Direct quantitative analysis of peptides using matrix assisted laser desorption ionization

The protocol and various matrices were examined for quantification of biomolecules in both the low ca. 1200 amu and mid mass 6000-12000 amu ranges using an internal standard. Comparative studies of different matrices of MALDI quantitative analysis showed that the best accuracy and standard curve linearity were obtained for two matrices: (a) 2,5-dihydroxybenzoic acid (DHB) combined with a comatrix of fucose and 5-methoxysalicylic acid (MSA) and (b) ferulic acid/fucose. In the low mass range, the quantitative limit was in the 30 fmol range and in the mid mass range the quantitative limit was in the 250 fmol range. Linear response was observed over 2-3 decades of analyte concentration. The relative error of the standard curve slope was 1.3-1.8% with correlation coefficients of 0.996-0.998.The main problem for quantitative measurement was suppression of the signal of the less concentrated component (analyte or internal standard) by the more concentrated component. The effect was identified with saturation of the matrix by the analyte. The threshold of matrix saturation was found to be in the range of 1/(3000-5000) analyte/matrix molar ratio. To avoid matrix saturation the (analyte+internal standard) to matrix molar ratio should be below this threshold. Thus the internal standard concentration should be as low as possible.DHB/MSA/fucose and ferulic acid/fucose matrices demonstrated good accuracy and linearity for standard curves even when the internal standard had chemical properties different from the analyte. However, use of an internal standard with different chemical properties requires highly stable instrumental parameters as well as constant (analyte+internal standard)/matrix molar ratio for all samples.     

Fast spectrophotometric determination of titanium in rocks with 3,4-dihydroxybenzoic acid

A fast Spectrophotometric method has been developed for titanium determination in geological matrices, based on the mixture of the sample solution with an exact volume of a single chromogenic solution containing acetate buffer, ascorbic acid and 3,4-dihydroxybenzoic acid DHB, which forms with titanium(IV) ions a yellow complex with absorption maximum at 380 nm. The following parameters were studied: complex stability, pH effect, amount of DHB, amount of acetate buffer, obedience to Beer's law, amount of ascorbic acid and iron masking. The results demonstrated that titanium can be determined in the pH range 4.0–5.0, with a molar absorptivity of 1.43 × 10⁴ 1·mol^–1 cm^–1 and a limit of detection of 2.3 ng/ml. The methodology that allows analysis of 30 samples per hour. Common anions and cations do not interfere, even when present in large amounts. Iron(III) interference can be easily eliminated by reduction to iron(II) using ascorbic acid. Analytical characteristics of the proposed procedure, such as calibration sensitivity, analytical sensitivity, limit of detection and coefficient of variation, were determined. The procedure was applied for titanium determination in various standard geological matrices, with results of satisfactory accuracy and precision (RSD<1%).     

Parameters contributing to efficient ion generation in aerosol MALDI mass spectrometry

The Bioaerosol Mass Spectrometry (BAMS) system was developed for the real-time detection and identification of biological aerosols using laser desorption ionization. Greater differentiation of particle types is desired; consequently MALDI techniques are being investigated. The small sample size ( approximately 1 microm3), lack of substrate, and ability to simultaneously monitor both positive and negative ions provide a unique opportunity to gain new insight into the MALDI process. Several parameters known to influence MALDI molecular ion yield and formation are investigated here in the single particle phase. A comparative study of five matrices (2,6-dihydroxyacetophenone, 2,5-dihydroxybenzoic acid, alpha-cyano-4-hydroxycinnamic acid, ferulic acid, and sinapinic acid) with a single analyte (angiotensin I) is presented and reveals effects of matrix selection, matrix-to-analyte molar ratio, and aerosol particle diameter. The strongest analyte ion signal is found at a matrix-to-analyte molar ratio of 100:1. At this ratio, the matrices yielding the least and greatest analyte molecular ion formation are ferulic acid and alpha-cyano-4-hydroxycinnamic acid, respectively. Additionally, a significant positive correlation is found between aerodynamic particle diameter and analyte molecular ion yield for all matrices. SEM imaging of select aerosol particle types reveals interesting surface morphology and structure.     

Parameterising matrix-assisted laser desorption/ionisation (MALDI): strategy for matrix—analyte selection and effect of radical co-additives on analyte peak intensities

Dihydroxybenzoic acid (DHB) analogues substituted at the 5-position can act as UV matrices at a wavelength of 337 nm, even when their absorption maxima are shifted past this particular wavelength.Modification of a matrix with a chiral ligand γ-(3-carboxy-4-hydroxy-anilide) (GCA) allowed it to differentiate between chiral isomers of tryptophan and also gave different intensities for glucose isomers, including structural dimers of glucose (cellobiose and maltose).An analogue that had one free hydroxyl group at the 2-OH position and a modification at the 5-position (MY10) gave protonated substance P (SP, analyte) peaks, similar in intensity to the not derivatised parent 2,5-dihydroxybenzoic acid indicating that the 5-OH position is not an important structural component.Another analogue that resembled a ‘dendrimeric’ structure of DHB (M552), also acted as a matrix, although its absorption maxima was at 552 nm suggesting the possibility of it being used at other wavelengths in addition to 337 nm.The DHB radical was complexed to a nitrone ‘spin-trap’. On complexion, the peptide (SP) peak intensity decreased. Addition of either radical initiators, such as 2,2-azobis(iso-butyronitrile) AIBN and tert-butylperoxide, or other radicals such as 2,2,6,6-tetramethyl-1-piperidinyloxy free radical (TEMPO) gave rise to higher analyte peak intensities for [SP+Na]⁺.It is thought that the DHB neutral radical is an intermediary in the protonation of the analyte. The photo-fragments of DHB, specifically the m/z 137 species, may also take part in proton transfer since possible mass analogues (hydroquinone, (deoxy)benzoin) can lead to analyte enhancement. Stabilization of or an increase in the matrix radical can also lead to analyte signal enhancement.     

Parameterising matrix-assisted laser desorption/ionization (MALDI): effect of solvents and co-additives on analyte peak intensities

The peak intensities obtained when 2,5-dihydroxybenzoic acid (DHB) was used as a 'classic' matrix were measured using substance P (SP) and betacyclodextrin (BCD) as analytes. Enhancements in peak intensities were observed going from 1:1 MeOH/H2O to dimethylforamide (DMF) as matrix solvents. Also non-covalent interactions between SP and solvent and DHB were observed suggesting close interactions between matrix, solvent and analyte in the gas-phase. Peak enhancements were previously reported with 'superDHB' (DHB and 2-hydroxy-5-methoxybenzoic acid at 10% v/v). Co-addition of structural analogues and their respective absorption coefficients were determined. It was found that other analogues used as co-matrices could give analyte peak enhancement similar to reported for sDHB with the additional benefit that some analogues could act as matrices with DHB addition. No direct correlation was observed between absorption coefficient and the ability of the molecule to act as a 'good' UV MALDI matrix.     

Analysis of three different types of fullerene derivatives by laser desorption/ionization time‐of‐flight mass spectrometry with new matrices

Three different types of fullerene derivatives, namely methano[60]fullerene dicarboxylate esters, [60]fulleropyrrolidines, and imino[60]fullerenes, were analyzed by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry using trans‐4‐tert‐butyl‐4′‐nitrostilbene (TBNS), 1,8,9‐anthracenetriol (dithranol), 6‐aza‐2‐thiothymine (ATT), 2,5‐dihydroxybenzoic acid (DHB) and carbazole as matrices. Unit mass resolution (sufficient to clearly resolve isotopic peaks), high signal‐to‐noise ratio, and clean mass spectra for all analytes were acquired by the optimization of experimental parameters and choice of optimal solvent for the matrix and molar matrix‐to‐analyte ratio. The new matrix, TBNS, gave the best results in the positive‐ion mode, as it can provide higher yields of analyte molecular ions at a lower laser threshold than the other four matrices, together with a very low degree of unwanted fragmentations. In the negative‐ion mode dithranol was better than TBNS, and the other three matrices gave relatively poor mass spectra for these fullerene derivatives. Copyright © 2005 John Wiley & Sons, Ltd.     

Improved silica xerogel film processing for MALDI-TOF–MS quantitative analysis of peptides and small molecules

In this work, sol–gel derived silica films were prepared for direct desorption/ionization of organic compounds in MALDI-TOF–MS analysis with the aim of improving method precision and of reducing interfering signals at low m/z values. Two commonly used MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (CHCA), were incorporated into the sol–gel network in order to absorb laser energy and to induce analyte desorption/ionization with low or absent background signals in the mass spectra. To achieve a reproducible xerogel film formation, experimental parameters for its deposition were optimized. The gel matrices were characterized by Fourier Transform Infrared (FT-IR) spectroscopy, X-ray Diffraction (XRD), and Scanning Electron Microscopy (SEM) analysis. The results proved the embedding of the matrix molecules in a disperse form into the homogeneous sol–gel material. The sol–gel matrix was then tested for the qualitative and quantitative analysis of two reference peptides, such as Bradykinin and P₁₄R. In addition, spectral quality and method performance were assessed for quantitation of melamine, a low-molecular weight compound of food safety concern. In all cases, high quality spectra and excellent mass accuracy (between 3.5 and 13 ppm) were observed. Furthermore, the experimental results evidenced a significant improvement of the measurement repeatability on spot and between spots (relative standard deviation <10%), with respect to the traditional dried-droplet sample deposition method. Good sensitivity and linearity in the concentration range explored were obtained for peptides and melamine, demonstrating the suitability of the sol–gel-based matrix to be used for quantitative analysis.     

On the use of DHB/aniline and DHB/<Emphasis Type="Italic">N,N</Emphasis>-dimethylaniline matrices for improved detection of carbohydrates: Automated identification of oligosaccharides and quantitative analysis of sialylated glycans by MALDI-TOF mass spectrometry

This study demonstrates the application of 2,5-dihydrohybenzoic acid/aniline (DHB/An) and 2,5-dihydroxybenzoic acid/N,N-dimethylaniline (DHB/DMA) matrices for automated identification and quantitative analysis of native oligosaccharides by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Both matrices are shown to be superior to pure DHB for native glycans in terms of signal intensities of analytes and homogeneity of sample distribution throughout the crystal layer. On-target formation of stable aniline Schiff base derivatives of glycans in DHB/An and the complete absence of such products in the mass spectra acquired in DHB/DMA matrix provide a platform for automated identification of reducing oligosaccharides in the MALDI mass spectra of complex samples. The study also shows how enhanced sensitivity is achieved with the use of these matrices and how the homogeneity of deposited sample material may be exploited for quick and accurate quantitative analysis of native glycan mixtures containing neutral and sialylated oligosaccharides in the low-nanogram to mid-picogram range.     

A 2,5-dihydroxybenzoic acid/N,N-dimethylaniline matrix for the analysis of oligosaccharides by matrix-assisted laser desorption/ionization mass spectrometry

The use of a novel 2,5-dihydroxybenzoic acid/N,N-dimethylaniline (DHB/DMA) matrix-assisted laser desorption/ionization (MALDI) matrix for detection and quantitative analysis of native N-linked oligosaccharides was investigated in this study. Substantial improvements in sensitivity were observed relative to the signals obtained with a traditional DHB matrix. Moreover, the morphology of the matrix crystal layer was very uniform, unlike that of DHB. This resulted in highly homogeneous sample distribution throughout the spot, allowing reproducible and consistent mass spectra to be obtained without spot-to-spot variations in signal. Here, we also demonstrate an approach for performing sensitive and accurate quantitative analysis of native N-linked glycans with this novel matrix using an internal standard method.     

Evaluation of three calibration methods to compensate matrix effects in environmental analysis with LC-ESI-MS

In quantitative analysis of environmental samples using high-performance liquid chromatography–electrospray ionization mass spectrometry (HPLC-ESI-MS) one of the major problems is the suppression or, less frequently, the enhancement of the analyte signals in the presence of matrix components. Standard addition is the most suitable method for compensating matrix effects, but it is time-consuming and laborious. In this study we compare the potential of three calibration approaches to compensate matrix effects that occurred when seven analytes (naphthalene sulfonates) were quantified in time series samples of waters with different matrices (untreated and treated industrial wastewater). The data obtained by external calibration, internal calibration with one standard, and external sample calibration (corresponding to matrix-matched calibration) were compared with those obtained by standard addition. None of the three approaches were suitable for a sample series of highly loaded, untreated wastewater with highly variable matrix. For less heavily loaded and less variable samples (treated wastewater effluents), the external sample calibration provided reasonable results for most analytes with deviations mostly below 25% as compared to standard addition. External sample calibration can be suitable to compensate matrix effects from moderately loaded samples with more uniform matrices, but it is recommended to verify this for each sample series against the standard addition approach.     

Comparison of mass spectra of peptides in different matrices using matrix-assisted laser desorption/ionization and a multi-turn time-of-flight mass spectrometer, MULTUM-IMG.

The mass spectra of peptides obtained with different matrices were compared using a matrix-assisted laser desorption/ionization (MALDI) ion source and a multi-turn time-of-flight (TOF) mass spectrometer, MULTUM-IMG, which has been developed at Osaka University. Two types of solid matrices, alpha-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB), and a liquid matrix made from a mixture of 3-aminoquinoline and CHCA were used. When measuring the peak signal intensity of human angiotensin II [M+H]+ from a fixed sample position, the liquid matrix produced a stable signal over 1000 laser shots, while the signal obtained with CHCA and DHB decayed after about 300 and 100 shots, respectively. Significant differences in the mass resolving power were not observed between the spectra obtained with the three matrices. Signal peak areas were measured as a function of the cycle number in a multi-turn ion trajectory, i.e., the total flight time over a millisecond time scale. For both [M+H]+ of human angiotensin II and bovine insulin, the decay of the signal peak area was the most significant with CHCA, while that measured with DHB was the smallest. The results of the mean initial ion velocity measurements suggested that the extent of metastable decomposition of the analyte ions increased in order of DHB, the liquid matrix, and CHCA, which is consistent with the difference in the decay of the signal peak area as the total flight time increased.     

Liquid chromatography/tandem mass spectrometry methods for quantitation of mevalonic acid in human plasma and urine: method validation,demonstration of using a surrogate analyte,and demonstration of unacceptable matrix effect in spite of use of a stable isotope analog internal standard

Selective, accurate, and reproducible liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods were developed and validated for the determination of mevalonic acid, an intermediate in the biosynthesis of cholesterol and therefore a useful biomarker in the development of cholesterol lowering drugs, in human plasma and urine. A hepta-deuterated analog of mevalonic acid was used as the internal standard. For both methods, calibration standards were prepared in water, instead of human plasma and urine, due to unacceptably high levels of endogenous mevalonic acid. The lower quality control (QC) samples were prepared in water while the higher QC samples were prepared in the biological matrices. For the isolation/purification of mevalonic acid from the plasma and urine matrices, the samples were first acidified to convert the acid analyte into its lactone form. For the plasma samples, the lactone analyte was retained on and then eluted off a polymeric solid-phase extraction (SPE) sorbent. For the urine method, the sample containing the lactone analyte was passed through a C-18 SPE column, which did not retain the analyte, with the subsequent analyte retention on and then elution off a polymeric SPE sorbent. Chromatographic separation was achieved isocratically on a polar-endcapped C-18 analytical column with a water/methanol mobile phase containing 0.5 mM formic acid. Detection was by negative-ion electrospray tandem mass spectrometry. The standard curve range was 0.500-20.0 ng/mL for the plasma method and 25.0-1,000 ng/mL for the urine method. Excellent accuracy and precision were obtained for both methods at all concentration levels tested. It was interesting to note that for certain batches of urine, when a larger sample volume was used for analysis, a high degree of matrix effect was observed which resulted not only in the attenuation of the absolute response, but also in a change of analyte/internal standard response ratio. This demonstrated that, under certain conditions, the use of a stable isotope analog internal standard does not, contrary to conventional thinking, guarantee the constancy of the analyte/internal response ratio, which is a prerequisite for a rugged bioanalytical method. On the other hand, under conditions where the sample matrix does not have such a deleterious effect, we have found that a stable isotope analog could serve as a surrogate (substitute) analyte. Thus, we have shown that using calibration standards prepared by spiking plasma with tri-deuterated or tetra-deuterated mevalonic acid, instead of mevalonic acid itself (the analyte), plasma QC samples that contain mevalonic acid can be successfully analyzed for the accurate and precise quantitation of mevalonic acid. The use of a surrogate analyte provides the opportunity to gauge the daily performance of the method for the low concentration levels prepared in the biological matrix, which otherwise is not achievable because of the endogenous concentrations of the analyte in the biological matrices.     

Matrix-assisted laser desorption/ionization mass spectrometry with additives to 2,5-dihydroxybenzoic acid

Selected benzoic acid derivatives and related substances were used as additives to 2,5-dihydroxybenzoic acid (2,5DHB) and the performance of the mixtures in matrix-assisted laser desorption/ionization mass spectrometry was investigated. Using benzoic acid derivatives substituted at position 2 and/or 5 or related substances as a co-matrix in the 1–10% range with 2,5DHB results in improved ion yields and signal-to-noise ratio of analyte molecules, especially for the high-mass range. The enhanced performance is prominent for 2-hydroxy-5-methoxybenzoic acid and exists for both proteins and oligosaccharides. It is suggested that the improvement is caused by a disorder in the 2,5DHB crystal lattice allowing ‘softer’ desorption. Charge transfer from matrix ions to additive molecules at the expense of analyte ionization gives a simple explanation for the deteriorating effects of some tested additives.     

Isoliquiritigenin (4,2′,4′-trihydroxychalcone): A new matrix-assisted laser desorption/ionization matrix with outstanding properties for the analysis of neutral oligosaccharides

A novel matrix of isoliquiritigenin (ISL), a flavonoid with a chalcone structure (4,2′,4′-trihydroxychalcone), was demonstrated to be advantageous in the analysis of neutral oligosaccharides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). With ISL as a matrix, adequate signal for an analyte can be obtained in much lower matrix concentrations and laser intensity compared to commonly used MALDI matrices. Four different sample preparation methods were tested, and the dried droplet method exhibited the best performance on MALDI-TOF-MS analysis of oligosaccharides with ISL as a matrix. For the analysis of carbohydrates, compared with popular matrices such as 2,5-dihydroxybenzoic acid (DHB) and 2,4,6-trihydroxyacetophenone (THAP), ISL exhibited outstanding matrix properties as follows: (1) higher homogeneity of crystallization thus allowing automatic data acquisition, (2) better spectral quality in terms of resolution and signal to noise ratio (S N⁻¹), (3) better salt tolerance, (4) higher sensitivity, and (5) enough fragmentation yield to use LIFT-TOF/TOF MS to get richer structural information. In addition, reliable quantitative analysis of oligosaccharides with a good linearity over two concentration orders (1–100 pmol μL⁻¹) and good reproducibility of the signal intensity (RSD less than 15%) were achieved using this matrix. These results give a new outlook on high-speed analysis of neutral carbohydrates by MALDI-TOF MS.     

Matrix-assisted laser desorption/ionization mass spectrometry of acidic glycoconjugates facilitated by the use of spermine as a co-matrix

Negative-ion matrix-assisted laser desorption/ionization mass spectra of sialylated glycoconjugates were acquired employing 2,5-dihydroxybenzoic acid (DHB) in conjunction with spermine as a co-matrix. The addition of spermine to DHB permitted an improved crystal formation as well as a higher analyte solubility. Moreover, DHB/spermine appears to minimize alkali adduct formation, thus allowing the sample analysis without desalting. The combined matrix permitted the analysis of complex sialylated and sialylated/fucosylated structures down to the femtomole range. The ability to use such a matrix also facilitates determination of the sialic acid linkages (in combination with a specific enzyme cleavage). The matrix also appears suitable for studies on gangliosides.     

The improved performance of MALDI‐TOF MS on the analysis of herbal saponins by using DHB‐GO composite matrix

Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) is an excellent analytical technique for rapid analysis of a variety of molecules with straightforward sample pretreatment. The performance of MALDI‐TOF MS is largely dependent on matrix type, and the development of novel MALDI matrices has aroused wide interest. Herein, we devoted to seek more robust MALDI matrix for herbal saponins than previous reported, and ginsenoside Rb1, Re, and notoginsenoside R1 were used as model saponins. At the beginning of the present study, 2,5‐dihydroxybenzoic acid (DHB) was found to provide the highest intensity for saponins in four conventional MALDI matrices, yet the heterogeneous cocrystallization of DHB with analytes made signal acquisition somewhat “hit and miss.” Then, graphene oxide (GO) was proposed as an auxiliary matrix to improve the uniformity of DHB crystallization due to its monolayer structure and good dispersion, which could result in much better shot‐to‐shot and spot‐to‐spot reproducibility of saponin analysis. The satisfactory precision further demonstrated that minute quantities of GO (0.1 μg/spot) could greatly reduce the risk of instrument contamination caused by GO detachment from the MALDI target plate under vacuum. More importantly, the sensitivity and linearity of the standard curve for saponins were improved markedly by DHB‐GO composite matrix. Finally, the application of detecting the Rb1 in complex biological sample was exploited in rat plasma and proved it applicable for pharmacokinetic study quickly. This work not only opens a new field for applications of DHB‐GO in herbal saponin analysis but also offers new ideas for the development of composite matrices to improve MALDI MS performance.     

Flavonoid–matrix cluster ions in MALDI mass spectrometry

The behaviour of 2,5‐dihydroxybenzoic acid (2,5‐DHB) matrix under matrix‐assisted laser desorption/ionisation (MALDI) conditions was investigated, and the formation of 2,5‐DHB cluster ions, mainly dehydrated 2,5‐DHB ions, is reported. Interestingly, in the mass spectra of this compound, besides dimers and trimers, protonated tetramers, pentamers, hexamers and heptamers were also found with significant abundance. The MALDI behaviour of four flavonoids, quercetin, myricetin, luteolin and kaempferol, using 2,5‐DHB as matrix, was also investigated. The mass spectra of the flavonoids studied revealed a number of flavonoid–2,5‐DHB cluster ions (mainly with the dehydrated 2,5‐DHB). The number of clusters formed is dependent on the structure of the analyte. For luteolin and kaempferol, in particular, evidence was found for the formation of cluster ions involving retro Diels Alder fragments and intact flavonoids molecules, as well as the corresponding protonated retro Diels Alder fragments with dehydrated DHB molecules. All ion compositions were attributed taking into account high accuracy mass measurements and tandem mass spectrometry experiments. Copyright © 2009 John Wiley & Sons, Ltd.     

Pre-column derivatization of rofecoxib for determination in serum by HPLC

An HPLC method for determination of rofecoxib in human serum is presented. The method is based on pre-column derivatization of analyte to a phenanthrene derivative of the drug. Rofecoxib and the internal standard were extracted from serum using liquid–liquid extraction. Upon exposure to UV light, the drug was found to undergo a photocyclization reaction, giving a species with high absorbance. Validation of the method has been studied in the concentration range 10–500 ng ml^–1.     

Influence of the laser intensity and spot size on the desorption of molecules and ions in matrix-assisted laser desorption/ionization with a uniform beam profile

The dependence of the number of desorbed particles on laser fluence has been investigated for matrix-assisted laser desorption/ionization (MALDI) of analyte and matrix ions as well as for (photoionized) neutral matrix molecules using a homogeneous “flat-top” laser profile. Laser spot diameters ranging from 10 to 200 μm in size have been used. 2,5-Dihydroxybenzoic acid (DHB) and 3,5-dimethoxy-4-hydroxycinnamic acid (sinapic acid) have been tested as matrices. The threshold (for ion detection) is higher and the dependence of the ion signal upon higher-than-threshold fluences is stronger for directly desorbed ions than for photoionized neutral molecules. Directly desorbed analyte ions exhibit the same dependence on fluence as the matrix ions with only minor differences between the two matrices tested, so both have approximately the same detection threshold. For both ions and photoionized neutral molecules, the fluence threshold increases with decreasing spot size while the slope of the intensity/fluence curves decreases. A quasi-thermal, sublimation/desportion model was found to describe the experimental results with excellent precision. For a complete explanation, non-equilibrium effects had to be taken into account.     

Analysis and validation of perfluorinated compounds in water,sediment and fish with LC-ESI–MS/MS

The analysis of perfluorinated compounds (PFCs) in environmental matrices is challenging, as the concentrations are generally low, but the risk of contamination is high. Sample preparation is a critical step and it is necessary to minimise the possibility of contamination. In this study, we successfully applied and validated a modified ion pair extraction method to quantify PFCs in sediment and fish samples. A large volume injection method was validated and used to quantify PFCs in different water matrices. Isotope internal standard of every analyte was applied to correct matrix effects. The recoveries of the analytes were 92–106% for water matrix, 93–119% for fish matrix and 86–103% for soil matrix whereas the achieved limit of quantitation values were 1.3–14.9 ng/L for water, 0.19–0.28 μg/kg for fish and 0.14–0.41 for soil samples. Thirty-one surface water, 8 stormwater and 41 sediment samples collected all over Estonia were analysed and 4 (out of 8 analysed) PFCs were found in quantitative amount. The most frequently detected analyte perfluorobutanoic acid (PFBA) was found in 26% of the water samples with a maximum concentration of 137 ng/L.