The authors would like to acknowledge the financial support of this project by The J.M. Smucker company.

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P., Buchanan, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Food Microbiology: Fundamentals and Frontiers. , (2013).</li><li>T&#367;ma, P., Samcov&#225;, E., &#352;tul&#236;k, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+the+Spectrum+of+Low+Molecular+Mass+Organic+Acids+in+Urine+by+Capillary+Electrophoresis+with+Contactless+Conductivity+and+Ultraviolet+Photometric+Detection-An+Efficient+Tool+for+Monitoring+of+Inborn+Metabolic+Disorders.">Determination of the Spectrum of Low Molecular Mass Organic Acids in Urine by Capillary Electrophoresis with Contactless Conductivity and Ultraviolet Photometric Detection-An Efficient Tool for Monitoring of Inborn Metabolic Disorders.</a> Anal Chim Acta. 685 (1), 84-90 (2011).</li><li>L&#243;pez-Bucio, J., Nieto-Jacobo, M. F., Ram&#305;&#769;rez-Rodr&#305;&#769;guez, V., Herrera-Estrella, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organic+Acid+Metabolism+in+Plants:+From+Adaptive+Physiology+to+Transgenic+Varieties+for+Cultivation+in+Extreme+Soils.">Organic Acid Metabolism in Plants: From Adaptive Physiology to Transgenic Varieties for Cultivation in Extreme Soils.</a> Plant Sci. 160 (1), 1-13 (2000).</li><li>Cebolla-Cornejo, J., Valc&#225;rcel, M., Herrero-Mart&#236;nez, J. 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M., Maquieira, A., Nuez, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simultaneous+Quantification+of+the+Main+Organic+Acids+and+Carbohydrates+Involved+in+Tomato+Flavour+Using+Capillary+Zone+Electrophoresis.">Simultaneous Quantification of the Main Organic Acids and Carbohydrates Involved in Tomato Flavour Using Capillary Zone Electrophoresis.</a> J Sci Food Agr. 82 (10), 1101-1106 (2002).</li><li>Wasielewska, M., Banel, A., Zygmunt, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Capillary+Electrophoresis+in+Determination+of+Low+Molecular+Mass+Organic+Acids.">Capillary Electrophoresis in Determination of Low Molecular Mass Organic Acids.</a> Int J Environ Sci Dev. 5 (4), 417-425 (2014).</li><li>Galli, V., Garc&#236;a, A., Saavedra, L., Barbas, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Capillary+Electrophoresis+for+Short-Chain+Organic+Acids+and+Inorganic+Anions+in+Different+Samples.">Capillary Electrophoresis for Short-Chain Organic Acids and Inorganic Anions in Different Samples.</a> Electrophoresis. 24 (1213), 1951-1981 (2003).</li><li>Klampfl, C. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+Organic+Acids+by+CE+and+CEC+Methods.">Determination of Organic Acids by CE and CEC Methods.</a> Electrophoresis. 28 (19), 3362-3378 (2007).</li><li>Kenney, B. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+Organic+Acids+in+Food+Samples+by+Capillary+Electrophoresis.">Determination of Organic Acids in Food Samples by Capillary Electrophoresis.</a> J Chromatogr A. 546, 423-430 (1991).</li><li>Galli, V., Barbas, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Capillary+Electrophoresis+for+the+Analysis+of+Short-Chain+Organic+Acids+in+Coffee.">Capillary Electrophoresis for the Analysis of Short-Chain Organic Acids in Coffee.</a> J Chromatogr A. 1032 (1-2), 299-304 (2004).</li><li>Schmitt-Kopplin, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Capillary+Electrophoresis:+Methods+and+Protocols.">Capillary Electrophoresis: Methods and Protocols.</a> Methods in Molecular Biology. , 384 (2008).</li><li>Nollet, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Chromatographic analysis of the environment 3rd ed. , (2006).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> ElixerOA Organic Acids/Anions Operating and Instruction Manual, MicroSolv Technology Corperation. , (2001).</li><li>Dahlen, J., Hagberg, J., Karlsson, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+low+molecular+weight+organic+acids+in+water+with+capillary+zone+electrophoresis+employing+indirect+photometric+detection.">Analysis of low molecular weight organic acids in water with capillary zone electrophoresis employing indirect photometric detection.</a> Fresenius J. Anal. Chem. 366 (5), 488-493 (2000).</li><li>Ibanez, A. B., Bauer, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analytical+method+for+the+determination+of+organic+acids+in+dilute+acid+pretreated+biomass+hydrolysate+by+liquid+chromatography-time-of-flight+mass+spectroscopy.">Analytical method for the determination of organic acids in dilute acid pretreated biomass hydrolysate by liquid chromatography-time-of-flight mass spectroscopy.</a> Biotech. For Biofuels. 7 (145), (2014).</li></ol>

The authors declare that they have no competing financial interests.

As with any analytical technique, there are several critical factors that can significantly impact the quality and reliability of the data generated. First, it is important to process samples efficiently, with a minimum of freeze/thaw cycles. Repeated freezing and thawing can compromise the chemical composition of the sample before processing or analysis. Second, it is critical to apply the steps of this protocol to all samples consistently and evenly. Technical errors arising from inconsistent sample preparation and handling can significantly impact the quality of the data generated, and result in increased &#34;noise&#34; in the SCCA measurements. For example, the particle size of the sample post-grinding will impact the speed and efficiency of SCCA extraction. It is therefore critical to ensure that the samples are ground to a uniform particle size, as this will maintain extraction efficiency across samples and help to reduce sample-to-sample variability. Similarly, accurate measurement and pipetting during the preparation of standard solutions, accurate measurement of sample masses, and careful monitoring (and normalization) of extraction times will result in the generation of more uniform data. Taking time to carefully normalize, measure, and record each of these parameters will ensure the reliability of the data and allow for accurate post-run correction of data for any processing errors which may occur. Third, it is critical to select and use an appropriate internal standard. Calculations of the final analyte concentration will rely heavily on accurate correction based on the peak area of the internal standard observed in each sample. Because of this, it is critical that the internal standard be both accurately and precisely measured; and should ideally not occur naturally in the sample or co-elute with other compounds. Not only does the proper selection and use of an internal standard in all samples enable the researcher to control for changes in metabolite levels observed due to differences in extraction efficiency; it also greatly simplifies downstream processing and peak identification. Finally, it is necessary to monitor the peak identification and integration process. While automated processing algorithms are useful, they are not perfect. The data generated by this technique rely on the accuracy of integration, and the traces must be checked manually to ensure the quality of integration events, particularly the definition of peak boundaries and baselines.
As with any analytical procedure, it is important to establish that the CZE method presented here is: a. accurate: able to determine the amount of a given SCCA present; b. precise: capable of reproducibly quantifying SCCAs within the same day and in measurements made across several days of analysis; and c. robust: capable of recovering most of the SCCAs present in the samples being analyzed. As shown above in the representative results, the method described here is capable of accurately determining the amounts of SCCAs present in samples. All the SCCAs measured (citric, malic, acetic, and lactic acid) and the internal standard (adipic acid) exhibited a linear response in the 0-80 ng/&#181;l concentration range. Additionally, the LOQs and LODs for these acids ranged from 2-4 ng/&#181;l and 1-2 ng/&#181;l, respectively. The method was also precise, as all of the SCCAs measured and the adipic acid internal standard exhibited low intra-day variability, falling between 2.0-5.5% of the peak area (or between 1.0-5.2% of the calculated concentration) for all SCCAs measured. The inter-day variability of SCCA measurements was also relatively low, falling between 3.05-10.10% of the peak area (or between 3.30-10.95% of the calculated concentration) for all SCCAs measured. Interestingly, with the exception of acetic acid, which was consistently at or close to the limit of detection/quantification in all coffee samples analyzed, correcting samples using adipic acid as an internal standard resulted in more reproducible measurements and a decrease in the coefficient of variability (see Representative Results, above). These data are consistent with previously published results indicating that correction with an internal standard is essential in maintaining precision in CE analyses over time16. While some methods have employed inorganic ions as an internal standard, we felt that adipic acid was a more appropriate standard for the CZE method presented here, as it is an organic acid and therefore more likely to experience loss in the sample preparation steps similar to that experienced by the SCCAs of interest in the sample. Adipic acid had the additional advantages of not being present in the coffee samples being examined, exhibiting a linear response across the same concentrations used for SCCAs in this study, exhibiting relatively low LOD/LOQ values (1 ng/&#181;l and 4 ng/&#181;l, respectively), and a high percent recoverability from the coffee matrix (100.19% &#177; 2.57), making it a useful standard for quantifying SCCAs in coffee samples. Interestingly, the high percent recovery observed for adipic acid was achievable for all organic acids measured in this study, which exhibited percent recovery values ranging from 91.94-106.08%. These data indicate that the CZE method presented here is capable of recovering most of the SCCAs present in coffee samples.
Adapting this protocol to new sample types requires the collection of preliminary data, based on literature or empirical evidence, concerning the expected amounts of targeted analytes. This information will help guide the experimental design, sample preparation, and standard curve construction. Determining the correct sample dilution to use can be easily accomplished empirically by running a dilution series of a test extract to find a proper working dilution. This protocol was designed to detect the SCCAs outlined in the example results, but it could easily be adapted to detect other SCCAs by altering the separation parameters, such as separation voltage, pressure, or time. It is important to remember, however, that altering the separation parameters may alter the number of runs that can be accomplished on a single set of separation buffers as these buffers degrade with use. Baseline degradation or changes in current are often manifestations of over-used/depleted buffers. Replacing the running buffer and reconditioning the capillary can often resolve these problems. After extended use, the ability of the capillary to resolve analytes will decrease as well. Decreased baseline stability, drastic shifts in retention time, and reduced peak resolution are all signs that the capillary may need to be replaced. It is also possible to receive a pressure error resulting from improper sealing between the sample vial and the capillary due to an ill-fitting vial cap or a defective vial. Ensure the caps fit snugly into the sample vials to prevent this error.
Traditionally, chromatographic methods such as GC-MS, GC-FID, or HPLC have been used to detect SCCAs in a wide range of matrices, including air, water, soil, and plant samples14. While effective, a major drawback in these methods is the need to derivatize SCCAs before detection. Derivatization uses hazardous reagents the limit of detection is often affected by the efficiency of the derivatization reaction13,14. The detection of non-derivatized SCCAs through CZE avoids analyte loss during processing, exposure to hazardous derivatizing agents, and reduces sample preparation time. These benefits can be seen in the high percent recovery rates (ranging between 91.94-106.08%) calculated for all SCCAs measured in this study. In addition, CZE quantification of SCCAs achieves limits of detection comparable to those reported in literature for GC-MS, GC-FID, and HPLC, in the range of parts per million to parts per billion13,14. When combined with high-speed run times, high-resolution separation power, the straight-forward sample processing protocols employed by this method of analysis, the sensitivity and convenience of CZE make it an attractive alternative to traditional GC or HPLC methods.
However, it is important to note that, while CZE provides several advantages over GC-MS HPLC, or LC-MS/MS based methods of SCCA analysis, it is not appropriate for all SCCA analyses. For example, since the CZE method described here relies solely on spectrophotometric detection, it does not allow for the identification of unknown SCCAs present in the sample, or the confirmation of SCCA identity via mass spectral profiling. Because of this, GC-MS or LC-MS/MS methods would be better suited for SCCA analyses in samples containing large numbers of unknown SCCAs, or samples in which it is critical to confirm the identity of all SCCAs present. Additionally, as previously reported LC-MS/MS based methods allow for lower limits of detection (LODs)-on average, 0.05 &#181;g/ml for LC-MS/MS17 vs. the 1 &#181;g/ml for CZE obtained using the method presented here-LC-MS/MS based quantification of SCCAs may be more appropriate for samples in which SCCAs are present in very low or trace amounts.
The protocol presented here focuses on the extraction and quantification of short chain carboxylic acids (SCCAs) from plant tissues. Obtaining proficiency in this technique will open the door to a wide range of applications of this technology for the individual researcher. This technique, with only slight variations in methodology, has been successfully employed in the analysis of SCCAs in a diverse population of samples and substrates, ranging from food products and tissue samples to environmental water and soil samples8. Additionally, gaining familiarity with the chemical principals underlying this technology though this protocol will provide researchers with the knowledge base needed to attempt the analysis of other compounds, such as carbohydrates or metals8,13. The analytical flexibility of capillary electrophoresis makes it an extraordinarily powerful tool suitable for a myriad of experimental applications.

Carboxylic acids are organic compounds containing one or more terminal carboxyl functional groups, each attached to an R-group containing one or more carbons (R-C[O]OH). Short chain, low molecular weight carboxylic acids (short chain carboxylic acids, SCCAs) containing between one and six carbons, are essential components of cellular respiration, and function in several biochemical pathways necessary for cell growth and development. SCCAs play critical roles in cellular metabolism1, cell signaling2, and organismal responses to the environment (such as antibiosis3). Because of this, SCCAs can serve as useful indicators of disruptions to cellular metabolism, plant stress responses4,5, and fruit quality6,7. To date, SCCAs have been quantified primarily through chromatographic techniques such as high performance liquid chromatography (HPLC) or gas chromatography-mass spectroscopy (GC-MS). While these methods, are capable of achieving very low limits of detection, they can be expensive, require the derivatization of target SCCAs using caustic and/or toxic reagents, and include lengthy separation runs on the GC or HPLC. Because of this, interest in the use of free zonal capillary electrophoresis (CZE), which does not require sample derivatization, to quantify organic acids has steadily increased8.
Free zonal capillary electrophoresis (CZE) is a chromatographic separation methodology that, due to its high number of theoretical plates, speed, and relative ease-of-use, is increasingly replacing both GC-MS and high-pressure liquid chromatography as an analytical method for the quantification (particularly for quality control purposes) of anions, cations, amino acids, carbohydrates, and short chain carboxylic acids (SCCAs)8,9,10. CZE-based separation of small molecules, including SCCAs, is based two primary principles: the electrophoretic movement of charged ions in an electrical field established across the buffer filling the capillary; and the electro-osmotic movement of the entire buffer system from one end of the capillary to the other, generally towards the negative electrode. In this system, small molecules move towards the negative electrode at varying speeds, with the speed of each molecule determined by the ratio of the net charge of the molecule to the molecular mass. As the movement of each individual molecule in this system is dependent on the charge state of the molecule and the overall rate of electro-osmotic flow (which is itself based on the ion content of the buffer used to fill the capillary), the buffer pH and ionic composition heavily impact the degree to which molecules can be efficiently separated using CZE. Because of this, SCCAs, with their relatively high charge-to-mass ratios, are ideal targets for CZE-based separation. Metabolites separated using CZE can be detected using a variety of methods, including UV absorbance, spectral absorbance (which is generally performed using a photo-diode array [PDA]), and/or mass spectroscopy (CE-MS or CE-MS/MS)8. The diversity of separation and detection methods provided by CZE makes it an extremely flexible and adaptable technique. Because of this, CZE has been increasingly applied as a standard method of analysis in the areas of food safety and quality11,12, pharmaceutical research13, and environmental monitoring13,14. 
Capillary electrophoresis has been used to detect and quantify short chain carboxylic acids for nearly two decades13. The resolving power (particularly for small, charged molecules), short run time, and low per sample cost of CZE analyses make CZE an ideal technique for the separation and quantification of SCCAs13. This method presents a protocol to utilize CZE to measure the concentration of organic acids from plant tissues. Example data was generated through the successful implementation of this protocol to measure the change in organic acid levels in coffee seeds following a secondary fermentation treatment. The protocol details the critical steps and common errors of CZE-based separation of SCCAs, and discusses the means by which this protocol can be successfully applied to quantify SCCAs in additional plant tissues.

<table><tbody><tr><td>Ceramic Moarter and Pestle</td><td>Coorstek</td><td>60310</td><td></td></tr><tr><td>Beckman Coulter P/ACE MDQ CE system</td><td>Beckman Coulter</td><td>Various</td><td></td></tr><tr><td>Glass sample vials</td><td>Fisher Inc.</td><td>033917D</td><td></td></tr><tr><td>1.5 ml microcentrifuge tubes&amp;nbsp;</td><td>Fisher Inc.</td><td>02-681-5</td><td></td></tr><tr><td>LC/MS grade water</td><td>Fisher Inc.</td><td>W6-1</td><td>Milli-Q water (18.2&amp;nbsp;M&amp;Omega;&amp;#183;cm) is also acceptable</td></tr><tr><td>15 ml glass tube/ Teflon lined cap&amp;nbsp;</td><td>Fisher Inc.</td><td>14-93331A</td><td></td></tr><tr><td>Parafilm M</td><td>Fisher Inc.</td><td>13-374-12</td><td></td></tr><tr><td>CElixirOA detection Kit pH 5.4&amp;nbsp;</td><td>MicroSolv</td><td>06100-5.4</td><td></td></tr><tr><td>BD Safety-Lok syringes</td><td>Fisher Inc.</td><td>14-829-32</td><td></td></tr><tr><td>17 mm Target Syringe filter, PTFE</td><td>Fisher Inc.</td><td>3377154</td><td></td></tr><tr><td>32 Karat, V. 8.0 control software</td><td>Beckman Coulter</td><td>285512</td><td></td></tr><tr><td>capillary electrophoresis (CE) sample vials&amp;nbsp;</td><td>Beckman Coulter</td><td>144980</td><td></td></tr><tr><td>caps for CE vials&amp;nbsp;</td><td>Beckman Coulter</td><td>144648</td><td></td></tr><tr><td>Liquid Nitrogen</td><td>N/A</td><td>N/A</td><td>Liquid nitrogen is available from most facilities services</td></tr></tbody></table>

using capillary electrophoresis to quantify organic acids from plant tissue: a test case examining coffea arabica seeds

Carboxylic acids are organic acids containing one or more terminal carboxyl (COOH) functional groups. Short chain carboxylic acids (SCCAs; carboxylic acids containing three to six carbons), such as malate and citrate, are critical to the proper functioning of many biological systems, where they function in cellular respiration and can serve as indicators of cell health. In foods, organic acid content can have significant impact on taste, with increased SCCA levels resulting in a sour or &#34;acid&#34; taste. Because of this, methods for the rapid analysis of organic acid levels are of particular interest to the food and beverage industries. Unfortunately, however, most methods used for SCCA quantification are dependent on time-consuming protocols requiring the derivatization of samples with hazardous reagents, followed by costly chromatographic and/or mass spectrometric analyses. This method details an alternate method for the detection and quantification of organic acids from plant material and food samples using free zonal capillary electrophoresis (CZE), sometimes simply referred to as capillary electrophoresis (CE). CZE provides a cost-effective method for measuring SCCAs with a low limit of detection (0.005 mg/ml). This article details the extraction and quantification of SCCAs from plant samples. While the method provided focuses on measurement of SCCAs from coffee beans, the method provided can be applied to multiple plant-based food materials.

This protocol has been successfully utilized to measure the effects of seed treatments on the SCCA content of green coffee seeds. In this experiment, the six treatments were: a saturated microbial suspension of Leuconostoc pseudomesenteroides strain GCP674 in its growth medium (1), an aqueous suspension of GCP674 microbes in water (2), an aqueous solution of acetic and lactic acids (0.15 and 0.4 mg/ml respectively) (3), a spent M1 growth medium treatment (4), dH2O water (5), and an un-treated control (no substance added to seeds) (6). Treatments were applied and allowed to ferment for 24 hours. Four independent replicates were assessed for each treatment. Analysis was conducted for citric (C), malic (M), acetic (A) and lactic (L) acid levels using adipic acid as an internal standard.
For each SCCA and the internal standard, standard curves spanning the range of concentrations predicted to be in coffee samples (5, 10, 20, 40, 60, and 80 ng/&#181;l) were generated. As expected, each acid exhibited a linear response for this concentration range with R-squared values of 0.9876 for citric acid, 0.9987 for malic acid, 0.9998 for acetic acid, and 0.9999 for lactic acid. The internal standard (adipic acid) also exhibited a linear response over this concentration range, yielding an R-squared value of 0.9984. Prior to sample analyses, limits of detection (LOD) and limits of quantitation (LOQ) were determined for each SCCA and the internal standard (adipic acid). The limit of detection of citric, malic, acetic, and adipic acid was 1 ng/&#181;l; and the LOD for lactic acid was 2 ng/&#181;l. The limit of quantitation of citric, adipic, acetic, and lactic acid was 4 ng/&#181;l; and the LOQ for malic acid was 2 ng/&#181;l. To calculate the percent recovery SCCAs and adipic acid, coffee was spiked with individual SCCAs or adipic acid and processed using the protocol described above. The percent recovery was then calculated by using the following formula ([{peak area spiked sample - peak area control sample}/theoretical peak area of calculated concentration of spiked sample {generated by analyzing buffer + SCCA/adipic acid spike}] x 100). Using this method, we calculated percent recoveries of 106.08% &#177; 12.66 for citric acid, 98.35% &#177; 1.15 for malic acid, 91.94% &#177; 3.07 for acetic acid, 97.42% &#177; 1.48 for lactic acid, and 100.19% &#177; 2.57 for adipic acid.
To determine the precision of the method, the intra- and inter-day variability of measurements made using CZE was also calculated. To determine intra-day variability, samples of each SCCA and adipic acid were measured from a single coffee sample five times across a 24-hour period, and coefficients of variability (COV; calculated by dividing the standard deviation in peak area [or concentration] for each SCCA by the average peak area [or concentration] for that SCCA, and then multiplying the result by 100) for each compound were calculated using the peak area. To assess the importance of correcting samples using the internal standard, the coefficient of variance for each SCCA was also calculated using the concentrations of each SCCA calculated using adipic acid as an internal standard. As expected, the CZE method was able to precisely measure SCCAs and adipic acid, with COVs of 3.02% for citric acid, 2.64% for malic acid, 3.74% for acetic acid, and 2.01% for adipic acid (lactic acid was below LOD/LOQ for all coffee samples measured). These measurements were repeated across a five-day period, and the CVs ranged from 2.11-5.25% for citric acid, 2.01-5.32% for malic acid, 1.72-3.74% for acetic acid, and 1.26-3.82% for adipic acid. When peak areas were corrected using the internal standard and calculated concentrations of SCCA were used to calculate COVs, the intra-day COVs ranged from 1.08-4.17% for citric acid, 1.47-3.40% for malic acid, and 2.68-5.10% for acetic acid. To assess inter-day variability, SCCAs in a single coffee sample were measured once per day across a five-day period. This experiment was then repeated five times for each SCCA and adipic acid. The COV for each SCCA was then calculated by dividing the standard deviation in peak area (or concentration) for each SCCA by the average peak area (or concentration) for that SCCA and multiplying by 100. To assess the importance of correcting samples using the internal standard, COVs were also calculated using the concentrations of each SCCA calculated using adipic acid as an internal standard. The CZE method was able to reliably reproduce SCCA measurements, with COVs ranging from 5.24-10.02% for citric acid, 6.55-9.47% for malic acid, 7.67-8.63% for acetic acid, and 3.08-6.57% for adipic acid. When peak areas were corrected using the internal standard and calculated concentrations of SCCA were used to calculated COVs, the inter-day COVs ranged from 4.56-6.23% for citric acid, 3.39-4.99% for malic acid, and 9.5-10.94% for acetic acid.
<img alt="Figure 2" src="/files/ftp_upload/54611/54611fig2.jpg" /> 
Figure 2: Example PDA traces with peaks indicated. Green coffee samples were diluted 1:10 before loading into CE vials. Acids of interest are indicated: acetic acid (A), citric acid (C), lactic acid (L), malic acid (M) and the internal standard, adipic acid (IS). <a href="https://cloudflare-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54611/54611fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Statistical analysis was conducted on corrected acid concentrations using a general linear model (GLM) to determine whether or not treatments altered organic acid levels. A model incorporating &#34;treatment&#34; x &#34;run&#34; (coded as a random factor) was implemented for the GLM. Tukey pairwise comparisons at 95% confidence were used to determine the directionality of changes.
Treatment altered SCCA concentrations in the green coffee. Acetic acid was significantly enriched in all treatments over the no treatment control (GLM, p &#60;0.0001).
<img alt="Figure 3" src="/files/ftp_upload/54611/54611fig3.jpg" /> 
Figure 3: Impact of treatment on organic acid levels in green coffee. Treatment had no impact on (a) citric or malic acid levels in green coffee. However, all treatments significantly increased (b) acetic acid levels compared to no treatment controls (GLM, p &#60;0.001). Increases in acetic acid levels were greatest with the microbe + medium treatment. Letters indicate significant difference by Tukey pairwise comparisons at 95%. <a href="https://cloudflare-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54611/54611fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The greatest increase was observed in the microbe + media treatment, which increased 0.25-fold (0.5 vs 0.4 mg/g coffee in GCP674 vs. NT). A similar trend was observed in lactic acid levels, though they were not significantly different. There were no significant changes or trends in the other acids tracked (citric and malic acid).

Watch this Scientific Journal Video about Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds at JoVE.com

Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

This article presents a method for the detection and quantification of organic acids from plant material using free zonal capillary electrophoresis. An example of the potential application of this method, determining the effects of a secondary fermentation on organic acid levels in coffee seeds, is provided.

Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

Carboxylic acids are organic acids containing one or more terminal carboxyl (COOH) functional groups. Short chain carboxylic acids (SCCAs; carboxylic ...

using-capillary-electrophoresis-to-quantify-organic-acids-from-plant

Nanyang Technological University

Research

JoVE Journal

Chemistry

9.8K Views.  The Ohio State University, OARDC.  Dit artikel presenteert een methode voor de detectie en kwantificering van organische zuren uit plantaardig materiaal met behulp van gratis zonale capillaire elektroforese. Een voorbeeld van de mogelijke toepassing van deze methode bepalen van de effecten van een tweede gisting op organische zuurgraad in koffiezaden is voorzien. 

Video: Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

Transcript and Metabolite Profiling for the Evaluation of Tobacco Tree and Poplar as Feedstock for the Bio-based Industry

The global demand for food, feed, energy, and water poses extraordinary challenges for future generations. It is evident that robust platforms for the exploration of renewable resources are necessary to overcome these challenges. Within the multinational framework MultiBioPro we are developing biorefinery pipelines to maximize the use of plant biomass. More specifically, we use poplar and tobacco tree (Nicotiana glauca) as target crop species for improving saccharification, isoprenoid, long chain hydrocarbon contents, fiber quality, and suberin and lignin contents. The methods used to obtain these outputs include GC-MS, LC-MS and RNA sequencing platforms. The metabolite pipelines are well established tools to generate these types of data, but also have the limitations in that only well characterized metabolites can be used. The deep sequencing will allow us to include all transcripts present during the developmental stages of the tobacco tree leaf, but has to be mapped back to the sequence of Nicotiana tabacum. With these set-ups, we aim at a basic understanding for underlying processes and at establishing an industrial framework to exploit the outcomes. In a more long term perspective, we believe that data generated here will provide means for a sustainable biorefinery process using poplar and tobacco tree as raw material. To date the basal level of metabolites in the samples have been analyzed and the protocols utilized are provided in this article.

Plant biomass offers a renewable resource for multiple products, including fuel, feed, food, and a variety of materials. In this paper we investigate the properties of tobacco tree (Nicotiana glauca) and poplar as suitable sources for a biorefinery pipeline.

The global demand for food, feed, energy, and water poses extraordinary challenges for future generations. It is evident that robust platforms for the ...

Environment

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis

Proton Transfer Reaction (PTR), combined with a Time-of-Flight (ToF) Mass Spectrometer (MS) is an analytical approach based on chemical ionization that belongs to the Direct-Injection Mass Spectrometric (DIMS) technologies. These techniques allow the rapid determination of volatile organic compounds (VOCs), assuring high sensitivity and accuracy. In general, PTR-MS requires neither sample preparation nor sample destruction, allowing real time and non-invasive analysis of samples. PTR-MS are exploited in many fields, from environmental and atmospheric chemistry to medical and biological sciences. More recently, we developed a methodology based on coupling PTR-ToF-MS with an automated sampler and tailored data analysis tools, to increase the degree of automation and, consequently, to enhance the potential of the technique. This approach allowed us to monitor bioprocesses (e.g. enzymatic oxidation, alcoholic fermentation), to screen large sample sets (e.g. different origins, entire germoplasms) and to analyze several experimental modes (e.g. different concentrations of a given ingredient, different intensities of a specific technological parameter) in terms of VOC content. Here, we report the experimental protocols exemplifying different possible applications of our methodology: i.e. the detection of VOCs released during lactic acid fermentation of yogurt (on-line bioprocess monitoring), the monitoring of VOCs associated with different apple cultivars (large-scale screening), and the in vivo study of retronasal VOC release during coffee drinking (nosespace analysis).

Proton Transfer Reaction Time of Flight Mass Spectrometry allows high-sensitivity, rapid and non-invasive analysis of volatile organic compounds. To demonstrate its potential, we give three examples: lactic acid fermentation of yogurt (on-line bioprocess monitoring), different apple genotypes (large-scale screening), and retronasal space after drinking coffee (nosespace analysis).

Proton Transfer Reaction (PTR), combined with a Time-of-Flight (ToF) Mass Spectrometer (MS) is an analytical approach based on chemical ionization that ...

Caffeine Extraction, Enzymatic Activity and Gene Expression of Caffeine Synthase from Plant Cell Suspensions

Caffeine (1,3,7-trimethylxanthine) is a purine alkaloid present in popular drinks such as coffee and tea. This secondary metabolite is regarded as a chemical defense because it has antimicrobial activity and is considered a natural insecticide. Caffeine can also produce negative allelopathic effects that prevent the growth of surrounding plants. In addition, people around the world consume caffeine for its analgesic and stimulatory effects. Due to interest in the technological applications of caffeine, research on the biosynthetic pathway of this compound has grown. These studies have primarily focused on understanding the biochemical and molecular mechanisms that regulate the biosynthesis of caffeine. In vitro tissue culture has become a useful system for studying this biosynthetic pathway. This article will describe a step-by-step protocol for the quantification of caffeine and for measuring the transcript levels of the gene (CCS1) encoding caffeine synthase (CS) in cell suspensions of C. arabica L. as well as its activity.

This protocol describes an efficient methodology for the extraction and quantification of caffeine in cell suspensions of C. arabica L. and an experimental process for evaluating the enzymatic activity of caffeine synthase with the expression level of the gene that encodes this enzyme.

Caffeine (1,3,7-trimethylxanthine) is a purine alkaloid present in popular drinks such as coffee and tea. This secondary metabolite is regarded as a ...

Biochemistry

Quantifying Plant Soluble Protein and Digestible Carbohydrate Content, Using Corn (Zea mays) As an Exemplar

Elemental data are commonly used to infer plant quality as a resource to herbivores. However, the ubiquity of carbon in biomolecules, the presence of nitrogen-containing plant defensive compounds, and variation in species-specific correlations between nitrogen and plant protein content all limit the accuracy of these inferences. Additionally, research focused on plant and/or herbivore physiology require a level of accuracy that is not achieved using generalized correlations. The methods presented here offer researchers a clear and rapid protocol for directly measuring plant soluble proteins and digestible carbohydrates, the two plant macronutrients most closely tied to animal physiological performance. The protocols combine well characterized colorimetric assays with optimized plant-specific digestion steps to provide precise and reproducible results. Our analyses of different sweet corn tissues show that these assays have the sensitivity to detect variation in plant soluble protein and digestible carbohydrate content across multiple spatial scales. These include between-plant differences across growing regions and plant species or varieties, as well as within-plant differences in tissue type and even positional differences within the same tissue. Combining soluble protein and digestible carbohydrate content with elemental data also has the potential to provide new opportunities in plant biology to connect plant mineral nutrition with plant physiological processes. These analyses also help generate the soluble protein and digestible carbohydrate data needed to study nutritional ecology, plant-herbivore interactions and food-web dynamics, which will in turn enhance physiology and ecological research.

Quantifying Plant Soluble Protein and Digestible Carbohydrate Content, Using Corn Zea mays As an Exemplar

The protocols described herein provide a clear and approachable methodology for measuring soluble protein and digestible (non-structural) carbohydrate content in plant tissues. The ability to quantify these two plant macronutrients has significant implications for advancing the fields of plant physiology, nutritional ecology, plant-herbivore interactions and food-web ecology.

Elemental data are commonly used to infer plant quality as a resource to herbivores. However, the ubiquity of carbon in biomolecules, the presence of ...

Quantification of Coenzyme A in Cells and Tissues

Emerging research has revealed that the cellular coenzyme A (CoA) supply can become limiting with a detrimental impact on growth, metabolism and survival. Measurement of cellular CoA is a challenge due to its relatively low abundance and the dynamic conversion of free CoA to CoA thioesters that, in turn, participate in numerous metabolic reactions. A method is described that navigates through potential pitfalls during sample preparation to yield an assay with a broad linear range of detection that is suitable for use in many biomedical laboratories.

This method describes sample preparation from cultured cells and animal tissues, extraction and derivatization of coenzyme A in the samples, followed by high pressure liquid chromatography for purification and quantification of the derivatized coenzyme A by absorbance or fluorescence detection.

Emerging research has revealed that the cellular coenzyme A (CoA) supply can become limiting with a detrimental impact on growth, metabolism and survival. ...

A Generalized Method for Determining Free Soluble Phenolic Acid Composition and Antioxidant Capacity of Cereals and Legumes

Phenolic acids are a class of organic compounds that bear both a phenolic group, and a carboxylic group. They are found in grains and concentrate in the bran of cereals or seed coat of legumes. They possess antioxidant properties that have generated much research interest in recent years, about their potential antioxidant protective health functions. This work presents a generalized method for the extraction of free soluble phenolic acids from whole grains and analysis of their antioxidant capacity. Five whole grain samples comprising two cereals (wheat and yellow corn) and three legumes (cowpea bean, kidney bean, and soybean), were used. The grains were milled into flour and their free soluble phenolic acids extracted using aqueous methanol. The compounds were then identified using a high-pressure liquid chromatograph (HPLC). The Folin-Ciocalteu method was used to determine their total phenolic content while their antioxidant capacities were determined using the DPPH radical scavenging capacity, Trolox equivalent antioxidant capacity (TEAC) and oxygen radical absorbance capacity (ORAC) assays. The phenolic acids identified included vanillic, caffeic, p-coumaric and ferulic acids. Vanillic acid was identified only in cowpea while caffeic acid was identified only in kidney bean. p-Coumaric acid was identified in yellow corn, cowpea, and soybean, while ferulic acid was identified in all the samples. Ferulic acid was the predominant phenolic acid identified. The total concentration of phenolic acids in the samples decreased in the following order: soybean &gt; cowpea bean &gt; yellow corn = kidney bean &gt; wheat. The total antioxidant capacity (sum of values of DPPH, TEAC and ORAC assays) decreased as follows: soybean &gt; kidney bean &gt; yellow corn = cowpea bean &gt; wheat. This study concluded that HPLC analysis as well as DPPH, TEAC, and ORAC assays provide useful information about the phenolic acid composition and antioxidant properties of whole grains.

Phenolic acids are important phytochemicals that are present in whole grains. They possess bioactive properties such as antioxidant protective functions. This work aimed at reporting on a generalized method for the HPLC identification, total phenolic content estimation, and determination of the antioxidant capacity of phenolic acids in cereals and legumes.

Phenolic acids are a class of organic compounds that bear both a phenolic group, and a carboxylic group. They are found in grains and concentrate in the ...

Enhanced Isomeric Separation of Ergot Alkaloids Using LC-IMS-MS

Detection of Regulated Ergot Alkaloids in Food Matrices by Liquid Chromatography-Trapped Ion Mobility Spectrometry-Time-of-Flight Mass Spectrometry

Ion mobility mass spectrometry (IMS) acts as an additional separation dimension when integrated into liquid chromatography-mass spectrometry (LC-MS) workflows. LC-IMS-MS methods provide higher peak resolution, enhanced separation of isobaric and isomeric compounds, and improved signal-to-noise ratio (S/N) compared to traditional LC-MS methods. IMS provides another molecular characteristic for the identification of analytes, namely the collision cross section (CCS) parameter, reducing false positive results. Therefore, LC-IMS-MS methods address important analytical challenges in the field of food safety (i.e., detection of compounds at trace levels in complex food matrices and unambiguous identification of isobaric and isomeric molecules).
Ergot alkaloids (EAs) are a family of mycotoxins produced by fungi that attack a wide variety of grass species, including small grains such as rye, triticale, wheat, barley, millet, and oats. Maximum levels (MLs) of these mycotoxins have been established in several foodstuffs, as detailed in the Commission Regulation EC/2023/915. This new legislation includes six main EAs and their corresponding epimers, so an efficient methodology is required to properly distinguish these isomeric molecules considering their co-occurrence.
Therefore, the goal of this protocol is to show how the integration of IMS in LC-MS workflows contributes to the separation of isomeric EAs, enhancing the selectivity of the analytical method. Additionally, it illustrates how the generation of CCS libraries through the characterization of analytical standards provides higher confidence for the identification of mycotoxins. This protocol is designed to clearly explain the benefits of implementing IMS in food safety, taking as an example the determination of EAs in cereals. A QuEChERS-based extraction followed by an LC-trapped ion mobility spectrometry (TIMS)-MS analysis provided limits of quantification ranging from 0.65 to 2.6 ng/g with acceptable accuracy (although low recovery for ergotaminine) at 1.5x, 1x, and 0.5x the ML and exhibited a negligible matrix effect.

This protocol presents a validated liquid chromatography-ion mobility-high resolution mass spectrometry method to determine the presence of ergot alkaloids in food in compliance with the recently released Commission Regulation (EU) 2023/915.

Ion mobility mass spectrometry (IMS) acts as an additional separation dimension when integrated into liquid chromatography-mass spectrometry (LC-MS) ...

Evaluation of Wild Peanut Species for Resistance to Aflatoxin Accumulation

Non-destructive SPE-UPLC-based Quantification of Aflatoxins and Stilbenoid Phytoalexins in Single Peanut (Arachis spp.) Seeds

Aflatoxins are highly carcinogenic secondary metabolites of some fungal species, particularly Aspergillus flavus. Aflatoxins often contaminate economically important agricultural commodities, including peanuts, posing a high risk to human and animal health. Due to the narrow genetic base, peanut cultivars demonstrate limited resistance to fungal pathogens. Therefore, numerous wild peanut species with tolerance to Aspergillus have received substantial consideration by scientists as sources of disease resistance.
Exploring plant germplasm for resistance to aflatoxins is difficult since aflatoxin accumulation does not follow a normal distribution, which dictates the need for the analyses of thousands of single peanut seeds. Sufficiently hydrated peanut (Arachis spp.) seeds, when infected by Aspergillus species, are capable of producing biologically active stilbenes&#160;(stilbenoids) that are considered defensive phytoalexins. Peanut stilbenes inhibit fungal development and aflatoxin production. Therefore, it is crucial to analyze the same seeds for peanut stilbenoids to explain the nature of seed resistance/susceptibility to the Aspergillus invasion. None of the published methods offer single-seed analyses for aflatoxins and/or stilbene phytoalexins.
We attempted to fulfill the demand for such a method that is environment-friendly, uses inexpensive consumables, and is sensitive and selective. In addition, the method is non-destructive since it uses only half of the seed and leaves the other half containing the embryonic axis intact. Such a technique allows germination and growth of the peanut plant to full maturity from the same seed used for the aflatoxin and stilbenoid analysis. The integrated part of this method, the manual challenging of the seeds with Aspergillus, is a limiting step that requires more time and labor compared to other steps in the method. The method has been used for the exploration of wild Arachis germplasm to identify species resistant to Aspergillus and to determine and characterize novel sources of genetic resistance to this fungal pathogen.

Author Spotlight: Quantification of Aflatoxins and Phytoalexins in Peanut Seeds to Identify Genetic Resistance Against Aspergillus

We demonstrate a medium-throughput method for quantification of aflatoxins and stilbenoid phytoalexins in single peanut seeds using ultra performance liquid chromatography. This method was specifically developed for the analyses of wild Arachis species challenged by the aflatoxigenic Aspergillus species.

Aflatoxins are highly carcinogenic secondary metabolites of some fungal species, particularly Aspergillus flavus. Aflatoxins often contaminate ...

Collection and Analysis of Arabidopsis Phloem Exudates Using the EDTA-facilitated Method

The plant phloem is essential for the long-distance transport of (photo-) assimilates as well as of signals conveying biotic or abiotic stress. It contains sugars, amino acids, proteins, RNA, lipids and other metabolites. While there is a large interest in understanding the composition and function of the phloem, the role of many of these molecules and thus, their importance in plant development and stress response has yet to be determined. One barrier to phloem analysis lies in the fact that the phloem seals itself upon wounding. As a result, the number of plants from which phloem sap can be obtained is limited. One method that allows collection of phloem exudates from several plant species without added equipment is the EDTA-facilitated phloem exudate collection described here. While it is easy to use, it does lead to the wounding of cells and care has to be taken to remove contents of damaged cells. In addition, several controls to prove purity of the exudate are necessary. Because it is an exudation rather than a direct collection of the phloem sap (not possible in many species) only relative quantification of its contents can occur. The advantage of this method over others is that it can be used in many herbaceous or woody plant species (Perilla, Arabidopsis, poplar, etc.) and requires minimal equipment and training. It leads to reasonably large amounts of exudates that can be used for subsequent analysis of proteins, sugars, lipids, RNA, viruses and metabolites. It is simple enough that it can be used in both a research as well as in a teaching laboratory.

Collection and Analysis of Arabidopsis Phloem Exudates Using the EDTA-facilitated Method

Knowledge of the composition of the phloem sap as well as the mechanism of its loading and long-distance transport is essential for the understanding of long-distance signaling in plant development and stress/pathogen response and of assimilate transport. This manuscript describes the collection of phloem exudates using the EDTA-facilitated method.

The plant phloem is essential for the long-distance transport of (photo-) assimilates as well as of signals conveying biotic or abiotic stress. It ...

Biology

Gas Chromatography (GC) with Flame-Ionization Detection

Source: Laboratory of Dr. B. Jill Venton - University of Virginia
Gas chromatography (GC) is used to separate and detect small molecular weight compounds in the gas phase. The sample is either a gas or a liquid that is vaporized in the injection port. Typically, the compounds analyzed are less than 1,000 Da, because it is difficult to vaporize larger compounds. GC is popular for environmental monitoring and industrial applications because it is very reliable and can be run nearly continuously. GC is typically used in applications where small, volatile molecules are detected and with non-aqueous solutions. Liquid chromatography is more popular for measurements in aqueous samples and can be used to study larger molecules, because the molecules do not need to vaporize. GC is favored for nonpolar molecules while LC is more common for separating polar analytes.
The mobile phase for gas chromatography is a carrier gas, typically helium because of its&#160;low molecular weight and being chemically inert. Pressure is applied and the mobile phase moves the analyte through the column. The separation is accomplished using a column coated with a stationary phase. Open tubular capillary columns are the most popular columns and have the stationary phase coated on the walls of the capillary. Stationary phases are often derivatives of polydimethylsiloxane, with 5&#8211;10% of the groups functionalized to tune the separation. Typical functional groups are phenyl, cyanopropyl, or trifluoropropyl groups. Capillary columns are usually 5&#8211;50 m&#160;long. Narrower columns have higher resolution but require higher pressures. Packed columns can also be used where the stationary phase is coated onto beads packed in the column. Packed columns are shorter, 1&#8211;5 m. Open tubular capillaries are generally preferred because they allow higher efficiencies, faster analyses, and have higher capacities.
Flame-ionization detection (FID) is a good general detector for organic compounds in GC that detects the amount of carbon in a sample. After the column, samples are burned in a hot, hydrogen-air flame. Carbon ions are produced by the combustion. While the overall efficiency of the process is low (only 1 in 105 carbon ions produce an ion in the flame) the total amount of ions is directly proportional to the amount of carbon in the sample. Electrodes are used to measure the current from the ions. FID is a destructive detector, as the entire sample is pyrolyzed. FID is unaffected by noncombustible gases and water.

Gas Chromatography GC with Flame-Ionization Detection

Source: Laboratory of Dr. B. Jill Venton - University of Virginia
Gas chromatography (GC) is used to separate and detect small molecular weight compounds ...

Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

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