Sample Preparation Strategies Research Articles

Recent advances in phosphoproteomics and application to neurological diseases.

Phosphorylation has an incredible impact on the biological behavior of proteins, altering everything from intrinsic activity to cellular localization and complex formation. It is no surprise then that this post-translational modification has been the subject of intense study and that, with the advent of faster, more accurate instrumentation, the number of large-scale mass spectrometry-based phosphoproteomic studies has swelled over the past decade. Recent developments in sample preparation, phosphorylation enrichment, quantification, and data analysis strategies permit both targeted and ultra-deep phosphoproteome profiling, but challenges remain in pinpointing biologically relevant phosphorylation events. We describe here technological advances that have facilitated phosphoproteomic analysis of cells, tissues, and biofluids and note applications to neuropathologies in which the phosphorylation machinery may be dysregulated, much as it is in cancer.

Absolute Quantification of Middle- to High-Abundant Plasma Proteins via Targeted Proteomics.

The increasing number of peptide and protein biomarker candidates requires expeditious and reliable quantification strategies. The utilization of liquid chromatography coupled to quadrupole tandem mass spectrometry (LC-MS/MS) for the absolute quantitation of plasma proteins and peptides facilitates the multiplexed verification of tens to hundreds of biomarkers from smallest sample quantities. Targeted proteomics assays derived from bottom-up proteomics principles rely on the identification and analysis of proteotypic peptides formed in an enzymatic digestion of the target protein. This protocol proposes a procedure for the establishment of a targeted absolute quantitation method for middle- to high-abundant plasma proteins waiving depletion or enrichment steps. Essential topics as proteotypic peptide identification and LC-MS/MS method development as well as sample preparation and calibration strategies are described in detail.

Development of a sample preparation strategy for the determination of tungsten in soil samples by inductively coupled plasma mass spectrometry using a response surface methodology

An alternative rapid digestion method has been developed for the determination of tungsten (W) in soil samples using fractionation studies and response surface methodology. The digestion method using the Kjeldahl instrument was applied to samples, and soluble tungsten was determined via inductively coupled plasma mass spectrometry. Digestion parameters were selected depending on the results of fractionation studies and optimized using a four-factor and five-level central composite design. The contributions of the phosphoric acid concentration (X$_{1})$, digestion temperature (X$_{2})$, digestion time (X$_{3})$, and hydrochloric acid concentration (X$_{4})$ were evaluated for the determination of W from samples in which its levels were maximum. Optimum conditions for factors were found to be X$_{1}$ = 9.00 M, X$_{2}$ = 124 $^{\circ}$C, X$_{3}$ = 45 min, and X$_{4}$ = 1.52 M using a predicted W level of 86.82 $\mu $g L$^{-1}$. This yielded an expected level of 1736.40 mg kg$^{-1}$ under the optimized conditions. Experimental W levels were in good agreement with this predicted level and found to be 1682.69 mg kg$^{-1}$. Thus, measured W levels showed the versatility of the central composite design in such a complex soil matrix for method development.

A comparison of sample preparation strategies for biological tissues and subsequent trace element analysis using LA-ICP-MS

Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) is one of the most commonly applied methods for lateral trace element distribution analysis in medical studies. Many improvements of the technique regarding quantification and achievable lateral resolution have been achieved in the last years. Nevertheless, sample preparation is also of major importance and the optimal sample preparation strategy still has not been defined. While conventional histology knows a number of sample pre-treatment strategies, little is known about the effect of these approaches on the lateral distributions of elements and/or their quantities in tissues. The technique of formalin fixation and paraffin embedding (FFPE) has emerged as the gold standard in tissue preparation. However, the potential use for elemental distribution studies is questionable due to a large number of sample preparation steps. In this work, LA-ICP-MS was used to examine the applicability of the FFPE sample preparation approach for elemental distribution studies. Qualitative elemental distributions as well as quantitative concentrations in cryo-cut tissues as well as FFPE samples were compared. Results showed that some metals (especially Na and K) are severely affected by the FFPE process, whereas others (e.g., Mn, Ni) are less influenced. Based on these results, a general recommendation can be given: FFPE samples are completely unsuitable for the analysis of alkaline metals. When analyzing transition metals, FFPE samples can give comparable results to snap-frozen tissues.Graphical abstractSample preparation strategies for biological tissues are compared with regard to the elemental distributions and average trace element concentrations.

Comparison of sample preparation strategies for target analysis of total thyroid hormones levels in serum by liquid chromatography-quadrupole time-of-flight-mass spectrometry

This paper describes a novel method based on liquid chromatography quadrupole time-of-flight-mass spectrometry (LC-QTOF-MS) for target analysis of total THs in serum. Several sample preparation strategies have been evaluated to reduce matrix effect (namely, HybridSPE cartridges, supported liquid extraction, SLE and solid phase extraction, SPE). Deproteinization and further clean-up with mixed-mode SPE was selected as the best strategy for sample preparation, since achieved the cleanest extracts and reduced ionization suppression effects (between −11 and −24%).Method validation was performed by the analysis of control human serum samples. Criteria for confirming THs identity in serum extracts were based on retention times, accurate masses, isotopic pattern and MS/MS fragmentation pattern. Moreover, the quantitation capabilities of the LC-QTOF-MS method were also evaluated in terms of linearity, precision, accuracy and sensitivity by the application of matrix-matched calibration.Additionally, the developed LC-QTOF-MS method successfully provides qualitative information on endogenous components responsible of ion suppression (e.g. lysophosphatidylcholines), via post acquisition data analysis. This demonstrates the significant advantage of using LC-QTOF-MS, as it allows retrospective querying of the acquired data without the need of re-injecting/re-processing the samples.

Systematic Assessment of Seven Solvent and Solid-Phase Extraction Methods for Metabolomics Analysis of Human Plasma by LC-MS.

The comparison of extraction methods for global metabolomics is usually executed in biofluids only and focuses on metabolite coverage and method repeatability. This limits our detailed understanding of extraction parameters such as recovery and matrix effects and prevents side-by-side comparison of different sample preparation strategies. To address this gap in knowledge, seven solvent-based and solid-phase extraction methods were systematically evaluated using standard analytes spiked into both buffer and human plasma. We compared recovery, coverage, repeatability, matrix effects, selectivity and orthogonality of all methods tested for non-lipid metabolome in combination with reversed-phased and mixed-mode liquid chromatography mass spectrometry analysis (LC-MS). Our results confirmed wide selectivity and excellent precision of solvent precipitations, but revealed their high susceptibility to matrix effects. The use of all seven methods showed high overlap and redundancy which resulted in metabolite coverage increases of 34–80% depending on LC-MS method employed as compared to the best single extraction protocol (methanol/ethanol precipitation) despite 7x increase in MS analysis time and sample consumption. The most orthogonal methods to methanol-based precipitation were ion-exchange solid-phase extraction and liquid-liquid extraction using methyl-tertbutyl ether. Our results help facilitate rational design and selection of sample preparation methods and internal standards for global metabolomics.

Quantitative secretomic analysis of pancreatic cancer cells in serum-containing conditioned medium.

Pancreatic cancer is a highly metastatic and chemo-resistant disease. Secreted proteins involved in cell-cell interactions play an important role in changing the tumor microenvironment. Previous studies generally focus on the secretome of cancer cell line from serum-free media, due to the serious interference of fetal bovine serum (FBS). However, serum-starvation may alter expression patterns of secreted proteins. Hence, efforts to decrease the interference of serum in proteomic analysis of serum-containing media have been hampered to quantitatively measure the tumor secretion levels. Recently, the metabolic labeling, protein equalization, protein fractionation and filter-aided sample preparation (FASP) strategy (MLEFF) has been successfully used to avoid the disturbance of serum on secretome analysis. Here, this efficient method was applied for comparative secretome analysis of two hamster pancreatic cancer cells with differentially metastatic potentials, enabling the observation of 161 differentially expressed proteins, including 106 proteins that had been previously reported and detected in plasma. By integrated analysis of our data and publicly available bioinformatics resources, we found that a combination panel consisting of CDH3, PLAU, and LFNG might improve the prognosis of overall pancreatic cancer survival. These secreted proteins may serve as a potential therapeutic targets for pancreatic cancer metastasis.

Instrument for Real-Time Digital Nucleic Acid Amplification on Custom Microfluidic Devices.

Nucleic acid amplification tests that are coupled with a digital readout enable the absolute quantification of single molecules, even at ultralow concentrations. Digital methods are robust, versatile and compatible with many amplification chemistries including isothermal amplification, making them particularly invaluable to assays that require sensitive detection, such as the quantification of viral load in occult infections or detection of sparse amounts of DNA from forensic samples. A number of microfluidic platforms are being developed for carrying out digital amplification. However, the mechanistic investigation and optimization of digital assays has been limited by the lack of real-time kinetic information about which factors affect the digital efficiency and analytical sensitivity of a reaction. Commercially available instruments that are capable of tracking digital reactions in real-time are restricted to only a small number of device types and sample-preparation strategies. Thus, most researchers who wish to develop, study, or optimize digital assays rely on the rate of the amplification reaction when performed in a bulk experiment, which is now recognized as an unreliable predictor of digital efficiency. To expand our ability to study how digital reactions proceed in real-time and enable us to optimize both the digital efficiency and analytical sensitivity of digital assays, we built a custom large-format digital real-time amplification instrument that can accommodate a wide variety of devices, amplification chemistries and sample-handling conditions. Herein, we validate this instrument, we provide detailed schematics that will enable others to build their own custom instruments, and we include a complete custom software suite to collect and analyze the data retrieved from the instrument. We believe assay optimizations enabled by this instrument will improve the current limits of nucleic acid detection and quantification, improving our fundamental understanding of single-molecule reactions and providing advancements in practical applications such as medical diagnostics, forensics and environmental sampling.

Dissolving capability difference based sequential extraction: A versatile tool for in-depth membrane proteome analysis

Profiling membrane proteins would facilitate revealing disease mechanism and discovering new drug targets as they play essential roles in cellular signaling, substrate transport, and cell adhesion. However, the analysis of membrane proteins still remains a challenge due to their high hydrophobicity, as well as the suppression effect of high abundant soluble proteins. In this work, to achieve a membrane proteome profiling, a sample preparation strategy based on sequential extraction at the protein level assisted by a range of extraction reagents with different dissolving capabilities, followed by nano-RPLC-ESI-MS/MS analysis was developed and applied for HeLa cell line analysis. It was found that with progressively harsher extraction reagents (i.e., 2 M NaCl, 4 M urea, 0.1 M Na2CO3, and 10% 1-dodecyl-3- methyl-imidazolium chloride (C12ImCl) performed, much more high hydrophobic proteins and low abundant proteins were identified. With our developed strategy, 5553 of the identified proteins (4419 gene products) were annotated to be membrane proteins and 2573 proteins (2183 gene products) have at least one transmembrane domain, to our best knowledge, which is the most comprehensive membrane proteome dataset for HeLa cell line. Notably, 110 of the identified membrane proteins were discovered in the “missing proteins” list referred to those in the neXtProt database. All above results indicated that our strategy has great potential to tackle the difficult but relevant task of identifying and profiling membrane proteins.

Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding.

The increasing application of soil metaproteomics is providing unprecedented, in-depth characterization of the composition and functionality of in situ microbial communities. Despite recent advances in high-resolution mass spectrometry, soil metaproteomics still suffers from a lack of effective and reproducible protein extraction protocols and standardized data analyses. This review discusses the opportunities and limitations of selected techniques in soil-, and leaf litter metaproteomics, and presents a step-by-step guideline on their application, covering sampling, sample preparation, extraction and data evaluation strategies. In addition, we present recent applications of soil metaproteomics and discuss how such approaches, linking phylogenetics and functionality, can help gain deeper insights into terrestrial microbial ecology. Finally, we strongly recommend that to maximize the insights environmental metaproteomics may provide, such methods should be employed within a holistic experimental approach considering relevant aboveground and belowground ecosystem parameters.

Simultaneous quantitation of trace level hydrazine and acetohydrazide in pharmaceuticals by benzaldehyde derivatization with sample ‘matrix matching’ followed by liquid chromatography–mass spectrometry

Hydrazine and acetohydrazide are potential genotoxins and therefore need to be controlled in APIs and drug products to ppm levels for patient safety in cases where there is a reasonable probability of either of them being present. They are structurally related and could both be formed in the same chemical process under certain circumstances. However, no previous studies have reported simultaneous trace level quantification of these two compounds. Herein, a chemical derivatization scheme using benzaldehyde followed by LC–MS analysis is presented to address that need. During method development, unexpectedly high recoveries were encountered and presented a major challenge. A systematic investigation was undertaken to understand the benzaldehyde derivatization reaction and determine the underlying causes of the unacceptable recovery. It was found that this was due to the presence of the counter ion of the API in the sample matrix. Employing a ‘matrix matching’ sample preparation strategy, which involved acidifying the derivatization reaction medium with benzoic acid, gave similar reaction rates for the chemical derivatization in the presence and absence of the API salt and accordingly more consistent recoveries. Resultantly, a robust method for simultaneous quantification of hydrazine and acetohydrazide (1–100ppm) was successfully developed and validated.

Analytical strategy for sample preparation in trace metal analysis

Analytical strategy for sample preparation in trace metal analysis

Visualizing fungal metabolites during mycoparasitic interaction by MALDI mass spectrometry imaging.

Studying microbial interactions by MALDI mass spectrometry imaging (MSI) directly from growing media is a difficult task if high sensitivity is demanded. We present a quick and robust sample preparation strategy for growing fungi (Trichoderma atroviride, Rhizoctonia solani) on glass slides to establish a miniaturized confrontation assay. By this we were able to visualize metabolite distributions by MALDI MSI after matrix deposition with a home‐built sublimation device and thorough recrystallization. We present for the first time MALDI MSI data for secondary metabolite release during active mycoparasitism.

Enhanced Sample Preparation for Proteomic Analysis Utilizing Reversible Biotinylation and Polymer Based Protein Engineering

Proteome sample preparation for gel‐based and mass spectrometry‐based studies has remained relatively unchanged for many years. The goal of these sample preparation schemes is to remove contaminants such as lipids, DNA, RNA, and carbohydrates from cell or tissue homogenates. The vast majority of current methods rely on protein precipitation followed by centrifugation and resolubilizing the proteins. Unfortunately none of these techniques provide an unbiased sampling of the tentire proteome. Regardless of the method (ammonium acetate precipitation, TCA/acetone precipitation, PEG precipitation, etc.), not all proteins will be precipitated and not all will be resolubilized. We have developed an unbiased method for proteome sample preparation based on protein capture, not precipitation. We recently showed that Biotin‐CDM can be used as a tool to reversibly tag the entire proteome for purification.1 Biotin‐CDM reacts with lysine residues present on the surface of proteins at elevated pH to covalently biotinylate proteins. Biotinylated proteins are bound to Avidin beads and then all non‐protein contaminants are washed away. The biotin tag is then reversed by lowering the pH to release the proteins from the Avidin beads, resulting in pur, unmodified, and unbiased proteome sample. Because an excess of Biotin‐CDM is required to tag all proteins, we utilized polymer based protein engineering to develope a novel method that separates free Biotin‐CDM from biotinylated proteins. Thus, we have developed a method to prepare proteome samples in an unbiased manner that could be used for any organism.

Simultaneous electrophoretic concentration and separation of herbicides in beer prior to stacking capillary electrophoresis UV and liquid chromatography-mass spectrometry.

Simultaneous electrophoretic concentration and separation (SECS) was used as a simple and environmental friendly sample preparation strategy for herbicides in beer samples. An electric field was used to facilitate the separation and concentration of the analytes based on their charge from a 20 mL sample of diluted beer into two separate 20 μL aliquots of an acceptor electrolyte housed inside a micropipette. The anionic organophosphonate and cationic quaternary ammonium herbicides were concentrated in the anodic and cathodic pipette, respectively. Under optimized conditions, SECS was completed in 30 min at an applied voltage of 150 V, which provided analyte concentration factors of up to 90. After sample preparation, the SECS concentrate of cationic and anionic herbicides was analyzed by stacking CE with UV detection and also by LC-MS, respectively. The method detection limit for the diluted and undiluted sample was as low as 3 and 15 ng/mL, respectively. The method was linear over two orders of concentration with repeatability and intermediate precision of better than 5.8 and 7.0%RSD, respectively. Accuracy values were between 91.0-115.1%.

Prevalence, Level, and Types of Salmonella Isolated from North American In-Shell Pecans over Four Harvest Years

In-shell pecan samples (500 g) were collected over four harvest seasons (2010 to 2014) from seven pecan shelling facilities located in five U.S. states. Four varieties of pecans were analyzed: Mexican Improved, Native Seedlings, Southern Improved, and Western Improved. Pecan samples (100 g) were sent to a third party laboratory for initial Salmonella screening. When a sample was positive for Salmonella, the pathogen level was determined by the most-probable-number (MPN) method (25, 2.5, and 0.25 g). Two sample preparation strategies were used for the MPN analysis, and both strategies were combined for the reported MPN values. Forty-four (0.95%) of 4,641 in-shell pecan samples were positive for Salmonella during initial screening; prevalence by year was 0.47 to 1.4%. Prevalence was not significantly different between varieties: Mexican Improved, 1.2%; Native/Seedling, 0.99%; Southern Improved, 0.97%; and Western Improved, 0.75%. Salmonella was not isolated from 31 of 44 samples upon retesting during MPN analysis (<0.47 MPN/100 g). When Salmonella was detected, the levels were 0.47 to 39 MPN/100 g, with a mean of 2.4 MPN/100 g. Thirty-one Salmonella serotypes were obtained from 42 Salmonella-positive pecan samples; Enteritidis was the most common (12% of samples) followed by Javiana (9%) and Braenderup (7%). All Salmonella Enteritidis isolates were phage type 8. Pulsed-field gel electrophoresis analysis (XbaI) revealed within-serotype diversity, indicating introduction of contamination from a variety of sources. Most (64%) of the isolates were resistant to streptomycin or tetracycline, and 13% were resistant to three or more antibiotics. Salmonella prevalence and level on in-shell pecans is comparable to that on other nuts.

Advances in experimental phasing.

Advances in experimental phasing.

Simultaneous determination of 16 organophosphorus flame retardants and plasticizers in fish by liquid chromatography-tandem mass spectrometry

In this work a method to analyze simultaneously sixteen organophosphorus flame retardants (OPFRs) by liquid chromatography-quadrupole-linear ion trap mass spectrometry (LC-QqLIT-MS) in fish samples was successfully developed. Sample preparation strategies, including different extraction techniques and clean-ups were tested. The chosen methodology is based on the extraction of 0.25g of dried fish by ultrasound and clean-up by solid phase extraction (SPE) with a tandem of C18 and basic alumina cartridges. Recoveries were between 45 to 115%, with RSDs lower than 25%. mLODs and mLOQs were between 0.34–11.6ng/g lw and 1.12–38.8ng/g lw, respectively, with the exception of Tris(tribromoneopentyl)phosphate (TBNPP) (37.4 and 125ng/g lw, respectively) and Tris(isopropyl-phenyl)phosphate (IPPP) (51.6 and 172ng/g lw, respectively) which had higher limits. The developed method was applied to twelve river fish samples. Thirteen out of sixteen analyzed compounds were detected. At least, one of the sixteen studied OPFRs was detected in all the analyzed samples, with ΣOPFR levels up to 2423ng/g lw. This is the first study reporting IPPP and Isodecyldiphenyl phosphate (IDPP) levels in biota samples. Moreover, levels found for IPPP are quite high (up to 601ng/g lw) and thus it is important to consider in the future development of analytical methodologies for OPFR analysis.

Matrix removal in state of the art sample preparation methods for serum by charged aerosol detection and metabolomics-based LC-MS

Investigations into sample preparation procedures usually focus on analyte recovery with no information provided about the fate of other components of the sample (matrix). For many analyses, however, and particularly those using liquid chromatography-mass spectrometry (LC-MS), quantitative measurements are greatly influenced by sample matrix. Using the example of the drug amitriptyline and three of its metabolites in serum, we performed a comprehensive investigation of nine commonly used sample clean-up procedures in terms of their suitability for preparing serum samples. We were monitoring the undesired matrix compounds using a combination of charged aerosol detection (CAD), LC-CAD, and a metabolomics-based LC-MS/MS approach. In this way, we compared analyte recovery of protein precipitation-, liquid-liquid-, solid-phase- and hybrid solid-phase extraction methods. Although all methods provided acceptable recoveries, the highest recovery was obtained by protein precipitation with acetonitrile/formic acid (amitriptyline 113%, nortriptyline 92%, 10-hydroxyamitriptyline 89%, and amitriptyline N-oxide 96%). The quantification of matrix removal by LC-CAD showed that the solid phase extraction method (SPE) provided the lowest remaining matrix load (48–123 μg mL−1), which is a 10–40 fold better matrix clean-up than the precipitation- or hybrid solid phase extraction methods. The metabolomics profiles of eleven compound classes, comprising 70 matrix compounds showed the trends of compound class removal for each sample preparation strategy. The collective data set of analyte recovery, matrix removal and matrix compound profile was used to assess the effectiveness of each sample preparation method. The best performance in matrix clean-up and practical handling of small sample volumes was showed by the SPE techniques, particularly HLB SPE. CAD proved to be an effective tool for revealing the considerable differences between the sample preparation methods. This detector can be used to follow matrix compound elution during chromatographic separations, and the facile monitoring of matrix signal can assist in avoiding unfavourable matrix effects on analyte quantification.

The impact of phospholipids and phospholipid removal on bioanalytical method performance.

Phospholipids (PLs) are a component of cellmembranes, biological fluids and tissues. These compounds are problematic for the bioanalytical chemist, especially when PLs are not the analytes of interest. PL interference with bioanalysis highly impacts reverse-phase chromatographic methods coupled with mass spectrometric detection. Phospholipids are strongly retained on hydrophobic columns, and can cause significant ionization suppression in the mass spectrometer, as they outcompete analyte molecules for ionization. Strategies for improving analyte detection in the presence of PLs are reviewed, including in-analysis modifications and sample preparation strategies. Removal of interfering PLs prior to analysis seems to be most effective atmoderating thematrix effects fromthese endogenous cellular components, and has the potential to simplify chromatography and improve column lifetime. Products targeted at PL removal for sample pre-treatment, as well as products that combine multiplemodes of sample preparation (i.e. Hybrid SPE), show significant promise inmediating the effect on PL interference in bioanalysis.