric avidin in the second dimension, and a reversed phase C18 HPLC-Chip in the third dimension that is coupled to a nano-ESI-Q-TOF mass spectrometer. The 3D-LC/MS setup is exemplified for the identification of biotinylated proteins from a simple protein mixture. Additionally, we describe an online 2D-nano-HPLC/nano-ESI-LTQ-Orbitrap-MS/MS setup for the enrichment, separation, and identification of cross-linked, biotinylated species from chemical cross-linking of cytochrome c and a calmodulin/peptide complex using a novel trifunctional cross-linker with two amine-reactive groups and a biotin label.

Structural stability–chromatographic retention relationship on exenatide diastereomer separation

In this study, the relationship of the structural stability of peptide diastereomers in elution solvents and their retention behaviors in reversed-phase chromatography (RPC) was examined to provide guidance on the solvent selection for a better separation of peptide diastereomers. We investigated the chromatographic retention behaviors of exenatide, a peptide drug for the treatment of type II diabetes mellitus and its three diastereomers using RPC and implicit molecular dynamics (MD) simulation analysis. Three diastereomers involved in the single serine residue mutation of d-form at the 11th, 32nd, and 39th residues were investigated in this study. Results show that the order of the solution structural stability of exenatide and its diastereomers is consistent with their retention order by 36?% acetonitrile/water elution. The sample loading solvent also affects the retention behaviors of exenatide peptide diastereomers in RPC column. Furthermore, a larger solution conformation energy difference of the critical pair of exenatide and its diastereomer (d-Ser39) at the elution solvent of 32?% tetrahydrofuran/water were obtained by MD simulation, and baseline separation was proved experimentally. In summary, we demonstrated that the solution structural stability–chromatographic retention relationship could be a powerful tool for elution solvent selection in peptide chromatographic purification, especially valuable for the separation of critical pair of diastereomers.

Improved chemical composition separation of ethylene–propylene random copolymers by high-temperature solvent gradient interaction chromatography

High-temperature solvent gradient interaction chromatography (HT-SGIC) is a fast and efficient fractionation technique for the chemical composition analysis of olefin copolymers. The separation of ethylene–propylene random copolymers (EPRs) was achieved on a graphitic stationary phase, Hypercarb, at 160 °C by using linear solvent gradient elution from 1-decanol to 1,2,4-trichlorobenzene (TCB). In the present work, the solvent gradient profile was modified to improve the chromatographic separation of EPRs. With the aim to obtain a better resolution in separation, a slow increase in the volume fraction of TCB was applied. This allowed for a relatively large retention region for linear polyethylene (PE) chains on the column; thereby, a broader elution volume zone between the start of the gradient and the PE elution was achieved. The efficiency of this new gradient profile was demonstrated by analysing two fully amorphous EPR samples. Clear differences in the chemical composition of these EPR samples with similar ethylene contents have been proven by using this modified solvent gradient. The comprehensive chemical composition and microstructure analysis of the SGIC-separated fractions by FTIR revealed that ethylene/propylene (EP) copolymer chains were eluted according to their ethylene/propylene contents and E or P sequence lengths, even though they are distributed in a random manner. These results showed that the solvent composition is an important factor to affect the interactive adsorption or desorption behaviour of EP chains on Hypercarb. In this way, for the first time, the determination of the complex composition and chain structure of EPR samples was achieved within short analysis time, which is not possible till now using other fractionation techniques reported.

Multisyringe ion chromatography with chemiluminescence detection for the determination of oxalate in beer and urine samples

The first multisyringe-based low-pressure ion chromatographic method is presented. It is based on the use of short surfactant coated octadecyl-silica monolithic columns. As a first application, we have determined oxalate in beer and human urine via post-column chemiluminescence detection. Oxalate is separated from the sample matrix in the monolithic column by precise programmable fluid handling, and then detected by reaction with on-line generated tris(2,2??-bipyridyl)ruthenium(III). Column coating, un-coating, ion chromatography and chemiluminescence detection are quickly performed by using a simple low-pressure multi-burette. The factors influencing the separation of oxalate and its subsequent detection, including the column coating with surfactants and its stability have been studied. The chromatographic behavior of the oxalate in presence of potentially interfering species also was assessed. The method has limits of detection and quantification of 0.025 and 0.035?mg?L^?1, respectively, a relative standard deviation of 3.1% (for 10 consecutive measurements without column re-coating) and a throughput of 48?h^?1. The results obtained with real samples were validated by using an enzymatic spectrophotometric test. The method is critically compared to recent methods for the determination of oxalate.

Continuous vs. segmented second-dimension system gradients for comprehensive two-dimensional liquid chromatography of sugarcane (Saccharum spp.)

A comprehensive two-dimensional liquid chromatography system in combination with photodiode array and mass spectrometry detection was developed for analysis of polyphenols in sugarcane (Saccharum spp.) leaf extracts. To achieve this, a micro cyano column and a partially porous octodecylsilica column were used in the first and the second dimension, respectively. The choice of the cyano column over other reversed-phase columns tested for the first-dimension separation was due to its lower correlation selectivity with respect to the octodecylsilica column, which was used for the second-dimension separation. Even when reversed-phase mode was used in both dimensions, a satisfactory degree of orthogonality was achieved by use of different gradient elution modes in the second dimension. By means of the setup investigated, 38 polyphenolic compounds were detected, and among them 24 were positively identified by means of complementary data from photodiode array and mass spectrometry detection and an in-house database. This is the first time such a powerful analytical technique has been used for polyphenolic characterization of sugarcane extracts.

Quinolinium ionic liquid-modified silica as a novel stationary phase for high-performance liquid chromatography

A novel stationary phase based on quinolinium ionic liquid-modified silica was prepared and evaluated for high-performance liquid chromatography. The stationary phase was investigated via normal-phase (NP), reversed-phase (RP), and anion-exchange (AE) chromatographic modes, respectively. Polycyclic aromatic hydrocarbons, phthalates, parabens, phenols, anilines, and inorganic anions were used as model analytes in chromatographic separation. Using the newly established column, organic compounds were separated successfully by both NP and RP modes, and inorganic anions were also separated completely by AE mode. The obtained results indicated that the stationary phase could be applied in different chromatographic modes, with multiple-interaction mechanism including van der Waals forces (dipole–dipole, dipole–induced dipole interactions), hydrophobic, π–π stacking, electrostatic forces, hydrogen bonding, anion-exchange interactions, and so on. The column packed with the stationary phase was applied to analyze phthalates and parabens in hexane extracts of plastics. Tap water and bottled water were also analyzed by the column, and nitrate was detected as 20.1 and 13.8 mg L^?1, respectively. The results illustrated that the stationary phase was potential in practical applications.

Ion exchange chromatographic separation and isolation of oligosaccharides of intact low-molecular-weight heparin for the determination of their anticoagulant and anti-inflammatory properties

It is well known that enoxaparin, a widely used anticoagulant and low-molecular-weight heparin containing a large number of oligosaccharides, possesses anti-inflammatory activity. Whilst enoxaparin has shown promising results in various inflammatory disorders, some of its oligosaccharides have anti-inflammatory properties and others increase the risk of bleeding due to their anticoagulant effects. The aim of this study was to develop an effective ion exchange chromatographic (IC) technique which allows the separation, isolation and, consequently, the identification of different oligosaccharides of enoxaparin with or without anticoagulant activity. The developed method utilises a semi-preparative CarboPac PA100 (9?×?250 mm) ion exchange column with sodium chloride gradient elution and UV detection at 232 nm. The method successfully resolved enoxaparin into more than 30 different peaks. IC-derived oligosaccharides with high, moderate, low or no anticoagulant activity were identified using an anti-factor Xa assay. The anti-inflammatory activity of selected oligosaccharides was investigated using the Griess assay. Using this technique, the oligosaccharides of enoxaparin with low or no anticoagulant activity, whilst exhibiting significant anti-inflammatory activity, could be fractionated. This technique can provide a platform to identify the oligosaccharides which are devoid of significant anticoagulant activity and are responsible for the therapeutic effects of enoxaparin that have been observed in various inflammatory conditions.

Further application of size-exclusion chromatography combined with small-angle X-ray scattering optics for characterization of biological macromolecules

Size-exclusion chromatography (gel filtration chromatography or gel permeation chromatography) in conjunction with online synchrotron radiation solution small-angle X-ray scattering optics, absorbance, and/or refractive index detectors was further assessed by application of biological macromolecules, such as the hollow sphere protein complex, apoferritin, and a linear polysaccharide, pullulan. The net X-ray scattering patterns of the eluted 24-mer molecule of apoferritin showed the specific character for the hollow spherical shape. The chromatographic (time-resolved) X-ray scattering data of the linear polysaccharide pullulan revealed the flexible chain structure during the chromatographic separation in an aqueous solution. These further applications demonstrated that the present measurement technique will be useful for not only the determination of the radius of gyration value of less than about 10?nm and molecular weight below several hundred thousand but also for the structural characterization of the various macromolecules during the chromatography.

Optimization in multidimensional gas chromatography applying quantitative analysis via a stable isotope dilution assay

Trace level analyses in complex matrices benefit from heart-cut multidimensional gas chromatographic (MDGC) separations and quantification via a stable isotope dilution assay. Minimization of the potential transfer of co-eluting matrix compounds from the first dimension (¹D) separation into the second dimension separation requests narrow cut-windows. Knowledge about the nature of the isotope effect in the separation of labeled and unlabeled compounds allows choosing conditions resulting in at best a co-elution situation in the ¹D separation. Since the isotope effect strongly depends on the interactions of the analytes with the stationary phase, an appropriate separation column polarity is mandatory for an isotopic co-elution. With 3-alkyl-2-methoxypyrazines and an ionic liquid stationary phase as an example, optimization of the MDGC method is demonstrated and critical aspects of narrow cut-window definition are discussed.

Energy Dependence of HCD on Peptide Fragmentation: Stepped Collisional Energy Finds the Sweet Spot

An understanding of the process of peptide fragmentation and what parameters are best to obtain the most useful information is important. This is especially true for large-scale proteomics where data collection and data analysis are most often automated, and manual interpretation of spectra is rare because of the vast amounts of data generated. We show herein that collisional cell peptide fragmentation, in this case higher collisional dissociation (HCD) in the Q Exactive, is significantly affected by the normalized energy applied. Both peptide sequence and energy applied determine what ion fragments are observed. However, by applying a stepped normalized collisional energy scheme and combining ions from low, medium, and high collision energies, we are able to increase the diversity of fragmentation ions generated. Application of stepped collision energy to HEK293T lysate demonstrated a minimal effect on peptide and protein identification in a large-scale proteomics dataset, but improved phospho site localization through increased sequence coverage. Stepped HCD is also beneficial for tandem mass tagged (TMT) experiments, increasing intensity of TMT reporters used for quantitation without adversely effecting peptide identification.

Implementation of Statistical Process Control for Proteomic Experiments Via LC MS/MS

Statistical process control (SPC) is a robust set of tools that aids in the visualization, detection, and identification of assignable causes of variation in any process that creates products, services, or information. A tool has been developed termed Statistical Process Control in Proteomics (SProCoP) which implements aspects of SPC (e.g., control charts and Pareto analysis) into the Skyline proteomics software. It monitors five quality control metrics in a shotgun or targeted proteomic workflow. None of these metrics require peptide identification. The source code, written in the R statistical language, runs directly from the Skyline interface, which supports the use of raw data files from several of the mass spectrometry vendors. It provides real time evaluation of the chromatographic performance (e.g., retention time reproducibility, peak asymmetry, and resolution), and mass spectrometric performance (targeted peptide ion intensity and mass measurement accuracy for high resolving power instruments) via control charts. Thresholds are experiment- and instrument-specific and are determined empirically from user-defined quality control standards that enable the separation of random noise and systematic error. Finally, Pareto analysis provides a summary of performance metrics and guides the user to metrics with high variance. The utility of these charts to evaluate proteomic experiments is illustrated in two case studies.

Simultaneous serum desalting and total protein determination by macroporous reversed-phase chromatography

Macroporous reversed-phase (mRP) chromatography was successfully used to develop an accurate and precise method for total protein in serum. The limits of detection (0.83 μg, LOD) and quantification (2.51 μg, LOQ) for the mRP method are comparable with those of the widely used micro BCA protein assay. The mRP method can be used to determine the total protein concentration across a wide dynamic range by detecting chromatographic peaks at 215 nm and 280 nm. The method has the added advantage of desalting and denaturing proteins, leading to more complete digestion by trypsin and to better LC–MS–MS identification in shotgun proteomics experiments.

Automated clean-up, separation and detection of polycyclic aromatic hydrocarbons in particulate matter extracts from urban dust and diesel standard reference materials using a 2D-LC/2D-GC system

A multidimensional, on-line coupled liquid chromatographic/gas chromatographic system was developed for the quantification of polycyclic aromatic hydrocarbons (PAHs). A two-dimensional liquid chromatographic system (2D-liquid chromatography (LC)), with three columns having different selectivities, was connected on-line to a two-dimensional gas chromatographic system (2D-gas chromatography (GC)). Samples were cleaned up by combining normal elution and column back-flush of the LC columns to selectively remove matrix constituents and isolate well-defined, PAH enriched fractions. Using this system, the sequential removal of polar, mono/diaromatic, olefinic and alkane compounds from crude extracts was achieved. The LC/GC coupling was performed using a fused silica transfer line into a programmable temperature vaporizer (PTV) GC injector. Using the PTV in the solvent vent mode, excess solvent was removed and the enriched PAH sample extract was injected into the GC. The 2D-GC setup consisted of two capillary columns with different stationary phase selectivities. Heart-cutting of selected PAH compounds in the first GC column (first dimension) and transfer of these to the second GC column (second dimension) increased the baseline resolutions of closely eluting PAHs. The on-line system was validated using the standard reference materials SRM 1649a (urban dust) and SRM 1975 (diesel particulate extract). The PAH concentrations measured were comparable to the certified values and the fully automated LC/GC system performed the clean-up, separation and detection of PAHs in 16 extracts in less than 24 h. The multidimensional, on-line 2D-LC/2D-GC system eliminated manual handling of the sample extracts and minimised the risk of sample loss and contamination, while increasing accuracy and precision.

Chemometric evaluation of the column classification system during the pharmaceutical analysis of lamotrigine and its related substances

This paper investigates the performance of a column classification system developed at the Katholieke Universiteit Leuven applied to pharmaceutical chromatographic analyses. The liquid chromatography assay of lamotrigine and related compounds was carried out according to the method prescribed in the European Pharmacopoeia monograph, using 28 brands of stationary phases. A ranking was built based on the F _KUL value calculated against the selected reference column, then compared with the column test performance established for the stationary phases studied. Therefore, the system suitability test prescribed by the European Pharmacopoeia in order to distinguish between suitable or unsuitable columns for this analysis was evaluated. Moreover, it was examined whether the classes of the stationary phases, determined using test parameter results, contain either suitable or unsuitable supports for the lamotrigine separation. This assay was performed using chemometric a technique, namely factor analysis.

A 3-D open-framework material with intrinsic chiral topology used as a stationary phase in gas chromatography

Compared with liquid chromatography and capillary electrophoresis, the diversity of gas chromatography chiral stationary phases is rather limited. Here, we report the fabrication of Co(d-Cam)_1/2(bdc)_1/2(tmdpy) (d-Cam?=?d-camphoric acid; bdc?=?1,4-benzenedicarboxylate; tmdpy?=?4,4′-trimethylenedipyridine)-coated open tubular columns for high-resolution gas chromatographic separation of compounds. The Co(d-Cam)_1/2(bdc)_1/2(tmdpy) compound possesses a 3-D framework containing enantiopure building blocks embedded in intrinsically chiral topological nets. In this study, two fused-silica open tubular columns with different inner diameters and lengths, including column A (30 m?×?530 μm i.d.) and column B (2 m?×?75 μm i.d.), were prepared by a dynamic coating method using Co-(d-Cam)_1/2(bdc)_1/2(tmdpy) as the stationary phase. The chromatographic properties of the two columns were investigated using n-dodecane as the test compound at 120 °C. The number of theoretical plates (plates/m) of the two metal–organic framework columns was 1,450 and 3,100, respectively. The separation properties were evaluated using racemates, isomers, alkanes, alcohols, and Grob's test mixture. The limit of detection and limit of quantification were found to be 0.125 and 0.417 ng for citronellal enantiomers, respectively. Repeatability (n?=?6) showed lower than 0.25 % relative standard deviation (RSD) for retention times and lower than 2.2 % RSD for corrected peak areas. The experimental results showed that the stationary phase has excellent selectivity and also possesses good recognition ability toward these organic compounds, especially chiral compounds.

Direct high-performance liquid chromatographic enantioseparation of free α-, β- and γ-aminophosphonic acids employing cinchona-based chiral zwitterionic ion exchangers

We report a chiral high-performance liquid chromatographic enantioseparation method for free α-aminophosphonic, β-aminophosphonic, and γ-aminophosphonic acids, aminohydroxyphosphonic acids, and aromatic aminophosphinic acids with different substitution patterns. Enantioseparation of these synthons was achieved by means of high-performance liquid chromatography on CHIRALPAK ZWIX(+) and ZWIX(-) (cinchona-based chiral zwitterionic ion exchangers) under polar organic chromatographic elution conditions. Mobile phase characteristics such as acid-to-base ratio, type of counterion, and solvent composition were systematically varied in order to investigate their effect on the separation performance and to achieve optimal separation conditions for the set of analytes. Under the optimized conditions, 32 of 37 racemic aminophosphonic acids studied reached baseline separation when we employed a single generic mass-spectrometry-compatible mobile phase, with reversal of the elution order when we used (+) and (-) versions of the chiral stationary phase.

Comprehensive two-dimensional liquid chromatography coupled to the ABTS radical scavenging assay: a powerful method for the analysis of phenolic antioxidants

The on-line combination of comprehensive two-dimensional liquid chromatography (LC?×?LC) with the 2,2′-azino-bis(3-ethylbenzothiazoline)-6 sulphonic acid (ABTS) radical scavenging assay was investigated as a powerful method to determine the free radical scavenging activities of individual phenolics in natural products. The combination of hydrophilic interaction chromatography (HILIC) separation according to polarity and reversed-phase liquid chromatography (RP-LC) separation according to hydrophobicity is shown to provide much higher resolving power than one-dimensional separations, which, combined with on-line ABTS detection, allows the detailed characterisation of antioxidants in complex samples. Careful optimisation of the ABTS reaction conditions was required to maintain the chromatographic separation in the antioxidant detection process. Both on-line and off-line HILIC?×?RP-LC–ABTS methods were developed, with the former offering higher throughput and the latter higher resolution. Even for the fast analyses used in the second dimension of on-line HILIC?×?RP-LC, good performance for the ABTS assay was obtained. The combination of LC?×?LC separation with an on-line radical scavenging assay increases the likelihood of identifying individual radical scavenging species compared to conventional LC–ABTS assays. The applicability of the approach was demonstrated for cocoa, red grape seed and green tea phenolics.

Highly hydrophilic and nonionic poly(2-vinyloxazoline)-grafted silica: a novel organic phase for high-selectivity hydrophilic interaction chromatography

A new hydrophilic and nonionic poly(2-vinyloxazoline)-grafted silica (Sil-VOX _n ) phase was synthesized and applied for the separation of nucleosides and nucleobases in hydrophilic interaction chromatography (HILIC). Polymerization and immobilization onto silica were confirmed by using characterization techniques including ¹H NMR spectroscopy, elemental analysis, and diffuse reflectance infrared Fourier transform spectroscopy. The hydrophilicity or wettability of Sil-VOX _n was observed by measuring the contact angle (59.9°). The chromatographic results were compared with those obtained with a conventional HILIC silica column. The Sil-VOX _n phase showed much better separation of polar test analytes than the silica column, and the elution order was different. Differences in selectivity between these two columns indicate that the stationary phase cannot function merely as an inert support for a water layer into which the solutes are partitioned from the bulk mobile phase. To elucidate the interaction mechanism, the separation of dihydroxybenzene isomers was performed on both columns in normal-phase liquid chromatography. Sil-VOX _n was very sensitive to the dipole moments of the positional isomers of polycyclic aromatic compounds in normal-phase liquid chromatography. The interaction mechanism for Sil-VOX _n in HILIC separation is also described.

Separation of dansylated 17β-estradiol, 17α-estradiol, and estrone on a single HPLC column for simultaneous quantitation by LC–MS/MS

We show here that baseline separation of dansylated estrone, 17β-estradiol, and 17α-estradiol can be done, contrary to previous reports, within a short run time on a single RP-LC analytical column packed with particles bonded with phenyl-hexyl stationary phase. The chromatographic method coupled with isotope dilution tandem MS offers a simple assay enabling the simultaneous analysis of these analytes. The method employs ¹³C-labeled estrogens as internal standards to eliminate potential matrix effects arising from the use of deuterated estrogens. The assay also offers adequate accuracy and sensitivity to be useful for biological samples. The practical applicability of the validated method is demonstrated by the quantitative analyses of in vivo samples obtained from rats treated with Premarin®.

A high-throughput three-capillary noise-cancelling viscometer for chromatographic systems

This paper describes an analytical three-capillary viscometer detector that eliminates the traditional viscometer ??hold-up?? volume (commonly found in four-capillary designs) while maintaining cancellation of short-term pump noise and long-term baseline drift of temperature and solvent flow rate that are inherent in chromatography systems. This improvement allows a staggered sample injection approach in chromatography, yielding a significant increase in sample throughput by cutting down the chromatographic run time. It also provides a more robust design as it does not require capillary rebalancing, complex purging, flushing or changing the hold-up volume to accommodate long-term chromatographic use.