D.P.B., K.J.R., and S.M.M. are supported by The Ian Potter Foundation, and J.P.V. is the recipient of an Australian Government Research Training Program, Stipend.

The cyanobacteria species Merismopedia was used for the present study38.
1. Raw sample preparation
<ol>
	<li>Collect the algal scum from the aquatic source of interest or from a cyanobacterial cultured flask and place it into 50 mL centrifuge tube38. 
	NOTE: The sample must be frozen at &#8722;20 &#176;C for later extractions and thawed prior to the following step.</li>
	<li>Centrifuge the tubes containing the sample at 3,500 x g&#160;for 10 min at 25 &#730;C. Decant the supernatant into a waste container and discard it into biological waste. 
	NOTE: The supernatant may be reserved for future analysis of the exosome.</li>
	<li>Cover the tube containing the sample pellet securely with a sealing film (see Table of Materials) and pierce a few holes in the film using a sharp, long nose tweezer. Store the tube in an upright position at &#8722;80 &#176;C for 30 min.</li>
	<li>Turn on and equilibrate the freeze dryer at 0.1 mbar and &#8722;80 &#176;C (~30 min). 
	&#8203;NOTE: The parameters (step 1.4) are optimized for the freeze dryer used for the present study (see Table of Materials). Follow standard operating procedures according to the freeze dryer model available in the laboratory or set the lowest possible temperature if the freeze dryer model does not go as low as &#8722;80 &#730;C.
	<ol>
		<li>Place the centrifuge tube(s) upright into a freeze dryer glass container and place it inside the &#8722;80 &#176;C freezer for 5 min to cool the jar.</li>
		<li>Remove the glass container from the freezer and attach the rubber lid.</li>
		<li>Ensure the handle on the rubber valve outlet of the freeze dryer is vented to the atmosphere (pointing upward) and attach the glass container firmly.</li>
		<li>Turn the handle of the rubber valve outlet very slowly to the pointing down position to expose the jar to the vacuum and allow up to 24 h of freeze-drying to ensure the sublimation of all the liquid.</li>
		<li>To release the vacuum in the jar, turn the handle to the pointing upward position, detach the glass container, and remove the freeze-dried samples.</li>
	</ol>
	</li>
	<li>Use an analytical balance to weigh 15-50 mg of dried sample pellets into a 15 mL centrifuge tube. 
	&#8203;NOTE: The samples may be placed into &#8722;80 &#176;C storage if not processed further at this stage.</li>
</ol>
2. Cell lysing and fractionation of free NPAAs
<ol>
	<li>Add 100 &#181;L of 100 ng/mL&#160;of D5-2,4-DAB (see Table of Materials) standard using a micropipette to the sample tube (optional).</li>
	<li>Add 300-600 &#181;L of 10% w/v aqueous trichloroacetic (TCA, see Table of Materials) or 300-600 &#181;L of 11.7%-13.3% TCA, respectively, if adding the D5-2,4-DAB standard. 
	NOTE: Choose a volume of aqueous TCA that fully covers the pellet.</li>
	<li>Place the sample tubes in a container filled with crushed ice.</li>
	<li>Use a probe sonicator (see Table of Materials) at medium-high power (70%) and lyse the sample for 1 min following the steps below. 
	&#8203;CAUTION: Ensure proper PPE with the use of noise-canceling earmuffs.
	<ol>
		<li>Follow the appropriate safety protocols in preparation for the use of the probe sonicator by placing in-use signage on the door, performing sonication in the fume hood, and using noise-canceling earmuffs.</li>
		<li>Switch on the sonicator and enter the following parameters: amplitude, 70%; time, 1 min.</li>
		<li>Spray 70% ethanol onto a lint-free paper wipe (see Table of Materials) and wipe down the probe.</li>
		<li>Fully immerse the end of the probe into the sample, and press start.</li>
		<li>When the probe sonicator stops, place the centrifuge tube containing the sample on ice for 1 min.</li>
		<li>To ensure the cells are lysed, repeat steps 2.4.3-2.4.5 once more.</li>
	</ol>
	</li>
	<li>Place the sample into a fridge at 4 &#176;C for 12-24 h to allow protein precipitation.</li>
	<li>Centrifuge the 10% aqueous TCA sample at 3,500 x g for 15 min at 8 &#176;C.</li>
	<li>Use a micropipette to transfer the supernatant to a 2 mL tube labeled &#34;Free Fraction&#34;.</li>
	<li>Micropipette 400 &#181;L of 10% aqueous TCA into the centrifuge tube containing the remaining sample pellet and break up the pellet either by vortex agitation or with the micropipette tip.</li>
	<li>Repeat steps 2.6-2.7, transferring the supernatant to the same 2 mL &#34;Free Fraction&#34; tube.</li>
	<li>Micropipette 400 &#181;L of 10% TCA/acetone into the centrifuge tube with the remaining pellet and break up the pellet with vortexing or the micropipette tip.</li>
	<li>Centrifuge the 10% TCA/acetone sample at 3,500 x g&#160;for 15 min at 8 &#176;C. Use a micropipette to transfer the supernatant to the 2 mL tube labeled &#34;Free Fraction&#34;.</li>
	<li>Place the &#34;Free Fraction&#34; tube with the lid open into a centrifugal evaporator (see Table of Materials) until all the volatile liquids are removed (at least 1 h).</li>
	<li>Once the sample is free of volatile liquids, cover the tube securely with sealing film and pierce the film with a few holes using a sharp, long nose tweezer. Place the sample into a &#8722;80 &#176;C freezer.</li>
	<li>Freeze dry the &#34;Free Fraction&#34; sample by repeating all the steps in step 1.4.</li>
	<li>Micropipette 200 &#181;L of 20 mM hydrochloric acid (HCl) into the &#34;Free Fraction&#34; tube to reconstitute the freeze-dried sample and place it in &#8722;80 &#176;C freezer storage. 
	NOTE: The &#34;Free Fraction&#34; of the sample is ready for filtration in step 4. The remaining pellet will be further processed in the following steps for protein fractionation.</li>
</ol>
3. Fractionation of the protein-bound NPAAs
<ol>
	<li>Use a glass engraver to label glass shell vials with the sample details for identification. 
	NOTE: Strong acid may dissipate ink labeling; therefore, engraving the labels on glass is recommended.</li>
	<li>Micropipette 100 &#181;L of 100 ng/mL&#160;D5-2,4-DAB standard onto the sample pellet (optional).</li>
	<li>Micropipette 400 &#181;L of 100% acetone onto the sample pellet and break up the pellet using either vortex agitation or the micropipette tip.</li>
	<li>Use a 1 mL micropipette set at 1,000 &#181;L to transfer the washed and resuspended pellet to the corresponding glass shell vial. 
	NOTE: Another 400 &#181;L of 100% acetone can be added to the agitated pellet to assist in the complete transfer of the pellet into the glass shell vial. This can be repeated a third time if necessary.</li>
	<li>Centrifuge at 8,000 x g for 5 min at 25 &#730;C and decant the liquid into biological waste.</li>
	<li>Place the remaining pellet into a centrifugal evaporator until all the liquid is removed and the pellet is dry (~1 h).</li>
	<li>Prepare the vacuum hydrolysis vial by adding 1 mL of 6 M HCl into the bottom of the hydrolysis vial.</li>
	<li>Use tweezers to carefully insert the labeled shell vials containing the dried samples into the hydrolysis vial, ensuring an upright, stable position. 
	NOTE: Empty shell vials can be used to help keep the sample vials upright if the number of samples is less than the capacity of the hydrolysis vial.</li>
	<li>Attach the lid to the hydrolysis vial and push the red knob on the lid to close the valve.</li>
	<li>Turn the vacuum pump on, attach the vacuum tube to the head of the hydrolysis vial lid, and press the green knob on the lid to open the valve.</li>
	<li>Allow the vacuum pump (see Table of Materials) to remove the air from the vial for 1 min.</li>
	<li>Close the vial by depressing the red knob on the hydrolysis vial lid, turn the vacuum pump off, and remove the vacuum tube.</li>
	<li>Attach a rubber tube to the nitrogen gas tap on the laboratory bench and open the tap slightly. Place the thumb at the tube&#39;s end, seal it, and count until the gas begins to escape as pressure builds up. This will be the timeframe for the next step. Adjust the gas flow to a suitable timeframe.</li>
	<li>Attach the other end of the rubber tube to the head of the hydrolysis vial lid and then immediately push the green knob of the lid. Count to the time determined in step 3.13 and quickly push the red knob on the lid and remove the rubber tube.</li>
	<li>Repeat steps 3.10-3.14 twice to ensure the glass hydrolysis vial is free of air and filled with nitrogen gas.</li>
	<li>Place the hydrolysis vial into a preheated oven set at 110 &#176;C for 16-18 h.</li>
	<li>Use oven gloves to remove the glass hydrolysis vial from the oven and allow it to cool inside the fume hood for 10 min. Inside the fume hood, while facing it away from you, push the green knob to release pressure and gas.</li>
	<li>Use tweezers to remove the shell vials from the hydrolysis vial.</li>
	<li>Reconstitute the hydrolyzed sample pellets by micro pipetting 200 &#181;L of 20 mM HCl into the shell vial. Ensure the pellet is resuspended by either vortexing or using a pipette tip.</li>
	<li>Centrifuge the shell vials containing the reconstituted sample pellets for 2 min at 5,300 x g&#160;and 25 &#730;C.</li>
</ol>
4. Sample filtering
<ol>
	<li>Label 2 mL filter tubes (see Table of Materials) containing 0.2 &#181;m pore membrane filters as &#34;Free Fraction&#34; and &#34;Protein Fraction&#34;.</li>
	<li>Transfer the reconstituted samples from step 2.15 (free fraction) and step 3.20 (protein fraction) into the corresponding filter tubes.</li>
	<li>Place them in the centrifuge for 30 min at 5,000 x g&#160;and 25 &#730;C.</li>
	<li>Remove the filters from the filter tubes and cap them. The samples are now ready for amino acid derivatization in step 5. 
	&#8203;NOTE: The samples can be placed into the &#8722;80 &#176;C freezer for storage for later derivatization and analysis.</li>
</ol>
5. Amino acid derivatization
<ol>
	<li>Derivatize the samples using propyl chloroformate (PCF)39 or 6-aminoquinolyl-N-hydrosysuccinimidyl carbamate (AQC)40 according to the manufacturer&#39;s instructions (see Table of Materials).</li>
</ol>

The authors have nothing to disclose.

The extraction protocol outlined here for the analysis of NPAAs applies to analyzing any amino acids in biological samples. For guides on isolating and culturing cyanobacterial strains, one can refer to the methods presented in the study by Violi et al.38. The first step in the protocol takes the sample to a point where normalization between samples against the dry weight can be achieved. The second step is cell lysis to release the analytes and can be performed using an array of techniques, including mechanical disruptions/lyses such as probe sonication as described in this protocol, freeze/thaw cycles, grinding and bead milling, and non-mechanical disruptions such as enzymatic, detergent and/or chemical lysis. Mechanical disruption is known to be advantageous over non-mechanical as it allows for a greater capacity of the sample to lyse while allowing the intracellular bonds and proteins to remain intact41, although the sample matrix may dictate the optimal method for cell lysing.
Protein precipitation is the critical third step of this protocol when extracting amino acids for analysis. TCA is the most commonly used solvent; however, perchloric acid, acetone, methyl tert-butyl ether (MTBE), methanol, and/or acetonitrile8,42 have also been used, where each extraction solvent is purposed to extract and precipitate different substrates. The model described here extracts the NPAA BMAA and its isomers from a cyanobacterial matrix, and although a range of different solvents have been utilized, the two most common are 10% TCA in water (aqueous) and 10% TCA in acetone. In general, protein precipitation with TCA is commonly used to extract amino acids to fractionate free amino acids from the protein-bound amino acids. Additionally, TCA extraction allows for determining the total protein content, reducing contaminants for the free fraction, and reducing the activity of proteases with minimal protein degradation43. The TCA extraction of the free fraction works by initially rinsing out organic-soluble substances, leaving behind proteins and insoluble compounds such as cell wall remnants in the precipitate, which is then followed by thermal hydrolysis extraction of the protein-bound amino acids (bound fraction) using a strong acid.
The fractionation of the free fraction with 10% aqueous TCA plus sonication produces the most extensive protein precipitation compared to other organic solvents44 and the best amino acid recoveries42. Some studies opt to use an acid combined with an organic solvent (i.e., 10%-20% TCA in acetone43) to precipitate more molecules, including smaller peptides/biomolecules, minimize protein degradation, and reduce contaminants such as salts43. Another advantage of 10% TCA in acetone is its faster drying rate in the preparation of the pellet for hydrolysis, minimizing moisture residue to prevent amino acid modification. However, 10% aqueous TCA plus sonication has better extraction efficiencies of free amino acids when compared to 10% TCA in acetone44 alone. Additionally, 10% aqueous TCA precipitation has limitations such as a long drying time, not being able to precipitate all proteins or small peptides/biomolecules, and depending on the analyte of interest (i.e., proteins or amino acids), requiring additives and reducing agents to prevent oxidization and degradation45,46.
This protocol uses a combination of 10% aqueous TCA and 10% TCA in acetone to increase protein precipitation, ensure smaller peptides/biomolecules are precipitated, allow for faster pellet drying times, and increase extraction efficiencies, taking advantage of both solvent extraction properties. However, the combination of 10% aqueous TCA and 10% TCA in acetone can precipitate small peptides/biomolecules in the free fraction after the 10% TCA in acetone supernatant is combined with the aqueous free fraction. In this case, the precipitates should be transferred to the bound fraction for hydrolysis.
The second half of this protocol involves the release of amino acids (i.e., BMAA) from the protein pellet via acid-vapor hydrolysis at elevated temperatures in an oxygen-free environment. The predominately limiting factor to the hydrolysis step is that it is time-consuming and laborious to prepare. The overnight incubation prevents fast and time-efficient sample preparation and analysis. In addition, the quantitative transfer of the pellet from a centrifuge tube to a shell vial (step 3.4) is an arduous process that requires diligence and patience to ensure an accurate point of normalization to the dry weight. Possible issues the user may face are the incomplete transfer of the pellet, wet precipitated proteins sticking to pipette tips and the original tube, and solid particles of the pellet blocking the pipette tip. A practical suggestion in aiding an easier transfer of the pellet is to remove about 0.3-0.5 mm off the end of the pipette tip with a pair of scissors, allowing larger pellet particles to be drawn and released into the shell vial. This transfer method is common practice for protein extraction for all amino acid analyses. However, modifications to improve the efficiency and accuracy of quantitatively transferring the pellet into the shell vial should be investigated.
Two forms of hydrolysis techniques can be employed to release amino acids from their protein-bound state: liquid-phase hydrolysis and acid-vapor hydrolysis. Liquid-phase hydrolysis, which involves the addition of 6 M HCl onto the sample, which is then placed in a 110 &#176;C oven overnight, is an alternative to the acid-vapor hydrolysis described in this protocol. Extraction techniques that employ liquid-phase hydrolysis may require further processing, such as desalination, especially if AQC derivatization is chosen, as it requires basic conditions for tagging40. Acid-vapor hydrolysis avoids desalination and allows the user the freedom to choose the derivatization technique upon reconstitution of the final pellet before filtration. Furthermore, independent of the chosen hydrolysis method, the samples may require further processing, such as SPE for matrix purification and concentration29,47,48, depending on the choice of derivatization technique and/or analytical analysis (e.g., reverse phase LC-MS/MS vs. hydrophilic interaction liquid chromatography [HILIC] LC-MS/MS37). The reconstitution of the final pellet in 20 mM HCl in this protocol is appropriate for derivatization using PCF reagents48&#160;via a commercially available amino acid hydrolysis kit39 (see Table of Materials). Both AQC and PCF will derivatize all the amino acids, protein, and non-protein in origin present in the sample, and the selectivity of the analytes is obtained through the use of LC-MS/MS and its combination of retention time matching and careful selection of the quantifier and qualifier MRMs38.
Current hydrolysis protocols are not optimized for the release of BMAA, 2,4-DAB, and AEG but for the 22 protein amino acids based on existing methods for protein hydrolysis32, where incubation for longer than 18 h results in the degradation and modification of certain amino acids, affecting LC-MS/MS analysis and, thus, the obtained concentrations32. Beach et al.49 investigated hydrolysis over time (0.5-120 h) to optimize hydrolysis for analyzing BMAA and the proteinogenic amino acids. They found that although there was an early rapid release of BMAA during the first 0.5 h of the hydrolysis, the BMAA levels continued to increase as the hydrolysis time increased, without degradation, even after 5 days49. There are also still different views and questions about the true nature of bound BMAA and its isomers, with some studies suggesting that rather than BMAA bonding50,51 or misincorporation into proteins14, BMAA-protein association is superficial52. However, the current consensus in the analysis of &#34;bound&#34; BMAA requires the validated and widely accepted hydrolysis step that breaks apart peptides/proteins to release amino acids and, thus, BMAA and its isomers.
The recovery rates of 20 protein amino acids were determined in a study by Sedgwick et al.42 using TCA extraction, resulting in approximately 100% recovery. In the case of BMAA and its isomers from algal matrices, studies comparing the efficiency of BMAA extraction using various extraction solvents have found 10% TCA to be the most efficient for free BMAA27. The recovery rates for protein-bound BMAA extracted using liquid-phase hydrolysis were established in studies by Glover et al.25 and by Faassen et al.53, where the accuracy was determined by spiked recovery methods, with an average BMAA recovery rate of 108.6% and 70%, respectively. Faassen et al. described procedures for spike-recovery experiments and illustrated how the recovery differs depending on the stage of the extraction process the spike was made53. Faassen et al. additionally determined the efficiency of the acid-vapor protocol presented here, with recovery rates of 83.6% for the BMAA isomers spiked prior to extraction and 68.6% for those spiked prior to hydrolysis24. These recoveries, methods of extraction, and analyses were further validated by Banack26, with recovery rates of 94%-106% for BMAA in a cyanobacterial matrix and a %Relative Standard Deviation (%RSD) between 5.6% and 20%, meeting the FDA criteria for accuracy54. It is recommended that each laboratory initially establish its recovery rates and accuracy before utilizing this protocol via spike recovery experiments. The recovery methods presented in Faassen et al.53 and Glover et al.25 may be followed as a guide.
Alternative forms of hydrolysis techniques can be utilized instead of overnight oven hydrolysis for faster protein-bound extraction of the analyte. For example, a microwave extractor could significantly reduce the hydrolysis time from 24 h to as little as 10 min55. Microwave hydrolysis for amino acids uses the same principles as the conventional thermal method, using a glove box to prepare and assemble the microwave vessel in an oxygen-free environment and adding 6 M HCl. Once air-tight, the vessel containing the sample undergoes microwave radiation. Microwave hydrolysis has been used to extract amino acids from various sample matrices56,57,58; however, microwave hydrolysis has yet to be developed and validated for the analysis of BMAA.
In conclusion, 10% aqueous TCA protein precipitation is the optimal method to extract free non-protein amino acids from cyanobacterial matrices27, and thermal hydrolysis provides a reliable and reproducible extraction of the protein-bound fraction. This protocol to extract the NPAA BMAA and its isomers from cyanobacteria is validated and widely accepted. Future directions to further optimize the extraction of BMAA will focus on the hydrolysis step, which is performed according to the specifications of the 22 protein amino acids. However, the extraction protocol presented here should still be considered efficient and effective for analyzing BMAA and its isomers via LC-MS/MS.

Amino acids are chemical compounds that contain at least one amine and carboxylic functional group. Some amino acids also contain an imino group, a functional acid group other than carboxylic; other amino acids have amine groups that are not attached to the &#945;-carbon group1. There are over 500 amino acids2, 22 of which are known as protein amino acids used for genetic coding in ribosomal protein synthesis3. These 22 amino acids can be further subdivided into essential and non-essential. Essential amino acids are necessary for an organism to function properly and can only be acquired by external sources. Non-essential amino acids can be synthesized within the organism. The classification of the 22 amino acids into essential/non-essential is unique to individual species. All other amino acids are non-protein amino acids (NPAAs) that are not encoded for protein synthesis. Amino acids, whether protein or non-protein, can also play a signaling role within an organism and act as metabolic intermediaries4. Due to their important and varying roles, amino acid levels can provide an insight into organism condition, functionality, and metabolic pathways, etc. There are two main mechanisms by which amino acids can be incorporated into a polypeptide chain: ribosomal protein synthesis, which utilizes the 22 amino acids in encoding, and non-ribosomal peptide synthesis, which, alongside protein amino acids, allows for the use of some NPAAs in synthesis. Certain NPAAs can mimic protein amino acids, potentially leading to their misincorporation into peptides and proteins. The misincorporation causes a misfolding of proteins, which, in turn, has detrimental effects5, such as the misincorporation of the NPAA L-3,4 dihydroxyphenylalanine (L-DOPA) in place of tyrosine, negatively impacting cellular function and health6,7. An additional source of incorporated NPAAs is through the post-translational modification (PTM) of amino acid residues. Amino acid residues are modified for various reasons, including changes to peptide or protein conformation, stability, and functionality. Upon hydrolysis of PTM-containing protein or peptides, these modified amino acid residues are released into their free NPAA form8,9.
The NPAA &#946;-methylamino-L-alanine (BMAA) produced by cyanobacteria, diatoms, and dinoflagellates10 is a suspected neurotoxin that is implicated as a contributing factor to various neurodegenerative diseases such as amyotrophic lateral sclerosis/parkinsonism-dementia complex (ALS-PDC)11,12, amyotrophic lateral sclerosis, and Alzheimer&#39;s disease13. It is suggested that BMAA is mistakenly incorporated into the polypeptide chain of proteins in place of L-serine14 and/or other protein amino acids. The misincorporation of BMAA can lead to the misfolding of proteins, resulting in the deposition of protein aggregates in neurons14. In the last decade, interest in BMAA has significantly increased. A wide range of cyanobacterial species from freshwater, marine, and brackish environments have been discovered to produce BMAA15, leading to their widespread distribution into various ecosystems16,17. Additionally, BMAA has been shown to biomagnify through the food chain to the human food web18,19. Due to the potential health effects, lack of understanding, and incongruences of BMAA toxicity, it is imperative to continue further research until either the toxicity of BMAA is ultimately understood or BMAA is deemed safe20,21.
The analysis of amino acids in biological samples can be divided into four main steps: sample preparation, amino acid derivatization, separation and detection, and identification and quantification. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is the preferred analysis method as it provides a targeted and reproducible separation and analysis of amino acids.
Sample preparation techniques for analyzing cyanobacterial and other algal samples predominantly involve an extraction method for amino acids in their free and protein-bound forms. Over the years, the extraction methods have remained relatively consistent with common elements, including the desolvation of the sample to separate the free amino acids from their bound form, followed by protein precipitation and the release of the bound amino acids through hydrolysis with hydrochloric acid (HCl) at elevated temperatures22. This extraction form has been optimized for protein amino acids and employed for NPAAs. However, the detection and quantification of BMAA and its isomers (Figure 1), aminoethylglycine (AEG) and 2,4-diaminobutyric acid (2,4-DAB), in the same species of cyanobacteria have shown inconsistent results in the literature, with a possible explanation lying in differences in the growth conditions and/or the strain of algae producing varying or no amounts of BMAA23. It has been argued that a more likely explanation for the inconsistencies in the detection and quantification of BMAA and its isomers is due to unvalidated experimental protocols, the use of a wide range of analytical techniques, and insufficient experimental detail in the reported methods16,24 leading to irreproducible inter-laboratory data. However, Glover et al.25 and Banack26 have recently developed and validated an analytical technique for the detection and quantification of BMAA and its isomers using ultra-performance liquid chromatography (UPLC)-MS/MS in accordance with the International Society of Analytical Chemists (AOAC), US Pharmacopeia, and FDA guidelines necessary for single-laboratory validation.
These validation experiments focused on the separation and detection of BMAA and its isomers and did not address the inconsistencies in sample preparation protocols. Lage et al.27 compared the performance of three common extraction methods for quantifying BMAA and its isomers in cyanobacterial samples via LC-MS/MS: solid phase extraction (SPE) of free amino acids28,29; a protein precipitation method involving a methanol extraction and acetone precipitation30; and the most commonly used extraction method for BMAA, protein precipitation with trichloroacetic acid (TCA)31. They concluded that the TCA protein precipitation was the optimal protocol, yielding higher BMAA concentrations in the test samples compared to the other extraction methods. Their study validated TCA extraction with derivatization of BMAA using 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) in a cyanobacteria matrix, providing an established guide to achieving reliable and reproducible BMAA data. TCA amino acid extraction is an accepted and common sample preparation technique that can also be applied to other matrices. However, the stability of the amino acid during hydrolysis needs to be considered to prevent degradation or oxidation, which can be overcome with the use of chemical modifiers and reducing agents32. TCA extraction is routinely used and taught to new research students, and although the protocol is widely reported, a visual aid in the application of this method is a valuable resource, ensuring proper and consistent execution.
Reverse-phase chromatography is commonly used to separate amino acids, requiring a derivatization step prior to analyses. The derivatization of amino acids such as BMAA allows for chromatographic retention and can increase resolution between isomers. It also increases the molecular mass and improves ionization in the mass spectrometer. Several derivatizing reagents have been used for the analysis of amino acids via LC-MS/MS, including propyl chloroformate (PCF)33, 6-aminoquinolyl-N-hydrosysuccinimidyl carbamate (AQC)27, 9-fluorenylmethyl chloroformate (FMOC)34, and dansyl chloride (DC)35. However, the only validated techniques for analyzing BMAA used either PCF36 or AQC24,26,37 as their derivatizing reagent.
The scope of this protocol is focused on the TCA extraction of NPAAs from cyanobacterial matrices. It is a labor-intensive method that is routinely used and taught in academic and industry research laboratories based on manuscripts that may be short on detail; therefore, this protocol provides details of the procedure and techniques involved in preparing samples for the analysis of free and bound BMAA as the model amino acid.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1 mL glass shell vials</td>
			<td>SHIMADZU</td>
			<td>REST-24663</td>
			<td></td>
		</tr>
		<tr>
			<td>10% TCA solution</td>
			<td></td>
			<td></td>
			<td>Dilute 100% (w/v) to 10% aqueous TCA&#160;</td>
		</tr>
		<tr>
			<td>100% TCA solution</td>
			<td></td>
			<td></td>
			<td>Dissolve TCA in water according to the following ratio 2.2 g:1 mL (TCA:H2O)</td>
		</tr>
		<tr>
			<td>1000 &#181;L micropipette</td>
			<td>Ependorf/Sigma-Aldrich</td>
			<td>Z683809</td>
			<td></td>
		</tr>
		<tr>
			<td>13.3% TCA solution</td>
			<td></td>
			<td></td>
			<td>Dilute 100% (w/v) to 13.3% aqueous TCA&#160;</td>
		</tr>
		<tr>
			<td>2 mL tubes</td>
			<td>MERCK</td>
			<td>BR780546-500EA</td>
			<td></td>
		</tr>
		<tr>
			<td>20 mM HCl</td>
			<td>Chem-Supply Pty Ltd</td>
			<td>7647-01-0</td>
			<td>Made from stock</td>
		</tr>
		<tr>
			<td>20-200 &#181;L micropipette</td>
			<td>Ependorf/Sigma-Aldrich</td>
			<td>Z740441</td>
			<td></td>
		</tr>
		<tr>
			<td>6 M HCl</td>
			<td>Chem-Supply Pty Ltd</td>
			<td>7647-01-0</td>
			<td>Made from stock</td>
		</tr>
		<tr>
			<td>70% ethanol</td>
			<td>Supelco</td>
			<td>1.11727</td>
			<td>Dilute 70:1 Ethanol:water</td>
		</tr>
		<tr>
			<td>-80 &#176;C Freezer</td>
			<td>Martin CHRIST</td>
			<td>102142</td>
			<td>Alpha 2-4 Ldplus</td>
		</tr>
		<tr>
			<td>AccQ-Tag Ultra Derivatisation Kit&#160;</td>
			<td>Waters</td>
			<td>186003836</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetone</td>
			<td>Chem-Supply Pty Ltd</td>
			<td>34967-2.5L</td>
			<td></td>
		</tr>
		<tr>
			<td>Analytical Scale Balance</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifugal evaporator</td>
			<td>Thermo Scientific</td>
			<td>13442549</td>
			<td>DNA120-115 SpeedVac Concentrator</td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>MERCK</td>
			<td>EP022620100-1EA</td>
			<td></td>
		</tr>
		<tr>
			<td>D5-2,4-DAB standard</td>
			<td>CDN Isotopes</td>
			<td>D-7568</td>
			<td></td>
		</tr>
		<tr>
			<td>Drying Oven</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Ez:faastTM Amino Acid Analysis Kit</td>
			<td>Phenomenex</td>
			<td>CEO-8492</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon tube holder</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon Tubes</td>
			<td>MERCK</td>
			<td>T2318-500EA</td>
			<td>Greiner centrifuge tubes</td>
		</tr>
		<tr>
			<td>Filter Tubes</td>
			<td>Sigma-Aldrich</td>
			<td>CLS8161-100EA</td>
			<td>Corning Costar Spin-X centrifuge tube filters (pore size 0.22 &#956;m)</td>
		</tr>
		<tr>
			<td>Glass engraver</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrolysis vial &#38; Lid</td>
			<td>Eldex Laboratories/Waters</td>
			<td>WAT007568 &#38; WAT007569</td>
			<td></td>
		</tr>
		<tr>
			<td>Ice and container</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Lint-free paper wipe</td>
			<td>Kimwipes/Sigma-Aldrich</td>
			<td>Z188956</td>
			<td></td>
		</tr>
		<tr>
			<td>Milli-Q water</td>
			<td></td>
			<td></td>
			<td>18.2 M&#937;.cm</td>
		</tr>
		<tr>
			<td>Nitrogen tap with hose</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>P1000 Micropipette</td>
			<td>MERCK</td>
			<td>EP3123000063</td>
			<td></td>
		</tr>
		<tr>
			<td>P1000 pipette tips</td>
			<td>MERCK</td>
			<td>Z740127</td>
			<td></td>
		</tr>
		<tr>
			<td>P200 Micropipette</td>
			<td>MERCK</td>
			<td>EP3123000055-1EA</td>
			<td></td>
		</tr>
		<tr>
			<td>P200 pipette tips</td>
			<td>MERCK</td>
			<td>Z740125</td>
			<td></td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>MERCK</td>
			<td>P7793</td>
			<td>Sealing film</td>
		</tr>
		<tr>
			<td>PPE - noise cancelling headphones</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>PPE - oven gloves</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Probe sonicator</td>
			<td>QSONICA Sonicators</td>
			<td>Q125 Sonicator</td>
			<td>Please ensure all appropriate PPE (i.e. noise cancelling headphones)</td>
		</tr>
		<tr>
			<td>Sample transfer spatula</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Trichloroacetic acid (TCA)</td>
			<td>Sigma-Aldrich</td>
			<td>T6399-1KG</td>
			<td></td>
		</tr>
		<tr>
			<td>Tweezers</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Vacuum Pump with hose</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

extraction of non-protein amino acids from cyanobacteria for liquid chromatography-tandem mass spectrometry analysis

Non-protein amino acids (NPAAs) are a large class of amino acids (AAs) that are not genetically encoded for translation into proteins. The analysis of NPAAs can provide crucial information about cellular uptake and/or function, metabolic pathways, and potential toxicity. &#946;-methylamino-L-alanine (BMAA) is a neurotoxic NPAA produced by various algae species and is associated with an increased risk for neurodegenerative diseases, which has led to significant research interest. There are numerous ways to extract AAs for analysis, with liquid chromatography-tandem mass spectrometry being the most common, requiring protein precipitation followed by acid hydrolysis of the protein pellet. Studies on the presence of BMAA in algal species provide contradictory results, with the use of unvalidated sample preparation/extraction and analysis a primary cause. Like most NPAAs, protein precipitation in 10% aqueous TCA and hydrolysis with fuming HCl is the most appropriate form of extraction for BMAA and its isomers aminoethylglycine (AEG) and 2,4-diaminobutyric acid (2,4-DAB). The present protocol describes the steps in a validated NPAA extraction method commonly used in research and teaching laboratories.

An illustration of the extraction protocol is provided in Figure 2 as a summarized reference guide. The results obtained by Violi et al.38 were chosen to represent a positive result from this extraction protocol for the analysis of BMAA isomers from cyanobacteria. Nineteen single species of cyanobacteria were cultured from 11 eastern Australian freshwater sites. Using the same protocol, the BMAA isomers were extracted into free and protein fractions, derivatized with PCF, and analyzed using LC-MS/MS. Seventeen of the cyanobacterial isolates were positive for BMAA, and all 19 contained the 2,4-DAB isomer. A positive result is confirmed by using a validated LC-MS/MS method and observing at least three multiple reaction monitoring (MRM) transitions, one as quantifier ion and two as qualifier ions at the expected retention time. A representative MRM chromatogram of a standard containing BMAA and its isomers, indicated by the color-coded lines, is shown in Figure 3. The presence and concentration of BMAA and isomers in all 19 samples, sectioned to show the BMAA and isomer concentration in the free and bound fractions, is summarized in Table 1. A positive detection for all three isomers was observed in the free fraction of the Merismopedia species collected from Lake Liddell (NSW, Australia), where the free fraction contained a BMAA concentration of 68.38 &#181;g/g dry weight (DW) &#177; 2.25 &#181;g/g DW, 2,4-DAB with a concentration of 1,223.98 &#181;g/g DW &#177; 20.7 &#181;g/g DW, and AEG with a concentration of 125.27 &#181;g/g DW &#177; 4.19 &#181;g/g DW. The chromatographic MRMs are shown in Figure 4. To illustrate a negative result for BMAA and its isomers in a sample, the bound fraction of the Microcystis flos-aquae species collected from Walka Water Works (NSW, Australia) is chromatographically presented in Figure 5. While the bound fraction contained no BMAA, 2,4-DAB, and/or AEG, its free fraction contained all three isomers, with concentrations of 79.86 &#181;g/g DW &#177; 1.59 &#181;g/g DW, 1,156.15 &#181;g/g DW &#177; 8.46 &#181;g/g DW, and 433.83 &#181;g/g DW &#177; 8.92 &#181;g/g DW, respectively.
Thus, through the use of this protocol, Violi et al.38 confirmed the presence of BMAA isomers in eastern Australian freshwater cyanobacteria and determined which cyanobacteria had toxin-producing capabilities.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/63779/63779fig01.jpg" /> 
Figure 1: The chemical structure of BMAA and its isomers 2,4-DAB and AEG. <a href="https://www.jove.com/files/ftp_upload/63779/63779fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/63779/63779fig02.jpg" /> 
Figure 2: Summarized reference diagram of the extraction protocol. <a href="https://www.jove.com/files/ftp_upload/63779/63779fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/63779/63779fig03.jpg" /> 
Figure 3: LC-MS/MS chromatogram of a calibration standard containing D5-2,4-DAB, 2,4-DAB, BMAA, and AEG for isomer identification based on retention, indicated by the highlighted peaks. Key: D5-2,4-DAB 338.01 m/z &#62; 278.10 m/z at 6.4 min (red), 2,4-DAB 333.01 m/z &#62; 273.10 m/z at 6.4 min (green), AEG 333.01 m/z &#62; 88.00 m/z at 7.4 min (orange), and BMAA 333.01 m/z &#62; 187.10 m/z at 7.8 min (blue). <a href="https://www.jove.com/files/ftp_upload/63779/63779fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/63779/63779fig04.jpg" /> 
Figure 4: LC-MS/MS chromatogram for detecting D5-2,4-DAB, 2,4-DAB, BMAA, and AEG&#160;in Merismopedia species collected from Lake Liddell (NSW, Australia), indicated by the highlighted peaks. Key: D5-2,4-DAB 338.01 m/z &#62; 278.10 m/z at 6.4 min (red),&#160;2,4-DAB 333.01 m/z &#62; 273.10 m/z at 6.4 min (green), AEG 333.01 m/z &#62; 88.00 m/z at 7.4 min (orange), and BMAA 333.01 m/z &#62; 187.10 m/z at 7.8 min (blue). <a href="https://www.jove.com/files/ftp_upload/63779/63779fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/63779/63779fig05.jpg" /> 
Figure 5: LC-MS/MS chromatogram of a negative control for 2,4-DAB, BMAA, and AEG in a bound fraction of Microcystis flos-aquae species collected from Walka Water Works (NSW, Australia). Key: D5-2,4-DAB 338.01 m/z &#62; 278.10 m/z at 6.4 min (red - peak highlighted), 2,4-DAB 333.01 m/z &#62; 273.10 m/z at 6.4 min (green), AEG 333.01 m/z &#62; 88.00 m/z at 7.4 min (orange), and BMAA 333.01 m/z &#62; 187.10 m/z at 7.8 min (blue). The dashed lines represent the retention times for missing 2,4-DAB, AEG, and BMAA. <a href="https://www.jove.com/files/ftp_upload/63779/63779fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Table 1: BMAA, AEG, and&#160;2,4-DAB concentrations in cyanobacterial isolates. Concentrations &#177; standard error of the mean (n = 3). ND denotes not detected. The highest concentration of each isomer detected is highlighted in green. The table is a modified version from Violi et al.38. <a href="https://www.jove.com/files/ftp_upload/63779/63779_Table 1.xlsx" target="_blank">Please click here to download this Table.</a>

Watch this Scientific Journal Video about Extraction of Non-Protein Amino Acids from Cyanobacteria for Liquid Chromatography-Tandem Mass Spectrometry Analysis at JoVE.com

Extraction of Non-Protein Amino Acids from Cyanobacteria for Liquid Chromatography-Tandem Mass Spectrometry Analysis

The present protocol describes the extraction of non-protein amino acids from biological matrices via trichloroacetic acid (TCA) protein precipitation and acid hydrolysis before analysis using liquid chromatography-tandem mass spectrometry.

Non-protein amino acids (NPAAs) are a large class of amino acids (AAs) that are not genetically encoded for translation into proteins. The analysis of ...

extraction-non-protein-amino-acids-from-cyanobacteria-for-liquid

Research

JoVE Journal

Chemistry

3.5K Views.  University of Technology Sydney. The present protocol describes the extraction of non-protein amino acids from biological matrices via trichloroacetic acid (TCA) protein precipitation and acid hydrolysis before analysis using liquid chromatography-tandem mass spectrometry. 

Video: Extraction of Non-Protein Amino Acids from Cyanobacteria for Liquid Chromatography-Tandem Mass Spectrometry Analysis

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)

Non-targeted metabolite profiling by ultra performance liquid chromatography coupled with mass spectrometry (UPLC-MS) is a powerful technique to investigate metabolism. The approach offers an unbiased and in-depth analysis that can enable the development of diagnostic tests, novel therapies, and further our understanding of disease processes. The inherent chemical diversity of the metabolome creates significant analytical challenges and there is no single experimental approach that can detect all metabolites. Additionally, the biological variation in individual metabolism and the dependence of metabolism on environmental factors necessitates large sample numbers to achieve the appropriate statistical power required for meaningful biological interpretation. To address these challenges, this tutorial outlines an analytical workflow for large scale non-targeted metabolite profiling of serum by UPLC-MS. The procedure includes guidelines for sample organization and preparation, data acquisition, quality control, and metabolite identification and will enable reliable acquisition of data for large experiments and provide a starting point for laboratories new to non-targeted metabolite profiling by UPLC-MS.

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS

Non-targeted metabolite profiling by ultra performance liquid chromatography coupled with mass spectrometry (UPLC-MS) is a powerful technique to investigate metabolism. This article outlines a typical workflow utilized for non-targeted metabolite profiling of serum including sample organization and preparation, data acquisition, data analysis, quality control, and metabolite identification.

Non-targeted metabolite profiling by ultra performance liquid chromatography coupled with mass spectrometry (UPLC-MS) is a powerful technique to ...

Untargeted Metabolomics from Biological Sources Using Ultraperformance Liquid Chromatography-High Resolution Mass Spectrometry (UPLC-HRMS)

Here we present a workflow to analyze the metabolic profiles for biological samples of interest including; cells, serum, or tissue. The sample is first separated into polar and non-polar fractions by a liquid-liquid phase extraction, and partially purified to facilitate downstream analysis. Both aqueous (polar metabolites) and organic (non-polar metabolites) phases of the initial extraction are processed to survey a broad range of metabolites. Metabolites are separated by different liquid chromatography methods based upon their partition properties. In this method, we present microflow ultra-performance (UP)LC methods, but the protocol is scalable to higher flows and lower pressures. Introduction into the mass spectrometer can be through either general or compound optimized source conditions. Detection of a broad range of ions is carried out in full scan mode in both positive and negative mode over a broad m/z range using high resolution on a recently calibrated instrument. Label-free differential analysis is carried out on bioinformatics platforms. Applications of this approach include metabolic pathway screening, biomarker discovery, and drug development.

Untargeted Metabolomics from Biological Sources Using Ultraperformance Liquid Chromatography-High Resolution Mass Spectrometry UPLC-HRMS

Untargeted metabolomics provides a hypothesis generating snapshot of a metabolic profile. This protocol will demonstrate the extraction and analysis of metabolites from cells, serum, or tissue. A range of metabolites are surveyed using liquid-liquid phase extraction, microflow ultraperformance liquid chromatography/high-resolution mass spectrometry (UPLC-HRMS) coupled to differential analysis software.

Here we present a workflow to analyze the metabolic profiles for biological samples of interest including; cells, serum, or tissue. The sample is first ...

A Straightforward Method for Glucosinolate Extraction and Analysis with High-pressure Liquid Chromatography (HPLC)

Glucosinolates are a well-studied and highly diverse class of natural plant compounds. They play important roles in plant resistance, rapeseed oil quality, food flavoring, and human health. The biological activity of glucosinolates is released upon tissue damage, when they are mixed with the enzyme myrosinase. This results in the formation of pungent and toxic breakdown products, such as isothiocyanates and nitriles. Currently, more than 130 structurally different glucosinolates have been identified. The chemical structure of the glucosinolate is an important determinant of the product that is formed, which in turn determines its biological activity. The latter may range from detrimental (e.g., progoitrin) to beneficial (e.g., glucoraphanin). Each glucosinolate-containing plant species has its own specific glucosinolate profile. For this reason, it is important to correctly identify and reliably quantify the different glucosinolates present in brassicaceous leaf, seed, and root crops or, for ecological studies, in their wild relatives. Here, we present a well-validated, targeted, and robust method to analyze glucosinolate profiles in a wide range of plant species and plant organs. Intact glucosinolates are extracted from ground plant materials with a methanol-water mixture at high temperatures to disable myrosinase activity. Thereafter, the resulting extract is brought onto an ion-exchange column for purification. After sulfatase treatment, the desulfoglucosinolates are eluted with water and the eluate is freeze-dried. The residue is taken up in an exact volume of water, which is analyzed by high-pressure liquid chromatography (HPLC) with a photodiode array (PDA) or ultraviolet (UV) detector. Detection and quantification are achieved by conducting comparisons of the retention times and UV spectra of commercial reference standards. The concentrations are calculated based on a sinigrin reference curve and well-established response factors. The advantages and disadvantages of this straightforward method, when compared to faster and more technologically advanced methods, are discussed here.

A Straightforward Method for Glucosinolate Extraction and Analysis with High-pressure Liquid Chromatography HPLC

Here, we describe in great detail an established and robust protocol for the extraction of glucosinolates from ground plant materials. After an on-column sulfatase treatment of the extracts, the desulfoglucosinolates are eluted and analyzed by high-pressure liquid chromatography.

Glucosinolates are a well-studied and highly diverse class of natural plant compounds. They play important roles in plant resistance, rapeseed oil ...

Real-time Breath Analysis by Using Secondary Nanoelectrospray Ionization Coupled to High Resolution Mass Spectrometry

Exhaled volatile organic compounds (VOCs) have aroused considerable interest, since they can serve as biomarkers for disease diagnosis and environmental exposure in a non-invasive manner. In this work, we present a protocol to characterize the exhaled VOCs in real time by using secondary nanoelectrospray ionization coupled to high resolution mass spectrometry (Sec-nanoESI-HRMS). The homemade Sec-nanoESI source was readily set up based on a commercial nanoESI source. Hundreds of peaks were observed in the background-subtracted mass spectra of exhaled breath, and the mass accuracy values are -4.0-13.5 ppm and -20.3-1.3 ppm in the positive and negative ion detection modes, respectively. The peaks were assigned with accurate elemental composition according to the accurate mass and isotopic pattern. Less than 30 s is used for one exhalation measurement, and it takes approximately 7 min for six replicated measurements.

A protocol for characterizing chemical composition of exhaled breath in real time by using secondary nanoelectrospray ionization coupled to high resolution mass spectrometry is demonstrated.

Exhaled volatile organic compounds (VOCs) have aroused considerable interest, since they can serve as biomarkers for disease diagnosis and environmental ...

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids

Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have been thought of as a type of molecular information storage. Mass spectrometry analysis has been considered the method of choice for sequencing peptoids. Peptoids can be synthesized via solid phase chemistry using a repeating two-step reaction cycle. Here we present a method to manually synthesize oligo-peptoids and to analyze the sequence of the peptoids using tandem mass spectrometry (MS/MS) techniques. The sample peptoid is a nonamer consisting of alternating N-(2-methyloxyethyl)glycine (Nme) and N-(2-phenylethyl)glycine (Npe), as well as an N-(2-aminoethyl)glycine (Nae) at the N-terminus. The sequence formula of the peptoid is Ac-Nae-(Npe-Nme)4-NH2, where Ac is the acetyl group. The synthesis takes place in a commercially available solid-phase reaction vessel. The rink amide resin is used as the solid support to yield the peptoid with an amide group at the C-terminus. The resulting peptoid product is subjected to sequence analysis using a triple-quadrupole mass spectrometer coupled to an electrospray ionization source. The MS/MS measurement produces a spectrum of fragment ions resulting from the dissociation of charged peptoid. The fragment ions are sorted out based on the values of their mass-to-charge ratio (m/z). The m/z values of the fragment ions are compared against the nominal masses of theoretically predicted fragment ions, according to the scheme of peptoid fragmentation. The analysis generates a fragmentation pattern of the charged peptoid. The fragmentation pattern is correlated to the monomer sequence of the neutral peptoid. In this regard, MS analysis reads out the sequence information of the peptoids.

A protocol is described for the manual synthesis of oligo-peptoids followed by sequence analysis by mass spectrometry.

Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have ...

Capillary Electrophoresis-based Hydrogen/Deuterium Exchange for Conformational Characterization of Proteins with Top-down Mass Spectrometry

Resolving conformational heterogeneity of multiple protein states that coexist in solution remains one of the main obstacles in the characterization of protein therapeutics and the determination of the conformational transition pathways critical for biological functions, ranging from molecular recognition to enzymatic catalysis. Hydrogen/deuterium exchange (HDX) reaction coupled with top-down mass spectrometric (MS) analysis provides a means to characterize protein higher-order structures and dynamics in a conformer-specific manner. The conformational resolving power of this technique is highly dependent on the efficiencies of separating protein states at the intact protein level and minimizing the residual non-deuterated protic content during the HDX reactions. 
Here we describe a capillary electrophoresis (CE)-based variant of the HDX MS approach that aims to improve the conformational resolution. In this approach, proteins undergo HDX reactions while migrating through a deuterated background electrolyte solution (BGE) during the capillary electrophoretic separation. Different protein states or proteoforms that coexist in solution can be efficiently separated based on their differing charge-to-size ratios. The difference in electrophoretic mobility between proteins and protic solvent molecules minimizes the residual non-deuterated solvent, resulting in a nearly complete deuterating environment during the HDX process. The flow-through microvial CE-MS interface allows efficient electrospray ionization of the eluted protein species following a rapid mixing with the quenching and denaturing modifier solution at the outlet of the sprayer. The online top-down MS analysis measures the global deuteration level of the eluted intact protein species, and subsequently, the deuteration of their gas-phase fragments. This paper demonstrates this approach in differential HDX for systems, including the natural protein variants coexisting in milk.

Presented here is a protocol for a capillary electrophoresis-based hydrogen/deuterium exchange (HDX) approach coupled with top-down mass spectrometry. This approach characterizes the difference in higher-order structures between different protein species, including proteins in different states and different proteoforms, by conducting concurrent differential HDX and electrophoretic separation.

Resolving conformational heterogeneity of multiple protein states that coexist in solution remains one of the main obstacles in the characterization of ...

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Exhaustive generation of molecular structures has numerous chemical and biochemical applications such as drug design, molecular database construction, exploration of alternative biochemistries, and many more. Mathematically speaking, these are graph generators with chemical constraints. In the field, the most efficient generator currently (MOLGEN) is a commercial product, limiting its use. Alternative to that, another molecular structure generator, MAYGEN, is a recent open-source tool with efficiency comparable to MOLGEN and the capacity for users to increase its performance by adding new features. One of the research fields that can benefit from this development is astrobiology; structure generators allow researchers to supplement experimental data with computational possibilities for alternative biochemistry. This protocol details one use case for structure generation in astrobiology, namely the generation and curation of alpha-amino acid libraries. Using open-source structure generators and cheminformatics tools, the practices described here can be implemented beyond astrobiology for the low-cost creation and curation of chemical structure libraries for any research question.

The purpose of this protocol is to efficiently generate and curate small-molecule structure libraries using open-source software.

Exhaustive generation of molecular structures has numerous chemical and biochemical applications such as drug design, molecular database construction, ...

Trimethylamine Detection in Animal-Derived Medicine by Headspace GC-MS

An Improved Technique for Trimethylamine Detection in Animal-Derived Medicine by Headspace Gas Chromatography-Tandem Quadrupole Mass Spectrometry

Animal-derived medicines have distinctive characteristics and significant curative effects, but most of them have an obvious fishy odor, resulting in the poor compliance of clinical patients. Trimethylamine (TMA) is one of the key fishy odor components in animal-derived medicine. It is difficult to identify TMA accurately using the existing detection method due to the increased pressure in the headspace vial caused by the rapid acid-base reaction after the addition of lye, which causes TMA to escape from the headspace vial, stalling the research progress of the fishy odor of animal-derived medicine. In this study, we proposed a controlled detection method that introduced a paraffin layer as an isolation layer between acid and lye. The rate of TMA production could be effectively controlled by slowly liquefying the paraffin layer through thermostatic furnace heating. This method showed satisfactory linearity, precision experiments, and recoveries with good reproducibility and high sensitivity. It provided technical support for the deodorization of animal-derived medicine.

Author Spotlight: An Improved Technique for Trimethylamine Detection in Animal-Derived Medicine by Headspace Gas Chromatography-Tandem Quadrupole Mass Spectrometry  

Here, a headspace gas chromatography-tandem quadrupole mass spectrometry (HS-GC-MS/MS) method suitable for the determination of trimethylamine (TMA) in animal-derived medicines is described. The protocol includes sample pretreatment, headspace treatment, analysis conditions, methodological validation, and the determination of TMA in animal-derived medicines.

Animal-derived medicines have distinctive characteristics and significant curative effects, but most of them have an obvious fishy odor, resulting in the ...

Analyzing Pesticides in Avocado Using the QuEChERS Method and CG-MS/MS

Determination of 45 Pesticides in Avocado Varieties by the QuEChERS Method and Gas Chromatography-Tandem Mass Spectrometry

Gas chromatography (GC) tandem mass spectrometry (MS/MS) stands as a preeminent analytical instrument extensively employed for the surveillance of pesticide residues in food. Nevertheless, these methods are vulnerable to matrix effects (MEs), which can potentially affect accurate quantification depending on the specific combination of analyte and matrix. Among the various strategies to mitigate MEs, matrix-matched calibration represents the prevailing approach in pesticide residue applications due to its cost-effectiveness and straightforward implementation. In this study, a total of 45 representative pesticides were analyzed in three different varieties of avocado (i.e., Criollo, Hass, and Lorena) using the Quick-Easy-Cheap-Effective-Rugged-Safe (QuEChERS) method with ammonium formate and GC-MS/MS. 
For this purpose, 5 g of the avocado sample was extracted with 10 mL of acetonitrile, and then 2.5 g of ammonium formate was added to induce phase separation. Subsequently, the supernatant underwent a cleanup process via dispersive solid-phase extraction employing 150 mg of anhydrous MgSO4, 50 mg of primary-secondary amine, 50 mg of octadecylsilane, 10 mg of graphitized carbon black, and 60 mg of a zirconium oxide-based sorbent (Z-Sep+). The GC-MS/MS analysis was successfully performed in less than 25 min. Rigorous validation experiments were carried out to assess the performance of the method. The examination of a matrix-matched calibration curve for each variety of avocado revealed that the ME remained relatively consistent and less than 20% (considered as a soft ME) for most pesticide/variety combinations. Furthermore, the method&#180;s limits of quantification were lower than 5 &#181;g/kg for all three varieties. Finally, the recovery values for most pesticides fell within the acceptable range of 70-120%, with relative standard deviation values below 20%.

Avocado Sample Preparation Using the QuEChERS Method with Ammonium Formate for Pesticide Analysis

The present protocol describes the analysis of multiclass pesticide residues in avocado varieties using the Quick-Easy-Cheap-Effective-Rugged-Safe (QuEChERS) method with ammonium formate, followed by gas chromatography-tandem mass spectrometry.

Gas chromatography (GC) tandem mass spectrometry (MS/MS) stands as a preeminent analytical instrument extensively employed for the surveillance of ...

Histone Proteomic Analysis and Post-Translational Modification Characterization

Histone Modification Screening using Liquid Chromatography, Trapped Ion Mobility Spectrometry, and Time-Of-Flight Mass Spectrometry

Histone proteins are highly abundant and conserved among eukaryotes and play a large role in gene regulation as a result of structures known as posttranslational modifications (PTMs). Identifying the position and nature of each PTM or pattern of PTMs in reference to external or genetic factors allows this information to be statistically correlated with biological responses such as DNA transcription, replication, or repair. In the present work, a high-throughput analytical protocol for the detection of histone PTMs from biological samples is described. The use of complementary liquid chromatography, trapped ion mobility spectrometry, and time-of-flight mass spectrometry (LC-TIMS-ToF MS/MS) enables the separation and PTM assignment of the most biologically relevant modifications in a single analysis. The described approach takes advantage of recent developments in dependent data acquisition (DDA) using parallel accumulation in the mobility trap, followed by sequential fragmentation and collision-induced dissociation. Histone PTMs are confidently assigned based on their retention time, mobility, and fragmentation pattern.

Author Spotlight: Enhanced Histone PTM Isomer Identification Through LC-TIMS-ToF MS/MS and PASEF

An analytical workflow based on liquid chromatography, trapped ion mobility spectrometry, and time-of-flight mass spectrometry (LC-TIMS-ToF MS/MS) for high confidence and highly reproducible "bottom-up" analysis of histone modifications and identification based on principal parameters (retention time [RT], collision cross section [CCS], and accurate mass-to-charge [m/z] ratio).