Glycan profiling of monoclonal antibodies using zwitterionic-type hydrophilic interaction chromatography coupled with electrospray ionization mass spectrometry detection

We present a new method for the analysis of glycans enzymatically released from monoclonal antibodies (MAbs) employing a zwitterionic-type hydrophilic interaction chromatography (ZIC–HILIC) column coupled with electrospray ionization mass spectrometry (ESI–MS). Both native and reduced glycans were analyzed, and the developed procedure was compared with a standard HILIC procedure used in the pharmaceutical industry whereby fluorescent-labeled glycans are analyzed using a TSK Amide-80 column coupled with fluorescence detection. The separation of isobaric alditol oligosaccharides present in monoclonal antibodies and ribonuclease B is demonstrated, and ZIC–HILIC is shown to have good capability for structural recognition. Glycan profiles obtained with the ZIC–HILIC column and ESI–MS provided detailed information on MAb glycosylation, including identification of some less abundant glycan species, and are consistent with the profiles generated with the standard procedure. This new ZIC–HILIC method offers a simpler and faster approach for glycosylation analysis of therapeutic antibodies.     

AmSUT1, a sucrose transporter in collection and transport phloem of the putative symplastic phloem loader Alonsoa meridionalis

A sucrose (Suc) transporter cDNA has been cloned from Alonsoa meridionalis, a member of the Scrophulariaceae. This plant species has an open minor vein configuration and translocates mainly raffinose and stachyose in addition to Suc in the phloem (C. Knop, O. Voitsekhovskaja, G. Lohaus [2001] Planta 213: 80-91). These are typical properties of symplastic phloem loaders. For functional characterization, AmSUT1 cDNA was expressed in bakers' yeast (Saccharomyces cerevisiae). Substrate and inhibitor specificities, energy dependence, and Km value of the protein agree well with the properties measured for other Suc transporters of apoplastic phloem loaders. A polyclonal antiserum against the 17 N-terminal amino acids of the A. meridionalis Suc transporter AmSUT1 was used to determine the cellular localization of the AmSUT1 protein. Using fluorescence labeling on sections from A. meridionalis leaves and stems, AmSUT1 was localized exclusively in phloem cells. Further histological characterization identified these cells as companion cells and sieve elements. p-Chloromercuribenzenesulfonic acid affected the sugar exudation of cut leaves in such a way that the exudation rates of Suc and hexoses decreased, whereas those of raffinose and stachyose increased. The data presented indicate that phloem loading of Suc and retrieval of Suc in A. meridionalis are at least partly mediated by the activity of AmSUT1 in addition to symplastic phloem loading.     

Separation of Organoarsenicals by Means of Zwitterionic Hydrophilic Interaction Chromatography (ZIC®‐HILIC) and Parallel ICP‐MS/ESI‐MS Detection

An analytical scheme was developed for the separation and detection of organoarsenicals using a zwitterionic stationary phase of hydrophilic interaction chromatography (ZIC^®‐HILIC) coupled in parallel to electrospray ionization mass spectrometry (ESI‐MS) and to inductively coupled plasma mass spectroscopy (ICP‐MS). The optimization of separation and detection for organoarsenicals was mainly focused on the influence of the percentage of acetonitrile (MeCN) used as a major component of the mobile phase. Isocratic and gradient elution was applied by varying the MeCN percentage from 78 % to 70 % MeCN and 22 % to 30 % of an aqueous solution of ammonium acetate (125 mM NH₄Ac; pH 8.3) on a ZIC^®‐HILIC column (150 × 2.1 mm id, 3.5 μm), to allow for the separation and successful detection of nine organoarsenicals (i.e., 3‐nitro‐4‐hydroxyphenylarsonic acid (roxarsone, Rox), phenylarsonic acid (PAA), p‐arsanilic acid (p‐ASA), phenylarsine oxide (PAO), dimethylarsinate (DMA), methylarsonate (MMA), arsenobetaine (AsB), arsenocholine (AsC) and trimethylarsine oxide (TMAO)) within 45 min. All analytes were prepared in the mobile phase. The flow rate of the mobile phase, the splitting ratio between ICP‐MS and ESI‐MS detection, and the oxygen addition were adapted to ensure that there appeared a stably burning inductively coupled plasma. Furthermore, the analytical method was evaluated by the identification and quantification of AsB in the reference material DORM‐2 (dogfish muscle) resulting in a 95‐% recovery with respect to the AsB concentration in the extract.     

丛枝菌根真菌萌发孢子利用不同氮素及外源葡萄糖对其代谢的影响

对各种含氮基质、葡萄糖和(或)根浸出液中培养的丛枝菌根真菌Glomus intraradices孢子,在萌发过程中对不同氮素的利用及其氨基酸的生物合成进行了研究.用稳定同位素标记及质谱仪来分析不同氮素的利用和氨基酸的生物合成.以高效液相色谱测量氨基酸的浓度.在缺少外源氮素的情况下,丛枝菌根真菌孢子萌发时可以利用内部储存的含氮化合物生物合成游离氨基酸.其中,丝氨酸和甘氨酸是大量合成的氨基酸.合成的氨基酸浓度在2周内随着萌发时间的增加而增加.在有可利用的外源无机氮(铵盐、硝酸盐和尿素)和有机氮(氨基酸)时,铵盐和尿素比硝酸盐更容易被AM真菌萌发孢子利用,而其利用氨基酸中的氮比无机氮源慢的多.孢子吸收同化外源无机氮,且将其整合到游离氨基酸中,这些新生氨基酸浓度比无外源氮添加时要高得多.在无葡萄糖添加的硝酸盐培养液中,AM真菌孢子中积累大量天冬酰胺.然而,在含有葡萄糖的培养液中,萌发孢子因葡萄糖的吸收促进了对外源氮的吸收,产生的游离氨基酸是无葡萄糖时的5倍,并且发现精氨酸转为含量最多的游离氨基酸.并且,从外源氮吸收同化的氮可以储存于精氨酸中,随之,精氨酸被整合到AM真菌孢子储存的蛋白质中.此外,根浸出原液在AM真菌孢子萌发2周后对氮的吸收作用不明显.     

Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection

The diversity and complexity of proteins and peptides in biological systems requires powerful liquid chromatography-based separations to optimize resolution and detection of components. Proteomics strategies often combine two orthogonal separation modes to meet this challenge. In nearly all cases, the second dimension is a reverse phase separation interfaced directly to a mass spectrometer. Here we report on the use of hydrophilic interaction chromatography (HILIC) as part of a multidimensional chromatography strategy for proteomics. Tryptic peptides are separated on TSKgel Amide-80 columns using a shallow inverse organic gradient. Under these conditions, peptide retention is based on overall hydrophilicity, and a separation truly orthogonal to reverse phase is produced. Analysis of tryptic digests from HeLa cells yielded numbers of protein identifications comparable to that obtained using strong cation exchange. We also demonstrate that HILIC represents a significant advance in phosphoproteomics analysis. We exploited the strong hydrophilicity of the phosphate group to selectively enrich and fractionate phosphopeptides based on their increased retention under HILIC conditions. Subsequent IMAC enrichment of phosphopeptides from HILIC fractions showed better than 99% selectivity. This was achieved without the use of derivatization or chemical modifiers. In a 300-microg equivalent of HeLa cell lysate we identified over 1000 unique phosphorylation sites. More than 700 novel sites were added to the HeLa phosphoproteome.     

Evaluation of reversed-phase columns for the analysis of heterocyclic aromatic amines by liquid chromatography-electrospray mass spectrometry

Liquid chromatography coupled to mass spectrometry (LC-MS), especially by the use of electrospray ionisation source (ESI), is currently used for the analysis of heterocyclic aromatic amines (HAs) in complex samples. The present paper describes the study of the performance of different narrow-bore reversed-phase columns to achieve the best chromatographic separation for the determination of 16 HAs by LC-ESI-MS in food samples. Different parameters such as peak symmetry, resolution and number of theoretical plates have been evaluated for each column, using different chromatographic conditions. The column that provided the best results was TSK Gel Semi-Micro ODS-80TS of Tosohaas. Quality parameters have been established, obtaining good short-term precision in all cases (relative standard deviation (R.S.D.) lower than 7.7%) and low limits of detection (<13 pg injected in MS and <16 pg injected in MS/MS). The content of HAs in two beef extracts have been determined.     

Chiral separation of underivatized amino acids in supercritical fluid chromatography with chiral crown ether derived column

The supercritical fluid chromatographic separation of underivatized amino acids was explored using immobilized chiral crown ether column CROWNPAK CR-I (+) and mass spectrometric detection. The type of modifier, acidic additives, and the role of water were investigated. Enantioseparation was achieved for all 18 amino acids investigated with short retention times (less than 3 minutes) and average resolution of greater than 5.0. Analysis of enantiomerically pure standards demonstrated the D enantiomer eluted first for all amino acids using a CROWNPAK CR-I (+) column.     

Comparison of rapid liquid chromatography-electrospray ionization-tandem mass spectrometry methods for determination of glycoalkaloids in transgenic field-grown potatoes

Two rapid methods for highly selective detection and quantification of the two major glycoalkaloids in potatoes, alpha-chaconine and alpha-solanine, were compared for robustness in high-throughput operations for over 1000 analytical runs using potato tuber samples from field trials. Glycoalkaloids were analyzed using liquid chromatography coupled to tandem mass spectrometry in multiple reaction monitoring mode. An electrospray interface was used in the detection of glycoalkaloids in positive ion mode. Classical reversed phase (RP) and hydrophilic interaction (HILIC) columns were investigated for chromatographic separation, ruggedness, recovery, precision, and accuracy. During the validation procedure both methods proved to be precise and accurate enough in relation to the high degree of endogenous biological variability found for field-grown potato tubers. However, the RP method was found to be more precise, more accurate, and, more importantly, more rugged than the HILIC method for maintaining the analytes' peak shape symmetry in high-throughput operation. When applied to the comparison of six classically bred potato cultivars to six genetically modified (GM) lines engineered to synthesize health beneficial inulins, the glycoalkaloid content in potato peels of all GM lines was found within the range of the six cultivars. We suggest complementing current unbiased metabolomic strategies by validating quantitative analytical methods for important target analytes such as the toxic glycoalkaloids in potato plants.     

Peptide analysis: solid phase extraction-elution on diamond combined with atmospheric pressure matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry

Electrospray ionization (ESI) has been an indispensable ion generation technique for mass spectrometric analysis of biopolymers such as intact proteins and protein digests operated at atmospheric pressure. Since its advent in 1998, atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) quickly became a popular alternative for the analysis of peptides. Although AP-MALDI sources typically share the same vacuum interface and ion transmission hardware with ESI, it is generally found that ESI is superior in detection sensitivity. Here we present a method based on solid phase extraction and elution with surface-functionalized diamond nanocrystals (which we previously referred to as "SPEED") that not only streamlines AP-MALDI mass spectrometric analyses of peptides and other small biomolecules under typical operational conditions but also outruns ESI in ultimate detectable concentration by at least one order of magnitude.     

Comprehensive proteomic mass spectrometric characterization of human cannabinoid CB2 receptor

The CB1 and CB2 cannabinoid receptors belong to the GPCR superfamily and are associated with a variety of physiological and pathophysiological processes. Both receptors, with several lead compounds at different phases of development, are potentially useful targets for drug discovery. For this reason, fully elucidating the structural features of these membrane-associated proteins would be extremely valuable in designing more selective, novel therapeutic drug molecules. As a first step toward obtaining information on the structural features of the drug-receptor complex, we describe the full mass spectrometric (MS) analysis of the recombinant human cannabinoid CB2 receptor. This first complete proteomic characterization of a GPCR protein beyond rhodopsin was accomplished by a combination of several LC/MS approaches involving nanocapillary liquid chromatography, coupled with either a quadrupole-linear ion trap or linear ion trap-FTICR mass spectrometer. The CB2 receptor, with incorporated N-terminal FLAG and C-terminal HIS6 epitope tags, was functionally expressed in baculovirus cells and purified using a single step of anti-FLAG M2 affinity chromatography. To overcome the difficulties involved with in-gel digestion, due to the highly hydrophobic nature of this membrane-associated protein, we conducted in-solution trypsin and chymotrypsin digestions of purified and desalted samples in the presence of a low concentration of CYMAL5. This was followed by nanoLC peptide separation and analysis using a nanospray ESI source operated in the positive mode. The results can be reported confidently, based on the overlapping sequence data obtained using the highly mass accurate LTQ-FT and the 4000 Q-Trap mass spectrometers. Both instruments gave very similar patterns of identified peptides, with full coverage of all transmembrane helices, resulting in the complete characterization of the cannabinoid CB2 receptor. Mass spectrometric identification of all amino acid residues in the cannabinoid CB2 receptor is a key step toward the "Ligand Based Structural Biology" approach developed in our laboratory for characterizing ligand binding sites in GPCRs using a variety of covalent cannabinergic ligands.     

Direct liquid introduction LC/MS microbore experiments for the analysis of nucleoside material present in human urine

In order to obtain detection limits low enough for the analysis of nucleoside material in biological samples, a direct liquid introduction (liquid chromatographic/mass spectrometric DLI) system was upgraded by inserting a self-built desolvation chamber between the DLI probe and the ion source and by switching to microbore high-performance liquid chromatography (HPLC) on a C-18 column. The system was evaluated for the analysis of pure nucleoside and 2'-deoxynucleoside compounds in CH3OH + H2O (80/20) and for the analysis of nucleoside mixtures which were separated using 0.01 M ammonium formate + methanol (97:3) as eluant. The detection of structurally important fragment ions in the lower mass region which could not be observed before and an enhanced sensitivity are considered to be the main improvements. In combination with an appropriate clean-up procedure the system was evaluated for the DLI liquid chromatographic/mass spectrometric analysis of some nucleosides present in a human urine sample. Pseudouridine and 5,6-dihydrouridine were detected and identified.     

Phloem loading and unloading of sugars and amino acids

In terrestrial higher plants, phloem transport delivers most nutrients required for growth and storage processes. Some 90% of plant biomass, transported as sugars and amino nitrogen (N) compounds in a bulk flow of solution, is propelled though the phloem by osmotically generated hydrostatic pressure differences between source (net nutrient export) and sink (net nutrient import) ends of phloem paths. Source loading and sink unloading of sugars, amino N compounds and potassium largely account for phloem sap osmotic concentrations and hence pressure differences. A symplasmic component is characteristic of most loading and unloading pathways which, in some circumstances, may be interrupted by an apoplasmic step. Raffinose series sugars appear to be loaded symplasmically. However, sucrose, and probably certain amino acids, are loaded into minor veins from source leaf apoplasms by proton symporters localized to plasma membranes of their sieve element/companion cell (se/cc) complexes. Sucrose transporters, with complementary kinetic properties, are conceived to function as membrane transporter complexes that respond to alterations in source/sink balance. In contrast, symplasmic unloading is common for many sink types. Intervention of an apoplasmic step, distal from importing phloem, is reserved for special situations. Effluxers that release sucrose and amino acids to the surrounding apoplasm in phloem loading and unloading are yet to be cloned. The physiological behaviour of effluxers is consistent with facilitated membrane transport that can be energy coupled. Roles of sucrose and amino acid transporters in phloem unloading remain to be discovered along with mechanisms regulating symplasmic transport. The latter is hypothesized to exert significant control over phloem unloading and, in some circumstances, phloem loading.     

Detection of the illegal use of ethinylestradiol in cattle urine by gas chromatography—mass spectrometry

A method for the detection of ethinylestradiol in cattle urine is described, based on enzymic hydrolysis of the sample, clean-up by means of disposable octadecyl and amino solid-phase extraction columns, fractionation by reversed-phase high-performance liquid chromatography, and detection by gas chromatography—mass spectrometry (selected-ion monitoring). Identification is based on both gas chromatographic and mass spectrometric data. The method has been tested on urine samples for a collaborative study and all the results found were correct.     

Hydrophilic interaction liquid chromatography and accurate mass measurement for quantification and confirmation of morphine, codeine and their glucuronide conjugates in human urine

A hydrophilic interaction liquid chromatography-time-of-flight mass spectrometry (HILIC-TOFMS) method for the quantification and confirmation of morphine (M), codeine (C), morphine-3-glucuronide (M3G), morphine-6-glucuronide (M6G) and codeine-6-glucuronide (C6G) is presented. The method was validated in terms of specificity, selectivity, extraction recovery, accuracy, repeatability, linearity and matrix effect. After a straightforward sample preparation by solid phase extraction (SPE) the compounds were analyzed directly without the need for hydrolysis, solvent transfer, evaporation or reconstitution. The HILIC technique provided good chromatographic separation which was critical for isomers M3G and M6G. The analytes were detected after electrospray ionization (ESI) in positive mode with mass accuracies below 2 mDa using a 5-mDa window. A measurement range of 50-5000 ng/ml was applied for calibration using deuterated analogs as internal standards. The precision of the method was 5.7% and 10.2% (RSD) within and between days, respectively. The applicability of the method was demonstrated with authentic urine samples known to contain codeine and/or morphine and their intact glucuronide conjugates. Identification of the analytes was based on in-source collision induced dissociation (ISCID), applying three diagnostic ions with accurate mass.     

Comparison of the sensitivity of evaporative universal detectors and LC/MS in the HILIC and the reversed-phase HPLC modes

It was hypothesized that the hydrophilic interaction liquid interface chromatography (HILIC) mode should produce more response than the reversed-phase HPLC mode on detectors with an evaporative component to the detection process. HILIC mobile phases are mostly composed of polar organic solvent and are more volatile than reversed-phase mobile phases. Therefore the more easily evaporated HILIC mobile phases should produce greater sensitivity for those detectors that remove mobile phase by evaporation. The responses of 12 compounds were measured in the reversed-phase mode and the HILIC mode with three detectors: evaporative light scattering detector (ELSD), corona charged aerosol detector (cCAD), and electrospray mass spectrometry (ESI-MS). The compounds studied were very polar compounds that were retained in the HILIC mode. Generally, the HILIC mode was able to achieve greater sensitivity than the reversed-phase mode for these compounds. The increases in sensitivity observed can be attributed to the more volatile HILIC mobile phase. For the ELSD, the HILIC mode produced slightly greater sensitivity than the reversed-phase mode. The cCAD was approximately 10 times more sensitive in the HILIC mode and the ESI-MS was approximately 5–10 times more sensitive in the HILIC mode. There was one instance in the study where a compound produced more response in the reversed-phase mode. Thymine yielded more sensitivity in the reversed-phase mode with the ESI-MS detector. In a given mode of operation, there was significant variation in the measured response factors for all compounds on each detector. While this is not unexpected for the ESI-MS detector, variation in the response factors between compounds indicates that the cCAD and ELSD are not truly universal detectors in the sense that all compounds have identical responses.     

Quantification of indole-3-acetic acid and amino acid conjugates in rice by liquid chromatography-electrospray ionization-tandem mass spectrometry

A method for quantifying indole-3-acetic acid (IAA) and its conjugates with the six amino acids, Ala, -Asp, -Ile, -Glu, -Phe and -Val, in rice (Oryza sativa) by using high-performance liquid chromatography coupled with electrospray ionization and tandem mass spectrometry (HPLC-ESI-MS/MS) is described. Samples from the rice plant or callus were treated with 80% acetone in water containing 2.5 mM diethyl dithiocarbamate. Each extract was partially purified in C18 cartridge column for solid-phase extraction (SPE) and subjected to HPLC-ESI-MS/MS without converting the product. The detection limit was 3.8 fmol for IAA, and 0.4-2.9 fmol for the IAA amino acid conjugates. The method was applied to the analysis of IAA and its conjugates in rice seedlings, dehulled rice and calli, using 20-100 mg tissue samples.     

MCX based solid phase extraction combined with liquid chromatography tandem mass spectrometry for the simultaneous determination of 31 endocrine-disrupting compounds in surface water of Shanghai

A novel analytical method employing MCX (mixed-mode cationic exchange) based solid phase extraction (SPE) coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS) was developed to detect 31 endocrine-disrupting compounds (EDCs) in surface water samples simultaneously. The target EDCs belong to five classes, including seven estrogens, eight androgens, six progesterones, five adrenocortical hormones and five industrial compounds. In order to simultaneously concentrate the target EDCs and eliminate matrix interferences in the water samples, MCX SPE cartridges were employed for SPE, and then followed by a simple and highly efficient three-step sequential elution procedure. Two electrospray ionization (ESI) detection modes, positive (ESI+) and (ESI-), were optimized for HPLC-MS/MS analysis to obtain the highest sensitivity for all the EDCs. The limits of detection (LODs) were 0.02-1.9 ng L(-1), which are lower than or comparable to these reported in references. Wide linear ranges (LOD-100 ng L(-1) for ESI+ mode, and LOD-200 ng L(-1) for ESI- mode) were obtained with determination coefficients (R(2)) higher than 0.99 for all the compounds. With five internal standards, good recoveries (84.4-103.0%) of all the target compounds were obtained in selected surface water samples. The developed method was successfully applied to investigate the EDCs occurrence in the surface water of Shanghai by analyzing surface water samples from 11 sites. The results showed that nearly all the target compounds (30 in 31) were present in the surface water samples of Shanghai, of which three industrial compounds (4-t-OP, BPA, and BPF) showed the highest concentrations (median concentrations were 11.88-23.50 ng L(-1)), suggesting that industrial compounds were the dominating EDCs in the surface water of Shanghai, and much more attention should be paid on these compounds. Our present research demonstrated that SPE with MCX cartridges combined with HPLC-MS/MS was convenient, efficient and reliable for multiclass analysis of EDCs in surface water.     

Mass determination of low-molecular-weight proteins in phloem sap using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The low-molecular-weight (LMW), low-abundance protein composition of lupin and pea phloem exudates was determined using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS)> Phloem sap was collected from lupin inflorescence stalks and pods (using shallow incisions) or pea seedlings (by placing cut stems in an EDTA solution). Western blot analysis of phloem exudate proteins with either a polyclonal antibody raised against Ricinus communis sieve-tube exudate proteins or pea Rubisco antibody revealed that the collected exudates contained phloem sap, and that contamination with other plant fluids was negligible. Three matrix combinations were tested to assess their ability to facilitate protein ionization. Sinapinic acid in combination with trifluoroacetic acid yielded the cleanest mass spectra, and revealed an array of LMW proteins ranging from 2 to 10 kDa. For pea phloem exudate, the addition of protease inhibitors to the exudate collection solution prevented proteolysis of endogenous proteins; the inhibitors did not interfere with the detection of proteins. The sensitivity of this technique was sufficient to detect changes in LMW phloem peptides throughout plant development in lupin, or to detect differences in the phloem peptide composition of two genotypes of pea. Because only limited sample preparation is required, MALDI-TOF-MS is a useful technique for characterizing complex fluids such as phloem sap.     

Determination of azatadine in human plasma by liquid chromatography/tandem mass spectrometry

A sensitive method using liquid chromatography with tandem mass spectrometric detection (LC-MS/MS) was developed and validated for the analysis of antihistamine drug azatadine in human plasma. Loratadine was used as internal standard (IS). Analytes were extracted from human plasma by liquid/liquid extraction using ethyl acetate. The organic phase was reduced to dryness under a stream of nitrogen at 30 °C and the residue was reconstituted with the mobile phase. 5 μL of the resulting solution was injected onto the LC-MS/MS system. A 4.6 mm × 150 mm, I.D. 5 μm, Agilent TC-C(18) column was used to perform the chromatographic analysis. The mobile phase consisted of ammonium formate buffer 0.010 M (adjusted to pH 4.3 with 1M formic acid)/acetonitrile (20:80, v/v) The chromatographic run time was 5 min per injection and flow rate was 0.6 mL/min. The retention time was 2.4 and 4.4 min for azatadine and IS, respectively. The tandem mass spectrometric detection mode was achieved with electrospray ionization (ESI) iron source and the multiple reaction monitoring (MRM) (291.3 → 248.2m/z for azatadine, 383.3 → 337.3m/z for IS) was operated in positive ion modes. The low limit of quantitation (LLOQ) was 0.05 ng/mL. The intra-day and inter-day precision of the quality control (QC) samples was 8.93-11.57% relative standard deviation (RSD). The inter-day accuracy of the QC samples was 96.83-105.07% of the nominal values.     

A comparative study of amino acid measurement in leaf extracts by gas chromatography-time of flight-mass spectrometry and high performance liquid chromatography with fluorescence detection

Gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF-MS) has become a promising technique for simultaneous and rapid analysis of small metabolites in complex mixtures. The aim of this work was to establish the quantitative nature of the information generated by amino acid analysis of crude leaf extracts using GC-TOF-MS. Dried aliquots of methanol/water extracts of Arabidopsis leaves were analysed in parallel by GC-TOF-MS following trimethylsilylation or high performance liquid chromatography and fluorescence detection of o-phthaldialdehyde derivatives (OPA-HPLC). Twenty amino acids could be routinely detected in leaf extracts by both methods. Because of instability of some trimethylsilylated derivatives, all GC-TOF-MS analyses were performed within a window of 2 h 30 min following derivatization. Repeatability studies showed that relative standard deviations for multiple injections of a single extract were below 20% for both techniques, though significantly smaller for OPA-HPLC. Similar between-extract variability and condition-independent biological variation were detected by OPA-HPLC and GC-TOF-MS, and both techniques detected similar environmentally induced changes in four major amino acids. Recovery of standard compounds through the extraction procedure was between 80% and 120% for OPA-HPLC but more variable when analysed by GC-TOF-MS. When quantified on the basis of tissue fresh weight according to response factors of mixed standards, the two techniques gave consistent values for a number of amino acids but divergent values for others. Taken together, the results suggest GC-TOF-MS analysis of Arabidopsis leaves with the present protocol can be used for absolute quantification of 4–7 amino acids, accurate relative quantification of 8–11 amino acids, and more limited quantification for five compounds of this class.