Identification of proteins by combination of size-exclusion chromatography with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and comparison of some desalting procedures for both intact proteins and their tryptic digests

Recent advances in top-down proteome sample processing ahead of MS analysis

Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.

Comparative proteomic analysis of oil palm (Elaeis guineensis Jacq.) during early fruit development

To gain insights on protein changes in fruit setting and growth in oil palm, a comparative proteomic approach was undertaken to study proteome changes during its early development. The variations in the proteome at five early developmental stages were investigated via a gel-based proteomic technique. A total of 129 variant proteins were determined using mass spectrometric analysis, resulting in 80 identifications. The majority of the identified protein species were classified as energy and metabolism, stress response/defence and cell structure during early oil palm development representing potential candidates for the control of final fruit size and composition. Seven prominent protein species were then characterised using real-time polymerase chain reaction to validate the mRNA expression against the protein abundant profiles. Transcript and protein profiles were parallel across the developmental stages, but divergent expression was observed in one protein spot, indicative of possible post-transcriptional events. Our results revealed protein changes in early oil palm fruit development provide valuable information in the understanding of fruit growth and metabolism during early stages that may contribute towards improving agronomic traits. BIOLOGICAL SIGNIFICANCE: Two-dimensional gel electrophoresis coupled with mass spectrometry approach was used in this study to identify differentially expressed proteins during early oil palm fruit development. A total of 80 protein spots with significant change in abundance were successfully identified and selected genes were analysed using real time PCR to validate their expression. The dynamic changes in oil palm fruit proteome during early development were mostly active in primary and energy metabolism, stress responses, cell structure and protein metabolism. This study reveals the physiological processes during early oil palm fruit development and provides a reference proteome for further improvements in fruit quality traits.

Influence of honeybee sting on peptidome profile in human serum

The aim of this study was to explore the serum peptide profiles from honeybee stung and non-stung individuals. Two groups of serum samples obtained from 27 beekeepers were included in our study. The first group of samples was collected within 3 h after a bee sting (stung beekeepers), and the samples were collected from the same person a second time after at least six weeks after the last bee sting (non-stung beekeepers). Peptide profile spectra were determined using MALDI-TOF mass spectrometry combined with Omix, ZipTips and magnetic beads based on weak-cation exchange (MB-WCX) enrichment strategies in the mass range of 1–10 kDa. The samples were classified, and discriminative models were established by using the quick classifier, genetic algorithm and supervised neural network algorithms. All of the statistical algorithms used in this study allow distinguishing analyzed groups with high statistical significance, which confirms the influence of honeybee sting on the serum peptidome profile. The results of this study may broaden the understanding of the human organism’s response to honeybee venom. Due to the fact that our pilot study was carried out on relatively small datasets, it is necessary to conduct further proteomic research of the response to honeybee sting on a larger group of samples.

Capillary-channeled polymer (C-CP) fibers for the rapid extraction of proteins from urine matrices prior to detection with MALDI-MS

PURPOSE

While MS is a powerful tool for biomarker determinations, the high salt content and the small molecules present in urine poses incredible challenges. Separation/extraction methods must be employed for the isolation of target species at relevant concentrations. Micropipette tips packed with capillary-channeled polymer (C-CP) fibers are employed for the SPE of proteins from a synthetic and a certified urine matrix.

EXPERIMENTAL DESIGN

Extractions are performed utilizing a very simple centrifugation method to spin-down species through the C-CP fiber tips. Proteins adsorb to the hydrophobic polypropylene fibers and are eluted in a solvent suitable for MALDI-MS analysis. Figures of merit are determined for representative compounds β2-microglobulin, retinol binding protein, and transferrin.

RESULTS

The optimum protein processing included a 100 μL aqueous rinse and an elution solvent composition was 10 μL of 55:45 ACN:water (with triflouroacetic acid). MALDI-MS responses for the target proteins are improved from nondetectable levels to eventually yield LOD ranging from 5 to 180 nM in 1 μL aliquots.

CONCLUSION AND CLINICAL RELEVANCE

C-CP fiber tips offer a plethora of advantages including low materials costs, high throughput, microvolume processing, and the determination of sub-nanogram quantities of analyte; allowing determination of biomarkers that are otherwise undetectable in urine matrices.

Accelerating trypsin digestion: the immobilized enzyme reactor

Sample preparation has lagged far behind the evolution of instrumentation used in mass-linked protein analysis. Trypsin digestion, for example, still takes a day, as it did 50 years ago, while mass spectral analyses are achieved in seconds. Higher order structure of proteins is frequently modified by varying digestion conditions: shifting the initial points of trypsin cleavage, changing digestion pathways, accelerating peptide bond demasking and altering the distribution of miscleaved products at the completion of proteolysis. Reduction and alkylation are even circumvented in many cases. This review focuses on immobilized enzyme reactor technology as a means to achieve accelerated trypsin digestion by exploiting these phenomena.

Solid phase extraction of proteins from buffer solutions employing capillary-channeled polymer (C-CP) fibers as the stationary phase

Polypropylene (PP) capillary-channeled polymer (C-CP) fibers are applied for solid phase extraction (SPE) of proteins from aqueous buffer solutions using a micropipette tip-based format. A process was developed in which centrifugation is used as the moving force for solution passage in the loading/washing steps instead of the previously employed manual aspiration. The complete procedure requires ~15 minutes, with the number of samples run in parallel limited only by the capacity of the centrifuge. The method performance was evaluated based on adsorption and elution characteristics of several proteins (cytochrome c, lysozyme, myoglobin, and glucose oxidase) from 150 mM phosphate buffered saline (PBS) solutions. Protein concentration ranges of ~2 to 100 μg mL(-1) were employed and the recovery characteristics determined through UV-Vis absorbance spectrophotometry for protein quantification. The protein loading capacities across the range of proteins was ~1.5 μg for the 5 mg fiber tips. Average recoveries from PBS were determined for each protein sample; cytochrome c ~86%, lysozyme ~80%, myoglobin ~86%, and glucose oxidase ~89%. Recoveries from more complex matrices, synthetic urine and synthetic saliva, were determined to be ~90%. A 10× dilution study for a fixed 1 μg protein application yielded 94 ± 3.2% recoveries. The C-CP tips provided significantly higher recoveries for myoglobin in a 150 mM PBS matrix in comparison to a commercially available protein SPE product, with the added advantages of low cost, rapid processing, and reusability.

Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry

Sample preparation and fractionation technologies are one of the most crucial processes in proteomic analysis and biomarker discovery in solubilized samples. Chromatographic or electrophoretic proteomic technologies are also available for separation of cellular protein components. There are, however, considerable limitations in currently available proteomic technologies as none of them allows for the analysis of the entire proteome in a simple step because of the large number of peptides, and because of the wide concentration dynamic range of the proteome in clinical blood samples. The results of any undertaken experiment depend on the condition of the starting material. Therefore, proper experimental design and pertinent sample preparation is essential to obtain meaningful results, particularly in comparative clinical proteomics in which one is looking for minor differences between experimental (diseased) and control (nondiseased) samples. This review discusses problems associated with general and specialized strategies of sample preparation and fractionation, dealing with samples that are solution or suspension, in a frozen tissue state, or formalin-preserved tissue archival samples, and illustrates how sample processing might influence detection with mass spectrometric techniques. Strategies that dramatically improve the potential for cancer biomarker discovery in minimally invasive, blood-collected human samples are also presented.

Digestion of native proteins for proteomics using a thermocycler

Efficient protein digestion is a critical step for successful mass spectrometry analysis. Here we describe simultaneous tryptic digestion and gradual unfolding of native proteins by application of a temperature gradient using a single cycle of 5 min or less in a PCR thermocycler. Chemicals typically used for chromatographic techniques did not affect the digestion efficiency. Tryptic digestion was performed in a small volume (3 microL) with 1.5 microg of trypsin without denaturing agents. This rapid procedure yielded more peptides than conventional methods utilizing chemical denaturation for 18 proteins out of 20. Samples were directly spotted on the MALDI-TOF target plate, without additional purification, thus reducing losses on reversed-phase resins.

Proteomic identification of technologically modified proteins in malt by combination of protein fractionation using convective interaction media and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A method for the fast separation of proteins and identification of their modifications based on the use of monolithic chromatographic media and mass spectrometric techniques is described. This method has been developed and applied to the analysis of malt proteins and its posttranslational modifications (glycation). Glycation, one of the most common forms of posttranslational modifications (PTM), can be detected in both biological and industrial samples. Our attention was focused on the investigations of possible chemical modifications of water-soluble barley proteins during malting process by combination of anion-exchange chromatography with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The malt extract was directly fractioned by anion-exchange chromatography using short monolithic columns and a linear gradient from 0 to 700 mM NaCl. Sufficient fractionation was obtained for malt sample, which demonstrates the potential of anion-exchange chromatography on this type of column. Proteins in separated fractions were identified by MALDI-TOF/TOF MS. Our proteomic analysis provided the identification of the major proteins present in the malt that were found to be heterogeneously glycated after malting. One of these proteins: nonspecific lipid transfer protein 1 (LTP1) can be used as a marker for characterization of glycation during malting. This protein and its modifications can be easily determined by the developed method.

Detection of hydrolysis of lipid post-translational modifications during gel-electrophoresis-based proteomic protocol

The influence of sample preparation on the identification of a lipid PTM was examined. Nonspecific lipid transfer protein 1 (LTP1) from barley is modified with a lipid-like molecule of mass of 294 Da. This modification was detected in the MS analysis of intact protein samples but no lipid-bound peptide was observed in the MS analysis of the in-gel digested LTP1 after an SDS-PAGE separation of the protein mixture. By using SEC instead of SDS-PAGE, the lipid-modified peptide was observed after in-solution enzymatic digestion of the SEC fraction containing LTP1. Conditions of individual steps of the gel-electrophoresis-based protocol were tested to find their effect on the removal of the lipid PTM from LTP1. The influences of particular solutions used in the gel-electrophoresis-based protocol on the hydrolysis of lipids were investigated. It was found that denaturing conditions, in combination with alkaline pH, have a major influence on the hydrolysis of the ester bond. Especially, the electrophoretic buffer has a strong influence on the hydrolysis of the lipid PTM (in the intact molecule) of LTP1.

Pipette tip solid-phase extraction and gas chromatography – mass spectrometry for the determination of methamphetamine and amphetamine in human whole blood

Methamphetamine and amphetamine were extracted from human whole blood samples using pipette tip solid-phase extraction (SPE) with MonoTip C(18) tips, on which C(18)-bonded monolithic silica gel was fixed. Human whole blood (0.1 mL) containing methamphetamine and amphetamine, with N-methylbenzylamine as an internal standard, was mixed with 0.4 mL of distilled water and 50 microL of 5 M sodium hydroxide solution. After centrifugation, the supernatant was extracted to the C(18) phase of the tip (pipette tip volume, 200 microL) by 25 repeated aspirating/dispensing cycles using a manual micropipettor. Analytes retained in the C(18) phase were eluted with methanol by five repeated aspirating/dispensing cycles. After derivatization with trifluoroacetic anhydride, analytes were measured by gas chromatography - mass spectrometry with selected ion monitoring in the positive-ion electron impact mode. Recoveries of methamphetamine and amphetamine spiked into whole blood were more than 87.6 and 81.7%, respectively. Regression equations for methamphetamine and amphetamine showed excellent linearity in the range of 0.5-100 ng/0.1 mL. The limits of detection for methamphetamine and amphetamine were 0.15 and 0.11 ng/0.1 mL, respectively. Intra- and interday coefficients of variation for both stimulants were not greater than 9.6 and 13.8%, respectively. The determination of methamphetamine and amphetamine in autopsy whole blood samples is presented, and was shown to validate the present methodology.

Simultaneous determination of methamphetamine and amphetamine in human urine using pipette tip solid-phase extraction and gas chromatography–mass spectrometry

Methamphetamine and amphetamine were extracted from human urine samples using pipette tip solid-phase extraction (SPE) with MonoTip C18 tips (pipette tip volume, 200 microl), in which C18-bonded monolithic silica gel was fixed. A sample of human urine (0.5 ml) containing methamphetamine, amphetamine, and N-methylbenzylamine as internal standard (IS), was mixed with 25 microl of 1M sodium hydroxide solution. The mixture was extracted into the C18 phase of the SPE tip by 25 repeated aspirating/dispensing cycles using a manual micropipettor. Analytes retained in the C18 phase were then eluted with methanol by five repeated aspirating/dispensing cycles. After derivatization with trifluoroacetic anhydride, analytes were measured by gas chromatography/mass spectrometry with selected ion monitoring in the positive-ion electron impact mode. Recoveries of methamphetamine, amphetamine, and IS spiked into urine were more than 82.9, 82.2, and 78.2%, respectively. Regression equations for methamphetamine and amphetamine showed excellent linearity in the range of 0.25-200 ng/0.5 ml. Limit of detection was 0.04 ng/0.5 ml for methamphetamine and 0.05 ng/0.5 ml for amphetamine. Intra- and inter-day coefficients of variations for both stimulants were not greater than 10.8%. The data obtained from actual determination of methamphetamine and amphetamine in autopsy urine samples are also presented for validation of the method.

Methods for samples preparation in proteomic research

Sample preparation is one of the most crucial processes in proteomics research. The results of the experiment depend on the condition of the starting material. Therefore, the proper experimental model and careful sample preparation is vital to obtain significant and trustworthy results, particularly in comparative proteomics, where we are usually looking for minor differences between experimental-, and control samples. In this review we discuss problems associated with general strategies of samples preparation, and experimental demands for these processes.

Sample Preparation for MALDI Mass Spectrometry Using an Elastomeric Device Reversibly Sealed on the MALDI Target

A new method for improving low-concentration sample recovery and reducing sample preparation steps in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is presented. In the conventional approach, samples are typically desalted and/or concentrated with various techniques and deposited on the MALDI target as small droplets. In this work, we describe a new approach in which an elastomeric device is reversibly sealed on the MALDI target to form a multi-well plate with the MALDI target as the base of the plate. The new format allows a larger volume (5-200 microL) of samples to be deposited on each spot and a series of sample handling processes, including desalting and concentrating, to be performed directly on the MALDI target. Several advantages have been observed: (i) multiple sample transferring steps are avoided; (ii) recovery of low-concentration peptides during sample preparation is improved using a novel desalting method that utilizes the hydrophobic surface of the elastomeric device; and (iii) sequence coverage of the peptide mass fingerprinting map is improved using a novel method in which proteins are immobilized on the hydrophobic surface of the elastomeric device for in-well trypsin digestion, followed by desalting and concentrating the digestion products in the same well.

Capillary-Channeled Polymer Fibers as a Stationary Phase for Desalting of Protein Solutions for Electrospray Ionization Mass Spectrometry Analysis

Micropipet solid-phase extraction (SPE) tips have been used to desalt and purify proteins and peptides from mixtures of buffers and biological solutions. Removing salts and buffers prior to electrospray ionization mass spectrometry (ESI-MS) characterization improves the detection limits and the sensitivity of the protein analyses. Recently, capillary-channeled polymer (C-CP) fibers have been investigated as stationary phases for high-performance liquid chromatography separations of proteins. Polypropylene C-CP fibers incorporated as sorbent materials in micro-SPE tips are shown to effectively remove both inorganic and organic buffers from proteins in defined solutions. The architecture of the fibers provides large surface areas in comparison to conventional round fibers and is readily packed into capillaries that can be affixed to micropipet tips. Desalting of protein solutions is demonstrated for ESI-MS analysis through increased signal-to-noise ratios and reduced spectral complexity.

Off-line combination of reversed-phase liquid chromatography and laser desorption/ionization time-of-flight mass spectrometry with seamless post-source decay fragment ion analysis for characterization of square-planar nickel(II) complexes

Characterization of square-planar nickel(II) complexes of the Schiff base of (S)-N-benzylproline (2-benzoylphenyl)amide and various amino acids that are used as efficient alpha-amino acids synthons was carried out using laser desorption/ionization time-of-flight mass spectrometry (LDI-TOF MS) in off-line combination with liquid chromatography. A mixture of four square-planar nickel(II) complexes was separated using reversed-phase liquid chromatography (RPLC) and the separated fractions from the chromatographic run were spotted on the metal target directly from the column outlet using a lab-made sample deposition device. The separated fractions were then analyzed by LDI-TOF MS. Seamless postsource decay (sPSD) fragment ion analysis was used for their structural characterization, which made possible the confirmation of expected chemical structures of the analyzed compounds. The off-line combination of the separation by RPLC and analysis by LDI-TOF MS allowed successful separation, sensitive detection and structure elucidation of the square-planar nickel(II) complexes.

Simultaneous determination of ten antihistamine drugs in human plasma using pipette tip solid-phase extraction and gas chromatography/mass spectrometry

Ten antihistamine drugs, diphenhydramine, orphenadrine, chlorpheniramine, diphenylpyraline, triprolidine, promethazine, homochlorcyclizine, cyproheptadine, cloperastine and clemastine, have been found to be extractable from human plasma samples using MonoTip C18 tips, inside which C18- bonded monolithic silica gel was fixed. Human plasma (0.1 mL) containing the ten antihistamines was mixed with 0.4 mL of distilled water and 25 microL of a 1 M potassium phosphate buffer (pH 8.0). After centrifugation of the mixture, the supernatant fraction was extracted to the C18 phase of the tip by 25 repeated aspirating/dispensing cycles using a manual micropipettor. The analytes retained on the C18 phase were then eluted with methanol by five repeated aspirating/dispensing cycles. The eluate was injected into a gas chromatography (GC) injector without evaporation and reconstitution steps, and was detected by a mass spectrometer with selected ion monitoring in the positive-ion electron impact mode. The separation of the ten drugs from each other and from impurities was generally satisfactory using a DB-1MS column (30 m x 0.32 mm i.d., film thickness 0.25 microm). The recoveries of the ten antihistamines spiked into plasma were 73.8-105%. The regression equations for the ten antihistamines showed excellent linearity with detection limits of 0.02-5.0 ng/0.1 mL. The within-day and day-to-day coefficients of variation for plasma were not greater than 9.9%. The data obtained from determination of diphenhydramine and chlorpheniramine in human plasma after oral administration of the drugs are also presented.