High-throughput Sample Preparation Research Articles

Development of an automated high-throughput sample preparation protocol for LC-MS/MS analysis of glycated peptides

Advanced glycation end products (AGEs) are known to play a leading part in the pathogenesis of human diseases, such as diabetes, Alzheimer's disease, lateral sclerosis, and atherosclerosis. It is for this reason that research on AGEs is crucial and large-scale studies are needed for the treatment of diseases. The aim of this study was to develop a reproducible method to analyze Amadori compounds using an automated enrichment protocol for high-throughput analysis of clinical samples. The developed method enabled the enrichment of Amadori compounds simultaneously from 96 samples, and it was applied to the discovery of biomarkers in AGEs related diseases. In this study, ten human serum samples were processed using automated filter-aided sample preparation (aFASP) in a 96-well filter plate, and the eluted peptide mixtures were enriched by Affinity Cellufine PB in a fritted 96-well filter plate using a liquid handling robotic system. The eluted glycated peptides were analyzed by a liquid chromatography-tandem mass spectrometry (LC-MS/MS) system. A total of 982 unique glycated peptides, corresponding to 524 unique glycated proteins, were identified from the analysis of ten human samples. The advantages and potentials of the automated sample preparation system were demonstrated through label free quantification of the glycated peptides.

Deterministic lateral displacement (DLD) in the high Reynolds number regime: high-throughput and dynamic separation characteristics

Recent progress in the development of biosensors has created a demand for high-throughput sample preparation techniques that can be easily integrated into microfluidic or lab-on-a-chip platforms. One mechanism that may satisfy this demand is deterministic lateral displacement (DLD), which uses hydrodynamic forces to separate particles based on size. Numerous medically relevant cellular organisms, such as circulating tumor cells (10–15 µm) and red blood cells (6–8 µm), can be manipulated using microscale DLD devices. In general, these often-viscous samples require some form of dilution or other treatment prior to microfluidic transport, further increasing the need for high-throughput operation to compensate for the increased sample volume. However, high-throughput DLD devices will require a high flow rate, leading to an increase in Reynolds numbers (Re) much higher than those covered by existing studies for microscale (≤ 100 µm) DLD devices. This study characterizes the separation performance for microscale DLD devices in the high-Re regime (10 < Re < 60) through numerical simulation and experimental validation. As Re increases, streamlines evolve and microvortices emerge in the wake of the pillars, resulting in a particle trajectory shift within the DLD array. This differs from previous DLD works, in that traditional models only account for streamlines that are characteristic of low-Re flow, with no consideration for the transformation of these streamlines with increasing Re. We have established a trend through numerical modeling, which agrees with our experimental findings, to serve as a guideline for microscale DLD performance in the high-Re regime. Finally, this new phenomenon could be exploited to design passive DLD devices with a dynamic separation range, controlled simply by adjusting the device flow rate.

Design and Application of a High-Throughput Sample Processing Module Based on Magnetic Beads

One of key challenges in diagnosis of infectious diseases is collecting a large quantity of purified nucleic acids from pathogens immediately. To address this challenge, a high-throughput magnetic separation module and a heating and vibrating module were developed to optimize the operation of biological sample preparation (like nucleic acid extraction) on our home-built liquid handing system. Both of the two modules have 4 working locations for Biomolecular Screening (BS) standard labware, and three functions (magnetic separation, heating and vibrating) were elaborately integrated into the two modules. Each module has its own core control circuit and a unique interface port containing a 24 V DC power supply connector and a CAN bus communication connector. When equipping with the two modules, the home-built liquid handing system transformed into an integrated automatic sample preparation workstation. Performance evaluations were carried out on the two modules and finally a nucleic acid extraction of human's whole blood was carried out on the workstation. Results showed that the two modules could cooperate well with the liquid handing system, and the workstation exhibited its ability for high-throughput sample preparation.

A method for analysis of marker persistent organic pollutants in low-volume plasma and serum samples using 96-well plate solid phase extraction

The objective of this study was to develop and validate a 96-well plate solid phase extraction method for analysis of 23 lipophilic persistent organic pollutants (POPs) in low-volume plasma and serum samples which is applicable for biomonitoring and epidemiological studies. The analysis of selected markers for internal exposure: 16 polychlorinated biphenyls (PCBs), 5 organochlorine pesticides (OCPs), octachlorinated dibenzo-p-dioxin (OCDD), and polybrominated diphenylether 47 (BDE 47) was evaluated by comparing two SPE sorbents and GC-HRMS or GC–MS/MS detection. The final method extracted 23 POPs from 150 μL of serum and plasma using a 96-well extraction plate containing 60 mg Oasis HLB sorbent per well prior to GC-HRMS magnetic sector analysis. The extraction method was applied to 40 plasma samples collected for an epidemiological study. The recovery of selected POPs ranged from 31% to 63% (n = 48), and detection limits ranged from 2.2 to 45 pg/mL for PCBs, 4.2 to 167 pg/mL for OCPs, 7.8 pg/mL for OCDD and 6.1 pg/mL for BDE 47. This method showed good precision with relative standard deviations of selected POP concentrations in quality control samples (n = 48) ranging from 11% to 25%. The trueness was determined with standard reference material serum (n = 48) and the deviation from certified values ranged from 1 to 27%. Of the 23 POPs analyzed, 18 were detected in 43% to 100% of plasma samples collected for the epidemiological study. The method showed good robustness with low inter-well plate variation (11–31%) determined by twelve 96-well plate extractions, and can extract 96 samples, including quality controls and procedural blanks in 2–3 days. Comparison with GC–MS/MS analysis showed that similar concentrations (within 0.5% to 30%) of most POPs could be obtained with GC-APCI-MS/MS. Larger deviations were observed for PCB 194 (60%) and trans-nonachlor (43%). The developed method produces accurate concentrations of low-level marker POPs in plasma and serum, providing a suitable high-throughput sample preparation procedure for biomonitoring and epidemiological studies involving large sample size and limited sample volume. GC-HRMS was chosen over GC–MS/MS, however the latter showed promising results, and could be used as an alternative to GC-HRMS analysis for most POPs.

NetoVIR: Modular Approach to Customize Sample Preparation Procedures for Viral Metagenomics.

The democratization of next-generation sequencing (NGS) technologies has enabled scientists to explore the diversity of microbial life in various ecological niches in an unpreceded depth. The role of viruses as a key player in health and disease is becoming increasingly clear. To address the need for an up scalable, reproducible protocol to purify RNA and DNA viruses from a sample, we describe our optimized method. The Novel Enrichment Technique Of Viromes (NetoVIR) allows researchers to attain a fast, reproducible, and high-throughput sample preparation protocol for NGS gut viromics studies. With appropriate prior homogenization steps, this protocol can be extended to any biological samples.

Protein Nanopore-Based Discrimination between Selected Neutral Amino Acids from Polypeptides.

Nanopore probing of biological polymers has the potential to achieve single-molecule sequencing at low cost, high throughput, portability, and minimal sample preparation and apparatus. In this article, we explore the possibility of discrimination between neutral amino acid residues from the primary structure of 30 amino acids long, engineered peptides, through the analysis of single-molecule ionic current fluctuations accompanying their slowed-down translocation across the wild type α-hemolysin (α-HL) nanopore, and molecular dynamics simulations. We found that the transient presence inside the α-HL of alanine or tryptophan residues from the primary sequence of engineered peptides results in distinct features of the ionic current fluctuation pattern associated with the peptide reversibly blocking the nanopore. We propose that α-HL sensitivity to the molecular exclusion at the most constricted region mediates ionic current blockade events correlated with the volumes that are occluded by at least three alanine or tryptophan residues, and provides the specificity needed to discriminate between groups of neutral amino acids. Further, we find that the pattern of current fluctuations depends on the orientation of the threaded amino acid residues, suggestive of a conformational anisotropy of the ensemble of conformations of the peptide on the restricted nanopore region, related to its relative axial orientation inside the nanopore.

ICP-MS measurement of toxic and essential elements in human breast milk. A comparison of alkali dilution and acid digestion sample preparation methods

BackgroundFor trace element measurement in human breast milk, an accurate high-throughput sample preparation method would be desirable. In this study, a quick alkali sample dilution method was systematically compared to the traditional acid digestion pretreatment for measuring 10 trace elements in 237 human breast milk samples by inductively coupled plasma mass spectrometry (ICP-MS). MethodsThe alkali method involved dilution of the breast milk samples with a solution consisting of 2% butanol, 0.05% EDTA, 0.05% Triton X-100 and 1% NH4OH. The mixtures were sonicated, centrifuged and analyzed by ICP-MS. Acid digestion was performed in HNO3 at 250°C using a Milestone Ultra CLAVE II microwave digestion system. ResultsOverall, the alkali dilution method gave higher analytical precision compared to acid digestion while LODs and recoveries were similar between the two methods. Spearman's correlations between measured element concentrations by the two sample preparation methods were strong (rS>0.70) for all elements, except for Ca and Cd (rS<0.50). Passing-Bablok regression analyses showed best agreement between the two methods for Li, Mg, Fe, Zn, Se and Cd (slopes 0.8–1.2). Evaluation of Bland-Altman difference plots showed best method agreement (lowest bias) for Na, Mg, Ca, Zn and Cd.Highest difference in element concentration between the methods was observed for iodine (96ng/g by alkali dilution and 33ng/g by acid digestion), probably due to formation of volatile species such as HI and I2 in the acid matrix. ConclusionsThe results indicate that the alkali dilution high-throughput sample preparation method is comparable to the more commonly used acid digestion method for ICP-MS measurements of some toxic and essential elements in human breast milk.

Use of monolithic supports for high-throughput protein and peptide separation in proteomics.

The exclusive properties of monolithic supports enable fast mass transfer, high porosity, low back pressure, easy preparation process and miniaturisation, and the availability of different chemistries make them particularly suitable materials for high-throughput (HTP) protein and peptide separation. In this review recent advances in monolith-based chromatographic supports for HTP screening of protein and peptide samples are presented and their application in HTP sample preparation (separation, enrichment, depletion, proteolytic digestion) for HTP proteomics is discussed. Development and applications of different monolithic capillary columns in HTP MS-based bottom-up and top-down proteomics are overviewed. By discussing the chromatographic conditions and the mass spectrometric data acquisition conditions an attempt is made to present currently demonstrated capacities of monolithic capillary columns for HTP identification and quantification of proteins and peptides from complex biological samples by MS-based proteomics. Some recent advances in basic monolith technology of importance for proteomics are also discussed.

Engineered Paper-Based Cell Culture Platforms.

Paper is used in various applications in biomedical research including diagnostics, separations, and cell cultures. Paper can be conveniently engineered due to its tunable and flexible nature, and is amenable to high-throughput sample preparation and analysis. Paper-based platforms are used to culture primary cells, tumor cells, patient biopsies, stem cells, fibroblasts, osteoblasts, immune cells, bacteria, fungi, and plant cells. These platforms are compatible with standard analytical assays that are typically used to monitor cell behavior. Due to its thickness and porous nature, there are no mass transport limitations to/from the cells in paper scaffolds. It is possible to pattern paper in different scales (micrometer to centimeter), generate modular configurations in 3D, fabricate multicellular and compartmentalized tissue mimetics for clinical applications, and recover cells from the scaffolds for further analysis. 3D paper constructs can provide physiologically relevant tissue models for personalized medicine. Layer-by layer strategies to assemble tissue-like structures from low-cost and biocompatible paper-based materials offer unique opportunities that include understanding fundamental biology, developing disease models, and assembling different tissues for organ-on-paper applications. Paper-based platforms can also be used for origami-inspired tissue engineering. This work provides an overview of recent progress in engineered paper-based biomaterials and platforms to culture and analyze cells.

Polymethacrylate-based monoliths as stationary phases for separation of biopolymers and immobilization of enzymes.

The experiences in the production and application of polymethacrylate-based monolithic supports, since their development almost thirty years ago, are presented. The main driving force for the development of new chromatographic supports was the necessity for the isolation and separation of physiologically active biopolymers and their use for therapeutic purposes. For this sake, a development of a method for fast separation, preventing denaturation and preserving their biological activity was necessary. Development of polysaccharide-based supports, followed by the introduction of polymer-based chromatographic media, is shortly described. This development was followed by the advances in monolithic media that are now used for both large- and small-scale separation of biopolymers and nanoparticles. Finally, a short overview is given about the applications of monoliths for sample displacement chromatography, resulting in isolation of physiologically active biomolecules, such as proteins, protein complexes, and nucleic acid, as well as high-throughput sample preparation for proteomic investigations.

High throughput human plasma N-glycan analysis using DNA analyzer and multivariate analysis for biomarker discovery

Carbohydrates form the majority of organic compounds found in nature and their presence on proteins influences many important bioactivities. Therefore, glycan profiling shows potential in clinical applications. This work demonstrates the use of a high-throughput GlycanAssure™ sample preparation technology and multi-capillary DNA analyzer for the analysis of the major N-linked glycans (N-glycans) found in human plasma. The application involves two biomarker studies: (1) in profiling patients with chronic kidney disease and (2) in differentiating heart disease patients with normal controls in response to an antiplatelet drug from hypo-responders. Due to complexity of the study data, bio-statistical methods were applied to data processing. 37 N-glycan peaks were observed from separation results, with confirmed structure for most glycans. Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were used to build models to differentiate the patient groups. The percentages of correct classification of the models reached 95.45% for the chronic kidney disease dataset and 85.42% for the anti-platelet drug response dataset. Given that blood N-glycan profiles had been shown to reflect certain disease states, this high-throughput platform could potentially be used for the simultaneous screening of multiple glycan biomarkers, with as little as one drop of blood sample.

High-throughput analysis of N-glycans using AutoTip via glycoprotein immobilization

Analysis of a large number of samples requires an efficient, rapid and reproducible method. Automation is an ideal approach for high-throughput sample preparation. Multi-plexing sample preparation via a 96-well plate format becomes popular in recent years; however, those methods lack specificity and require several cleanup steps via chromatography purification. To overcome these drawbacks, a chemoenzymatic method has been developed utilizing protein conjugation on solid-phase. Previously, sample preparation was successfully performed in a snap-cap spin-column (SCSC) format. However, sample preparation using SCSC is time-consuming and lacks reproducibility. In this work, we integrated the chemoenzymatic technique in a pipette tip (AutoTip) that was operated by an automated liquid handler. We established a multi-step protocol involving protein immobilization, sialic acid modification, and N-glycan release. We first optimized our automated protocol using bovine fetuin as a standard glycoprotein, and then assessed the reproducibility of the AutoTip using isobaric tags for relative N-linked glycan quantification. We then applied this methodology to profile N-glycans from 58 prostate cancer patient urine samples, revealing increased sialyation on urinary N-glycans derived from prostate cancer patients. Our results indicated AutoTip has applications for high-throughput sample preparation for studying the N-linked glycans.

Solid-phase analytical derivatization for gas-chromatography–mass-spectrometry-based metabolomics

A novel derivatization method for gas chromatography/mass spectrometry (GC/MS)-based metabolomics was developed, based on solid-phase analytical derivatization (SPAD) with methoximation followed by trimethylsilylation. This SPAD method realized derivatization on solid phases combining strong anion exchange with strong cation exchange. To omit a sample condensation process, GC/MS injection was performed using a large-volume injection mode. This mode uses a stomach-shaped insert, and enables a large quantity of sample to be vaporized and introduced into the GC/MS system. In the present study, several parameters were investigated for each SPAD step. The optimal derivatization conditions were determined to be 3-min-methoximation with 5μL of >5% methoxyamine solution, and 10-min-trimethylsilylation with 25μL of N-methyl-N-trimethylsilyl-trifluoroacetamide (MSTFA). Derivatized analytes were effectively eluted with 25μL of n-hexane. The influences of coexisting substances were also investigated. Coexisting saccharides did not significantly affect the derivatization of analytes. Moreover, saccharides were efficiently washed out using 80% (v/v) acetonitrile in water. The influences of coexisting sodium chloride were negated by dilution of the sample solution with water. The developed method enables the derivatization of both anionic and cationic metabolites, and high-throughput sample preparation. The coverage of detectable metabolites for the developed method was similar to that of the conventional method. This is the first report of a SPAD-based human plasma metabolome analysis protocol.

ZEISS Crossbeam - Advancing Capabilities in High Throughput 3D Analysis and Sample Preparation

ZEISS Crossbeam - Advancing Capabilities in High Throughput 3D Analysis and Sample Preparation

Quick 96FASP for high throughput quantitative proteome analysis

Filter aided sample preparation (FASP) is becoming a central method for proteomic sample cleanup and peptide generation prior to LC-MS analysis. We previously adapted this method to a 96-well filter plate, and applied to prepare protein digests from cell lysate and body fluid samples in a high throughput quantitative manner. While the 96FASP approach is scalable and can handle multiple samples simultaneously, two key advantages compared to single FASP, it is also time-consuming. The centrifugation-based liquid transfer on the filter plate takes 3–5 times longer than single filter. To address this limitation, we now present a quick 96FASP (named q96FASP) approach that, relying on the use of filter membranes with a large MWCO size (~30kDa), significantly reduces centrifugal times. We show that q96FASP allows the generation of protein digests derived from whole cell lysates and body fluids in a quality similar to that of the single FASP method. Processing a sample in multiple wells in parallel, we observed excellent experimental repeatability by label-free quantitation approach. We conclude that the q96FASP approach promises to be a promising cost- and time-effective method for shotgun proteomics and will be particularly useful in large scale biomarker discovery studies. SignificanceHigh throughput sample processing is of particular interests for quantitative proteomics. The previously developed 96FASP is high throughput and appealing, however it is time-consuming in the context of centrifugation-based liquid transfer (~1.5h per spin). This study presents a truly high throughput sample preparation method based on large cut-off 96-well filter plate, which shortens the spin time to ~20min. To our knowledge, this is the first multi-well method that is entirely comparable with conventional FASP. This study thoroughly examined two types of filter plates and performed side-by-side comparisons with single FASP. Two types of samples, whole cell lysate of a UTI (urinary tract infection)-associated Klebsiella pneumoniae cell and human urine, were tested which demonstrated its capability for quantitative proteomics. The q96FSAP approach makes the filter plate-based approach more appealing for protein biomarker discovery projects, and could be broadly applied to large scale proteomics analysis.

High Throughput and Quantitative Measurement of Microbial Metabolome by Gas Chromatography/Mass Spectrometry Using Automated Alkyl Chloroformate Derivatization.

The ability to identify and quantify small molecule metabolites derived from gut microbial-mammalian cometabolism is essential for the understanding of the distinct metabolic functions of the microbiome. To date, analytical protocols that quantitatively measure a complete panel of microbial metabolites in biological samples have not been established but are urgently needed by the microbiome research community. Here, we report an automated high-throughput quantitative method using a gas chromatography/time-of-flight mass spectrometry (GC/TOFMS) platform to simultaneously measure over one hundred microbial metabolites in human serum, urine, feces, and Escherichia coli cell samples within 15 min per sample. A reference library was developed consisting of 145 methyl and ethyl chloroformate (MCF and ECF) derivatized compounds with their mass spectral and retention index information for metabolite identification. These compounds encompass different chemical classes including fatty acids, amino acids, carboxylic acids, hydroxylic acids, and phenolic acids as well as benzoyl and phenyl derivatives, indoles, etc., that are involved in a number of important metabolic pathways. Within an optimized range of concentrations and sample volumes, most derivatives of both reference standards and endogenous metabolites in biological samples exhibited satisfactory linearity (R2 > 0.99), good intrabatch reproducibility, and acceptable stability within 6 days (RSD < 20%). This method was further validated by examination of the analytical variability of 76 paired human serum, urine, and fecal samples as well as quality control samples. Our method involved using high-throughput sample preparation, measurement with automated derivatization, and rapid GC/TOFMS analysis. Both techniques are well suited for microbiome metabolomics studies.

Application of volumetric absorptive microsampling for robust, high-throughput mass spectrometric quantification of circulating protein biomarkers

Volumetric absorptive micro sampling (VAMS™) allows accurate sampling of 10µL of blood from a minimally invasive finger prick and could enable remote personalized health monitoring. Moreover, VAMS overcomes effects from hematocrit and sample heterogeneity associated with dried blood spots (DBS). We describe the first application of VAMS with the Mitra® microsampling device for the quantification of protein biomarkers using an automated, high-throughput sample preparation method coupled with mass spectrometric (MS) detection.The analytical performance of the developed workflow was evaluated for 10 peptides from six clinically relevant proteins: apolipoproteins A-I, B, C-I, C-III, E, and human serum albumin (HSA). Extraction recovery from blood with three different levels of hematocrit varied between 100% and 111% for all proteins. Within-day and total assay reproducibility (i.e., 5 replicates on 5days) ranged between 3.2–10.4% and 3.4–12.6%, respectively. In addition, after 22weeks of storage of the Mitra microsampling devices at −80°C, all peptide responses were within ±15% deviation from the initial response. Application to data-independent acquisition (DIA) MS further demonstrated the potential for broad applicability and the general robustness of the automated workflow by reproducible detection of 1661 peptides from 423 proteins (average 15.7%CV (n=3) in peptide abundance), correlating to peptide abundances in corresponding plasma (R=0.8383).In conclusion, we have developed an automated workflow for efficient extraction, digestion, and MS analysis of a variety of proteins in a fixed small volume of dried blood (i.e., 10µL). This robust and high-throughput workflow will create manifold opportunities for the application of remote, personalized disease biomarker monitoring.

Development of high throughput LC/MS/MS method for analysis of perfluorooctanoic acid from serum, suitable for large-scale human biomonitoring.

A simple method for determination of perfluorooctanoic acid (PFOA) from human serum by liquid chromatography/tandem mass spectrometry (LC/MS/MS) and utilizing high-throughput sample preparation was developed by New York State Public Health Emergency Preparedness Laboratory and used for biomonitoring studies. 50μl of serum was mixed with a 0.4ml of acetonitrile containing isotopically labeled internal standard, followed by phospholipid removal/protein precipitation. The extract was partially dried and analyzed by LC/MS/MS. The linear range of PFOA analysis was 0.5-100ng/ml. LLOQ was selected as 0.5ng/ml. The method was validated following APHL guidelines for LRN-C laboratories and about 6000 specimens were successfully prepared and analyzed using this simple LC/MS method. Due to sample preparation simplicity, the presented method can be used in large-scale clinical testing, such as public health surveillance studies.

Droplet-based light-sheet fluorescence microscopy for high-throughput sample preparation, 3-D imaging and quantitative analysis on a chip.

We report a novel fusion of droplet microfluidics and light-sheet microscopy, to achieve high-throughput sample compartmentalization, manipulation and three-dimensional imaging on a chip. This optofluidic device characterized by orthogonal plane illumination and rapid liquid handling is compact and cost-effective, and capable of preparing sample droplets with tunable size, frequency and ingredient. Each droplet flowing through the device's imaging region is self-scanned by a laser-sheet, three-dimensionally reconstructed and quantitatively analysed. This simple-and-robust platform combines fast 3-D imaging with efficient sample preparation and eliminates the need of a complicated mechanical scan at the same time. Achieving 500 measurements per second and screening over 30 samples per minute, it shows great potential for various lab-on-a-chip biological studies, such as embryo sorting and cell growth assays.

High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR.

Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of combining reactions together. We designed and evaluated a panel based on this principle to rapidly identify the presence of common disease agents in dogs and horses with acute respiratory illness. This manuscript describes a nanoscale diagnostic PCR workflow for sample preparation, amplification, and analysis of target pathogen sequences, focusing on procedures that are different from microliter scale reactions. In the respiratory panel presented, 18 assays were each set up in triplicate, accommodating up to 48 samples per plate. A universal extraction and pre-amplification workflow was optimized for high-throughput sample preparation to accommodate multiple matrices and DNA and RNA based pathogens. Representative data are presented for one RNA target (influenza A matrix) and one DNA target (equine herpesvirus 1). The ability to quickly and accurately test for a comprehensive, syndrome-based group of pathogens is a valuable tool for improving efficiency and ergonomics of diagnostic testing and for acute respiratory disease diagnosis and management.