scholarly journals SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS

2021 ◽  
Vol 12 ◽  
Author(s):  
Kamil Mikulášek ◽  
Hana Konečná ◽  
David Potěšil ◽  
Renata Holánková ◽  
Jan Havliš ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Magnetic Particles ◽  
Protein Extraction ◽  
Solid Phase ◽  
Handling Time ◽  
Plant Sample ◽  
Preparation Methods ◽  
Wide Range ◽  
Contaminants Removal ◽  
Paramagnetic Beads

Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the filter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample preparations (SP3) on carboxylated or HILIC paramagnetic beads, and protein suspension trapping method (S-Trap) were evaluated for SDS removal and protein digestion from Arabidopsis thaliana (AT) lysate. Finally, the optimized carboxylated SP3 workflow was benchmarked closely against the routine FASP. Ultimately, LC-MS/MS analyses revealed that regarding the number of identifications, number of missed cleavages, proteome coverage, repeatability, reduction of handling time, and cost per assay, the SP3 on carboxylated magnetic particles proved to be the best alternative for SDS and other contaminants removal from plant sample lysate. A robust and efficient 2-h SP3 protocol for a wide range of protein input is presented, benefiting from no need to adjust the amount of beads, binding and rinsing conditions, or digestion parameters.

scholarly journals Modern Methods of Sample Preparation for the Analysis of Oxylipins in Biological Samples

Molecules ◽  
2019 ◽  
Vol 24 (8) ◽  
pp. 1639 ◽  
Author(s):  
Liakh ◽  
Pakiet ◽  
Sledzinski ◽  
Mika
Keyword(s):  
Mass Spectrometry ◽  
Sample Preparation ◽  
Biological Samples ◽  
Solid Phase ◽  
Biological Tissues ◽  
Gas Chromatography Mass Spectrometry ◽  
Liquid Liquid Extraction ◽  
Wide Range ◽  
Popular Subject ◽  
Technological Platforms

Oxylipins are potent lipid mediators derived from polyunsaturated fatty acids, which play important roles in various biological processes. Being important regulators and/or markers of a wide range of normal and pathological processes, oxylipins are becoming a popular subject of research; however, the low stability and often very low concentration of oxylipins in samples are a significant challenge for authors and continuous improvement is required in both the extraction and analysis techniques. In recent years, the study of oxylipins has been directly related to the development of new technological platforms based on mass spectrometry (LC–MS/MS and gas chromatography–mass spectrometry (GC–MS)/MS), as well as the improvement in methods for the extraction of oxylipins from biological samples. In this review, we systematize and compare information on sample preparation procedures, including solid-phase extraction, liquid–liquid extraction from different biological tissues.

scholarly journals Comparison of an Offline SPE–GC–MS and Online HS–SPME–GC–MS Method for the Analysis of Volatile Terpenoids in Wine

Molecules ◽  
2020 ◽  
Vol 25 (3) ◽  
pp. 657 ◽  
Author(s):  
Cody Williams ◽  
Astrid Buica
Keyword(s):  
Sample Preparation ◽  
Solid Phase ◽  
White Wine ◽  
Gas Chromatography Mass Spectrometry ◽  
Wine Quality ◽  
White Wines ◽  
Preparation Methods ◽  
Odor Thresholds ◽  
Spe Method ◽  
Sample Preparation Methods

The aroma profile is an important marker for wine quality. Various classes of compounds are responsible for the aroma of wine, and one such class is terpenoids. In the context of this work, a validated gas chromatography–mass spectrometry (GC–MS) method for the quantitation of terpenoids in red and white wine using headspace solid-phase microextraction (HS–SPME) and solid-phase extraction (SPE) was established. Calibrations were performed in the respective base wine using both sample preparation methods. The linearity, precision and accuracy evaluated for the respective matrices were excellent for both sample preparations. However, the HS–SPME approach was more sensitive and more accurate. For both sample preparations, the quantification limits were lower than the odor thresholds in wine. The terpenoid concentrations (µg/L) were evaluated for 13 white wines using both sample preparation methods. Importantly, the online HS–SPME approach was more sensitive than the offline SPE method. The major terpenoids identified in the white wines evaluated were linalool (0.2–63 µg/L), geraniol (nd–66 µg/L) and α-terpineol (nd–85 µg/L).

Analytical Methodology for the Determination of Organochlorine Pesticides in Vegetation

2012 ◽  
Vol 95 (5) ◽  
pp. 1291-1310 ◽  
Author(s):  
Elisa Beceiro-González ◽  
María J González-Castro ◽  
Soledad Muniategui-Lorenzo ◽  
Purificación López-Mahía ◽  
Darío Prada-Rodríguez
Keyword(s):  
Sample Preparation ◽  
Solid Phase Extraction ◽  
Organochlorine Pesticides ◽  
Pesticide Residues ◽  
Solid Phase ◽  
Liquid Extraction ◽  
Stir Bar Sorptive Extraction ◽  
Phase Extraction ◽  
Chromatographic Techniques ◽  
Wide Range

Abstract Due to the extensive use of organochlorine pesticides (OCPs) for agricultural purposes and their high persistence and low biodegradability, they have become an important group of contaminants. Detection and quantification of pesticide residues in food, particularly fruits and vegetables, is of growing concern for producers, consumers, and governments. The most widely used pretreatment for the extraction of pesticides in plants is based on solvent extraction liquid-solid extraction (LSE). LSE can be carried out using Soxhlet, shake-flask, homogenization, sonication, and, more recently, microwave-assisted extraction, pressurized liquid extraction, and supercritical fluid extraction. Furthermore, new analytical procedures using the extraction with sorbents, such as solid-phase micro-extraction, stir bar sorptive extraction, and matrix solid-phase dispersion, have also been used. On the other hand, a wide range of cleanup methods (liquid–liquid extraction, solid-phase extraction, gel permeation chromatography, and dispersive solid-phase extraction; and chromatographic techniques with electron capture detector and mass spectrometry detector; and HPLC with a ultraviolet detector are reported in the literature. This article reviews the applicability, advantages, and disadvantages of various sample preparation techniques (traditional and new techniques) for the analysis of OCPs in different plants and plant materials. It covers more than 15 years of published methods in which pesticide residues have been determined in a wide range of vegetation samples (fruits, horticultural samples, medicinal plants, tree leaves, etc.) by the use of chromatographic techniques after various sample preparation steps. A great number of applications in different plant material are provided. To the best of the authors' knowledge, previously published reviews have not covered as wide and exhaustive range of vegetation matrixes as presented here. A summary of pesticide levels cited in the literature is included.

scholarly journals On sample preparation methods for fermented beverage VOCs profiling by GCxGC-TOFMS

Metabolomics ◽  
2020 ◽  
Vol 16 (10) ◽  
Author(s):  
Penghan Zhang ◽  
Silvia Carlin ◽  
Cesare Lotti ◽  
Fulvio Mattivi ◽  
Urska Vrhovsek
Keyword(s):  
Sample Preparation ◽  
Solid Phase ◽  
White Wine ◽  
Stir Bar Sorptive Extraction ◽  
Metabolomic Analysis ◽  
Preparation Methods ◽  
Fermented Beverages ◽  
Targeted Profiling ◽  
The Impact ◽  
Sample Preparation Methods

Abstract Introduction Aromas and tastes have crucial influences on the quality of fermented beverages. The determination of aromatic compounds requires global non-targeted profiling of the volatile organic compounds (VOCs) in the beverages. However, experimental VOC profiling result depends on the chosen VOC collection method. Objectives This study aims to observe the impact of using different sample preparation techniques [dynamic headspace (DHS), vortex-assisted liquid–liquid microextraction (VALLME), multiple stir bar sorptive extraction (mSBSE), solid phase extraction (SPE), and solid phase micro-extraction (SPME)] to figure out the most suitable sample preparation protocol for profiling the VOCs from fermented beverages. Methods Five common sample preparation methods were studied with beer, cider, red wine, and white wine samples. After the sample preparation, collected VOCs were analyzed by two-dimensional gas chromatography coupled with time of flight mass spectrometry (GCxGC-TOFMS). Results GCxGC oven parameters can be optimized with the Box–Behnken surface response model and response measure on peak dispersion. Due to the unavoidable column and detector saturation during metabolomic analysis, errors may happen during mass spectrum construction. Profiling results obtained with different sample preparation methods show considerable variance. Common findings occupy a small fraction of total annotated VOCs. For known fermentative aromas, best coverage can be reached by using SPME together with SPE for beer, and VALLME for wine and cider. Conclusions GCxGC-TOFMS is a promising tool for non-targeted profiling on VOCs from fermented beverages. However, a proper data processing protocol is lacking for metabolomic analysis. Each sample preparation method has a specific profiling spectrum on VOC profiling. The coverage of the VOC metabolome can be improved by combining complementary methods.

Levoglucosan in speleothems: An evaluation of various sample preparation methods.

2021 ◽  
Author(s):  
Julia Homann ◽  
Thorsten Hoffmann ◽  
Denis Scholz ◽  
Sebastian Breitenbach
Keyword(s):  
Sample Preparation ◽  
Biomass Burning ◽  
Solid Phase ◽  
Ice Cores ◽  
Soxhlet Extraction ◽  
Atmospheric Particulate Matter ◽  
Preparation Methods ◽  
Local Climate ◽  
Solid Liquid ◽  
Global And Local

<p>Secondary mineral deposits in caves, such as stalagmites or flowstones, are valuable paleoclimate archives because they have several advantages over other environmental archives. These include stable in-cave conditions, protecting the speleothems from external influences, and the potential to precisely date samples up to 600,000 years using <sup>230</sup>Th/U-dating. [1] Supplementing established climate proxies, such as stable isotopes and trace elements, organic proxies have been increasingly used in recent years to inform on local vegetation and soil dynamics. [2]</p><p>Biomass burning events are major sources of atmospheric particulate matter that influences global and local climate. [3] Investigating fire proxies in paleoclimate archives may therefore help determine the interactions of climate, hydrology, and fire activity. Levoglucosan, an anhydrosugar, naturally only originates from the combustion of cellulose and thus constitutes a biomass burning marker. Analysis of levoglucosan in sediments has shown high correlation with traditional burning markers, such as black charcoal. [4] Mannosan and galactosan, both stereoisomers of levoglucosan, are formed during combustion of hemicellulose. Previous work suggests that rather than absolute levoglucosan concentrations the ratio of levoglucosan to its isomers should be considered when characterizing burning events. [5] To date, no data on levoglucosan or its isomers in speleothems has been published, whereas the anhydrosugars are already utilised in other paleoclimate archives, such as sediments and ice cores. [2,3]</p><p>We test three approaches (solid phase extraction (SPE), soxhlet extraction and solid/liquid extraction) for the isolation and quantification of anhydrosugars using HILIC-MS instrumentation. As the anhydrosugars are highly polar molecules, extraction from the calcium carbonate matrix and subsequent sample preparation proved challenging. We evaluate the different approaches and compare the resulting concentrations and assumed recoveries. We find that the anhydrosugars do not show significant retention on any of the evaluated SPE materials. While solid/liquid extractions lead to detectable analyte concentrations, soxhlet extractions with methanol or dichloromethane/methanol mixtures are more efficient.</p><p> </p><p>[1] D. Scholz, D. Hoffmann, Quat. Sci. J. 57 (2008) 52–76 [2] A. Blyth et al. Quat. Sci. Rev. 149 (2016) 1-17 [3] P. Yao et al. J. of Glaciology 59 (2013) 599-611 [4] V. O. Elias et al. Geochim. et Cosmochim. Acta 65 (2001) 267-272. [5] D. Fabbri et al. Atmos. Env. 43 (2009) 2286–2295</p>

scholarly journals Sample Preparation Methods for Lipidomics Approaches Used in Studies of Obesity

Molecules ◽  
2020 ◽  
Vol 25 (22) ◽  
pp. 5307
Author(s):  
Ivan Liakh ◽  
Tomasz Sledzinski ◽  
Lukasz Kaska ◽  
Paulina Mozolewska ◽  
Adriana Mika
Keyword(s):  
Sample Preparation ◽  
Metabolic Pathways ◽  
Chemical Structure ◽  
Analytical Procedure ◽  
Preparation Methods ◽  
Wide Range ◽  
Obese Subjects ◽  
Composition Properties ◽  
Important Branch ◽  
Sample Preparation Methods

Obesity is associated with alterations in the composition and amounts of lipids. Lipids have over 1.7 million representatives. Most lipid groups differ in composition, properties and chemical structure. These small molecules control various metabolic pathways, determine the metabolism of other compounds and are substrates for the syntheses of different derivatives. Recently, lipidomics has become an important branch of medical/clinical sciences similar to proteomics and genomics. Due to the much higher lipid accumulation in obese patients and many alterations in the compositions of various groups of lipids, the methods used for sample preparations for lipidomic studies of samples from obese subjects sometimes have to be modified. Appropriate sample preparation methods allow for the identification of a wide range of analytes by advanced analytical methods, including mass spectrometry. This is especially the case in studies with obese subjects, as the amounts of some lipids are much higher, others are present in trace amounts, and obese subjects have some specific alterations of the lipid profile. As a result, it is best to use a method previously tested on samples from obese subjects. However, most of these methods can be also used in healthy, nonobese subjects or patients with other dyslipidemias. This review is an overview of sample preparation methods for analysis as one of the major critical steps in the overall analytical procedure.

scholarly journals Solid Phase Microextraction and Related Techniques for Drugs in Biological Samples

2014 ◽  
Vol 2014 ◽  
pp. 1-24 ◽  
Author(s):  
Mohammad Mahdi Moein ◽  
Rana Said ◽  
Fatma Bassyouni ◽  
Mohamed Abdel-Rehim
Keyword(s):  
Sample Preparation ◽  
Biological Samples ◽  
Solid Phase Microextraction ◽  
Solid Phase ◽  
Biological Fluids ◽  
Drug Analysis ◽  
Primary Objective ◽  
Small Sample ◽  
Preparation Methods ◽  
Recent Developments

In drug discovery and development, the quantification of drugs in biological samples is an important task for the determination of the physiological performance of the investigated drugs. After sampling, the next step in the analytical process is sample preparation. Because of the low concentration levels of drug in plasma and the variety of the metabolites, the selected extraction technique should be virtually exhaustive. Recent developments of sample handling techniques are directed, from one side, toward automatization and online coupling of sample preparation units. The primary objective of this review is to present the recent developments in microextraction sample preparation methods for analysis of drugs in biological fluids. Microextraction techniques allow for less consumption of solvent, reagents, and packing materials, and small sample volumes can be used. In this review the use of solid phase microextraction (SPME), microextraction in packed sorbent (MEPS), and stir-bar sorbtive extraction (SBSE) in drug analysis will be discussed. In addition, the use of new sorbents such as monoliths and molecularly imprinted polymers will be presented.

Comparison of Sample Preparation Methods for Recovering Salmonella from Raw Fruits, Vegetables, and Herbs

2001 ◽  
Vol 64 (10) ◽  
pp. 1459-1465 ◽  
Author(s):  
ANDREA B. BURNETT ◽  
LARRY R. BEUCHAT
Keyword(s):  
Sample Preparation ◽  
Pathogenic Bacteria ◽  
Preparation Method ◽  
Morphological Characteristics ◽  
Processing Method ◽  
Sample Processing ◽  
Processing Methods ◽  
Preparation Methods ◽  
Wide Range ◽  
The Mean

Methods for preparing raw fruits, vegetables, and herbs for enrichment or direct plating to determine the presence and populations of pathogenic bacteria vary greatly. A study was done to compare three sample processing methods (washing in 0.1% peptone, stomaching, and homogenizing) for their influence on recovery of Salmonella inoculated onto 26 types of raw produce. The mean numbers of Salmonella recovered from 10 fruits, 11 vegetables, and 5 herbs using all three processing methods were 7.17, 7.40, and 7.27 log10 CFU/sample, respectively. Considering all 26 types of produce and all processing methods, the number of Salmonella recovered ranged from 7.24 to 7.29 log10 CFU/sample, with no significant differences attributable to a particular sample processing method. Mean percent recoveries of Salmonella from washed, stomached, and homogenized produce were 39.4, 44.7, and 42.4%, respectively. Mean percent recoveries from fruits, vegetables, and herbs, regardless of sample preparation method, were 41.7, 50.1, and 25.9%, respectively. The number of Salmonella recovered from stomached and homogenized produce, but not washed produce, with pH ≤ 4.53 was significantly less than the number recovered from produce with pH from 5.53 to 5.99, suggesting that the acidic environment in stomachates and homogenates was lethal to a portion of Salmonella. Reduced percent recoveries from herbs (pH 5.94 to 6.34) is attributed, in part, to antimicrobials released from plant cells during sample preparation. Overall, the type of processing method did not substantially affect the number of Salmonella recovered from the 26 types of raw produce representing a wide range of structural and morphological characteristics, composition, and pH. The influence of sample size, diluent composition, and processing time on efficiency of recovery of Salmonella and other pathogens needs to be evaluated before a method(s) for processing samples of raw produce can be recommended.

Recent achievements and applications of solid – phase microextraction in pesticide residues analysis in food

2015 ◽  
Vol 8 (2) ◽  
pp. 178-190
Author(s):  
Mária Andraščíková ◽  
Svetlana Hrouzková
Keyword(s):  
Sample Preparation ◽  
Pesticide Residues ◽  
Solid Phase Microextraction ◽  
Method Development ◽  
Solid Phase ◽  
Current Trend ◽  
Preparation Methods ◽  
Pesticides Residues ◽  
Fiber Coating ◽  
Food Matrices

Abstract The current trend in sample preparation methods is devoted to minimizing or eliminating the volume of extractive solvent. In this review, the focus on solid phase microextraction (SPME) as a solvent free sample preparation method for the isolation of pesticides residues in different food matrices is given. To achieve satisfactory extraction efficiency, selection of the fiber coating is an important step in the method development. Here, recent trends in new supporting materials and new fiber coatings development are discussed. Finally, applicability of SPME for the pesticide residues analysis in various food matrices using mainly chromatographic methods is also reviewed.

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