Bioconjugation with Aminoalkylhydrazine for Efficient Mass

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Article Cite This: ACS Omega 2019, 4, 13447−13453

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Bioconjugation with Aminoalkylhydrazine for Efficient Mass Spectrometry-Based Detection of Small Carbonyl Compounds Senthil K. Thangaraj,† Sanni Voutilainen,‡ Martina Andberg,‡ Anu Koivula,‡ Janne Jänis,† and Juha Rouvinen*,† †

Department of Chemistry, University of Eastern Finland, PO Box 111, FI-80101 Joensuu, Finland VTT Technical Research Centre of Finland Ltd, PO Box 1000, FI-020444 VTT, Espoo, Finland



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S Supporting Information *

ABSTRACT: Bioconjugation through oxime or hydrazone formation is a versatile strategy for covalent labeling of biomolecules in vitro and in vivo. In this work, a mass spectrometry-based method was developed for the bioconjugation of small carbonyl compounds (CCs) with an aminoalkylhydrazine to form stable hydrazone conjugates that are readily detectable with electrospray ionization mass spectrometry (ESI-MS). Out of all hydrazine reagents tested, 2-(dimethylamino)ethylhydrazine (DMAEH) was selected for further analysis due to the fastest reaction rates observed. A thorough study of the reaction kinetics between structurally varied short-chain CCs and DMAEH was performed with the second-order reaction rate constants spanning in the range of 0.23−208 M−1 s−1. In general, small aldehydes reacted faster than the corresponding ketones. Moreover, a successful reaction monitoring of a deoxyribose-5-phosphate aldolase-catalyzed reversible retro−aldol cleavage of deoxyribose was demonstrated. Thus, the developed method shows potential also for ESI-MS-based enzyme kinetics studies.



INTRODUCTION Various bioconjugation reactions have become an essential route to investigate the chemical and biological molecules in vitro and in vivo.1 Hydrazone and oxime formations are the examples of widely utilized covalent labeling reactions for biomolecules under physiological conditions.2 These reactions are older than many other bioconjugation reactions and have already been studied by German scientists in the late 1800s.3−6 In particular, hydrazines are commonly used as nucleophiles due to their high reactivity toward carbonyl compounds (CCs), forming stable hydrazone conjugates. Hydrazone conjugates are of great interest due to their high specificity and bioorthogonality (i.e., potential use in living systems without interfering with biological processes).1 The hydrazone formation follows a two-step mechanism: first, an α-effect nucleophile (hydrazine) reacts with an electrophile (aldehyde or ketone) to form a tetrahedral hemiaminal intermediate, which then dehydrates to produce the final product (Figure 1).1 In general, the reaction is slow, especially at neutral pH; thus, a general acid catalyst can be used to enhance the reaction rate. The fastest rates are observed around pH ∼4.5, where carbonyl carbon is protonated but hydrazine is not yet protonated. This limits the use of hydrozone conjugation in in © 2019 American Chemical Society

vivo applications where physiological pH is desired. Another approach is to use nucleophilic catalysts such as aromatic amines and phenols.7−9 However, many of these are toxic to human cells; therefore, new types of nontoxic catalysts, like imidazoles or bifunctional amines, have been proposed for cellular applications.10 Different CCs are widespread organic molecules in nature, particularly in environmental samples and food stuff, including milk products, meat, fish, fresh vegetables, and fruits.11 Moreover, they can be used as preservatives in food processing, brewery, and beverage industry due to their sensory nature.12 Certain aldehydes are produced during the process of fermentation of alcoholic beverages13 and in high-temperature frying via degradation of fatty acids, lipids, and proteins.14 Many of them are toxic and potentially carcinogenic, especially formaldehyde,15,16 acetaldehyde,16 benzaldehyde,11,14 and furfural.13,17 For instance, according to the US Environmental Protection Agency (EPA), the daily reference dose (RfD) of formaldehyde is about 0.2 mg kg−1 of body weight.11 Thus, Received: June 9, 2019 Accepted: July 25, 2019 Published: August 7, 2019 13447

DOI: 10.1021/acsomega.9b01691 ACS Omega 2019, 4, 13447−13453

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Figure 1. Hydrazone formation between carbonyl compound (CC) and hydrazine. R1, R2, and R3 are varying alkyl, substituted alkyl, or aryl groups. Breakdown of the hemiaminal intermediate is usually the rate-limiting step of the reaction.

sensitive detection of these compounds is an important task. However, sampling and detection of short-chain CCs are challenging due to their low molecular weight and high volatility. One way to overcome these challenges is to transform CCs into the corresponding hydrazone or oxime conjugates, which improves their chromatographic separation and detection sensitivity in conventional GC−MS or LC−MS analysis.18,19 Most common reagents used for this purpose are 2,4-dinitrophenylhydrazine (DNPH), o-(2,3,4,5,6pentafluorobenzyl)hydroxylamine (PFBHA),20 methoxyphenylhydrazine (MPH), and 4-hydrazinobenzoic acid (HBA) (Figure 2). For example, DNPH has been successfully used for

Thus, the ESI-MS-based method should be more universal, as it can also be used to detect aliphatic or alicyclic compounds without the need for chromophores in the structure. Here, bioconjugation of four hydrazines and a hydroxylamine was performed with a wide variety of small CCs (i.e., 9 aldehydes, 6 ketones, and 2 sugars) and 2-(dimethylamino)ethylhydrazine (DMAEH) was selected for further analysis due to the fastest reaction rates observed in the applied conditions. Moreover, a successful reaction monitoring of a deoxyribose-5-phosphate aldolase (DERA) catalyzed retro−aldol reaction of Ddeoxyrobise (DR) to form D-glyceraldehyde and acetaldehyde was demonstrated, suggesting that the developed method holds a vast potential also for ESI-MS-based enzyme kinetics studies.



RESULTS AND DISCUSSION Bioconjugation of Short-Chain CCs for Detection with ESI-MS. To compare the efficiency of different compounds promoting hydrazone/oxime-based bioconjugation of various CCs at neutral pH, we selected four hydrazines (DNPH, MPH, HBA, and DMAEH) for initial reaction kinetics studies (Figure 2). In the previous study of Kool and co-workers, relative rate constants (krel) of DNPH, MPH, HBA, and DMAEH (at 25 °C and pH 7.4) with 2formylpyridine were determined to be 1.4, 2.0, 4.9, and 23, respectively. Additionally, PFBHA (hydroxylamine) was included in our study since it is frequently used for the fast derivatization of aldehydes for GC-MS detection.29 Among all hydrazine reagents tested, DMAEH was clearly the fastest nucleophile as compared to three phenylhydrazines or hydroxylamine (data not shown), consistent with the studies of Kool and co-workers.27,28 In addition, the terminal dimethylamino group present in DMAEH provides a very high ionization efficiency in the positive-ion ESI, which is beneficial for the detection of both free hydrazine (m/z 104.1181 for [DMAEH + H]+) and the corresponding bioconjugate. Besides, DMAEH was fully converted into specific hydrazone products with all CCs studied, except with a few low-reactive ketones due to their less electrophilic nature (Figures S1−S3). In addition, not only the small aldehydes and ketones but also the sugar molecules (DR and DRP) reacted with DMAEH and yielded the corresponding conjugated products (Figure S4). Thus, DMAEH was selected for further reaction kinetics studies. Reaction Kinetics Analysis of CCs with DMAEH. A representative ESI-MS-based reaction-monitoring analysis for the bioconjugation of formaldehyde (FA) with DMAEH is presented in Figure 3. The reaction rate plots (ln R vs treact) at an increasing formaldehyde concentration were sufficiently linear (R2 > 0.99), showing that the reactions in these conditions followed a pseudo-first-order kinetics. Only at the highest aldehyde concentrations tested (i.e., fastest rates), a

Figure 2. Chemical structures of hydrazine/hydroxylamine reagents tested for the bioconjugation of various carbonyl compounds.

a simultaneous detection of various aldehydes and ketones from cigarette smoke and urine samples.21,22 PFBHA is one of the first synthesized derivatization reagents to determine volatile carbonyl compounds present in air samples23,24 or, e.g., uric acid in human serum.25 Both are also chromophores, making it possible to use UV−vis for their detection. The drawbacks of DNPH and PFBHA are that they are electrondeficient α-nucleophiles and perform relatively slowly at pH ≈7.1 Moreover, DNPH has a poor solubility in water, which hinders the determination of some endogenous aldehydes like formaldehyde.26 Kool and co-workers have recently reported alternative “fast α-nucleophiles”, which react much faster at physiological pH and even without a catalyst.1,27,28 These compounds can be used for rapid bioconjugation reactions of various biomolecules in vitro or in vivo. In this study, a mass spectrometry based method was developed for the bioconjugation of small carbonyl compounds (CCs) with an aminoalkylhydrazine to form stable hydrazone conjugates, which are readily detectable with electrospray ionization mass spectrometry (ESI-MS). Due to their small size and high volatility, many CCs are difficult to detect directly with ESI-MS or other atmospheric-pressure ionization (API) techniques. Moreover, previous studies have relied on the chromophoric nature of the formed hydrazone conjugates when utilizing UV−vis spectrophotometry for detection.27,28 13448

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Figure 3. (A) Reaction monitoring of the bioconjugation of formaldehyde (FA) with 2-(dimethylamino)ethylhydrazine (DMAEH) at pH 7 with positive-ion ESI-MS. (b) Pseudo-first-order reaction rate plots at five different formaldehyde concentrations. The concentration of DMAEH was always 10 μM. (c) Plot of the observed pseudo-first-order rate constant (k1) as a function of formaldehyde concentration to determine the secondorder rate constant (k2) for the reaction.

Table 1. Second-Order (k2) and Relative (krel) Rate Constants for Hydrazone Formation of Various Carbonyl Compounds (CCs) with 2-(Dimethylamino)ethylhydrazine (DMAEH) at Neutral pH Determined with ESI-MSa

Conditions used: The DMAEH concentration was 5 μM for CCs 5, 7, 9, 12, 13, and 16; 10 μM for CCs 1−3, 6, 8, 10, 14, 17, and 18; 50 μM for CC 4; and 200 μM for CC 15. The relative second-order rate constants (krel) are relative to that of acetophenone (CC 15), which had the lowest k2 among all the CCs studied (given krel = 1). a

M−1 s−1, which is slightly higher than that observed for 2formylpyridine in the previous study.28 Table 1 shows the structures and the determined reaction rate constants (k2 and krel) for the other investigated CCs with DMAEH at neutral pH by using ESI-MS (the reaction rate

slight deviation from linearity can be seen. Therefore, we limited the reaction times generally to treact < 4000 s and/or the extent of the reaction to ∼60% conversion (ln R > −1.0). The second-order rate constant (obtained from the secondary plot, k1 vs [FA]) for formaldehyde was determined to be k2 = 4.7 13449

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these results cannot simply be rationalized in terms of electronic and steric effects, and more detailed studies are therefore needed. The lowest rate among all CCs was observed for acetophenone (15; krel = 1), which can be explained by the disturbed aryl conjugation upon the formation of a tetrahedral hemiaminal intermediate.27 Reactive carbonyl groups (aldehydes and/or ketones) are naturally present in many carbohydrates. Therefore, we tested whether DMAEH can also be used for the bioconjugation of some simple sugar molecules. Two monosaccharides, 2-deoxyD-ribose (DR) and 2-deoxy-D-ribose-5-phosphate (DRP), were evaluated in this context. Both DR and DRP were converted into the corresponding hydrazone conjugates within the extended reaction times, proving that the developed method is equally good for detecting reactive sugar molecules. Interestingly, DR had a comparable reaction rate (krel = 5.8) with the smallest aliphatic aldehydes but DRP had a roughly 7fold higher rate than DR (krel = 41.3), which suggests that the phosphate group present in the structure can enhance the breakdown of the hemiaminal intermediate, which is believed to be the rate-limiting step of the reaction. Figure 4 presents a bar plot to compare the relative reaction rate constants of all CCs studied (Figure 4).

plots can be found as Supporting Figures S5−S21). The slowest rate was observed with acetophenone (k2 = 0.23 M−1 s−1; krel = 1) and the fastest rate with pyruvaldehyde (k2 = 208 M−1 s−1; krel = 910.1). Pyruvaldehyde (also known as methylglyoxal) is a ketoaldehyde that exists exclusively in its hydrated form in aqueous solution (Keq ≈ 8 × 103).30 Some general trends can be observed from the kinetics data presented in Table 1. First, aldehydes reacted faster than the corresponding methyl ketones. For example, acetaldehyde (entry 2) had ∼2.6-fold higher rate than acetone (11), butyraldehyde (5) had ∼3.9-fold higher rate than 2-pentanone (13), and isovaleraleraldehyde/valeraldehyde (7/8) had ∼2.5fold higher rate than 2-hexanone (14). Also, benzaldehyde (9) reacted much faster (17.6-fold) than acetophenone (15). Second, the rates generally increased with increasing carbon chain length, except for formaldehyde and acetaldehyde, which reacted faster than propionaldehyde. In aqueous solution, formaldehyde exists exclusively in its hydrated form (Keq ≈ 2000) and acetaldehyde is partially hydrated (Keq ≈ 1); thus, it is possible that these two compounds may react in hydrazone formation via an SN2-type substitution reaction (Figure S22), which should have a lower activation energy than nucleophilic addition, especially in the absence of an acid catalyst and/or nonbulky substituents. Kool et al. previously studied the reaction rates of aliphatic vs aromatic CCs and confirmed that simple aliphatic compounds react more rapidly than aromatic ones, and that the steric effects are moderate to small, except in case of very bulky aldehydes.27,28 It was concluded that electron-deficient CCs generally react faster than electron-rich ones in hydrazone formation. This is in line with our observations. However, there were some notable exceptions. Butanone (12) had a 3.4fold higher rate than propionaldehyde (3), which cannot be explained by either electronic or steric effects. In addition, lactaldehyde (4) reacted rather slowly (krel = 3.6) as compared to other aldehydes, although the hydroxyl group present at the α-carbon should increase the reactivity. However, lactaldehyde exists mainly in the dimeric form in aqueous solution,31 which may considerably decrease its reactivity. The fastest rate observed for pyruvaldehyde (krel = 910.1) is probably because the compound has two adjacent carbonyl groups, both of which can react in hydrazone formation with a very little steric hindrance. Moreover, pyruvaldehyde also exists mainly in its hydrated form in water,30 which may increase its reactivity via an SN2-type reaction (Figure S23). In both cases, the hemiaminal intermediate can be stabilized by an intramolecular hydrogen bond. In comparison, some aromatic dialdehydes have been reported to undergo very rapid bioconjugation reactions with hydroxylamines by virtue of a cyclic intermediate formed during the reaction.32 Due to the very rapid reactions in the applied conditions, the rate constants for pyruvaldehyde were determined in the molar excess of DMAEH rather than CC. The trend in the observed rates for ketones was not so clear. Unlike aldehydes showing an increasing rate with an increasing carbon chain length, aliphatic ketones did not show a clear dependence; 2-butanone (12) reacted considerably faster (krel = 24.4) than acetone (11; krel = 4.6), but 2-pentanone (13) and 3-pentanone (16) had very comparable rates (krel = 6.6 and 6.1, respectively) to that of acetone. The lower rate observed for 3-pentanone could be explained by a greater steric hindrance (two ethyl groups) as compared to the other aliphatic methyl ketones but not for 2-pentanone. Overall,

Figure 4. Relative second-order rate constants (krel) of varied carbonyl compounds (CCs) with 2-(dimethylamino)ethylhydrazine (DMAEH) at neutral pH in methanol. Acetophenone (15) serves as a reference with krel = 1.

Hydrazone Formation of DERA Substrates and Products. Deoxyribose-5-phosphate aldolase (DERA; E.C. 4.1.2.4) is an enzyme that catalyzes the enantioselective formation of carbon−carbon (C−C) bonds under mild reaction conditions.33,34 DERA has an important role in nucleic acid metabolism in bacteria and attracted attention as a potential industrial biocatalyst for the synthesis of pharmaceutically important intermediates. Naturally, DERA catalyzes a retro−aldol cleavage of DRP into two aldehydes, namely, Dglyceraldehyde-3-phosphate (GAP) and acetaldehyde (AA), as part of the pentose phosphate pathway. However, the reaction is reversible and the reverse C−C bond formation in aldol reaction has high potential in synthetic chemistry. DERA also shows weaker activity in the cleavage of DR.35 Consequently, DERA has been subjected to biochemical engineering to tailor its activity, specificity, and stability against high aldehyde concentrations.33 Since we observed efficient bioconjugation of both DR and DRP with DMAEH, we further tested if the DERA-catalyzed C−C bond cleavage of DR could be efficiently monitored by using the developed ESI-MS-based 13450

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in methanol and hydrazines samples were prepared in water (HPLC grade) solution. Cloning, Expression, and Purification of 2-Deoxy-Dribose-5-phosphate Aldolase (DERA) Enzyme. DERA encoding gene (deoC) from E. coli was purchased as a G-block from Integrated DNA Technologies as a codon optimized for E. coli. The gene having an N-terminal 6× His-tag was cloned into the E. coli expression vector pBAT436 using the Gibson assembly method. DERA was produced in E. coli BL21(DE3) strain in LB medium containing 100 μg mL−1 ampicillin and purified from the E. coli cell extract in a single step using NiNTA chromatography. Conjugation Reactions and Reaction Kinetic Analysis. The stock solutions of hydrazines, DNPH, DMAEH, PFBHA, MPH, and HBA, were prepared in water to the concentration of 2 mg mL−1. The stock solutions of CCs were prepared in methanol to 500 μM concentration. The conjugation reactions were performed at room temperature (23 ± 2 °C) by mixing appropriate aliquots of hydrazine and CC stock solutions to obtain 5−200 μM hydrazine concentration and a varying CC concentration. The reaction rates were measured under pseudo-first-order conditions, i.e., excess amount of CC. All reactions were performed in water/methanol (50:50, v/v) solvent mixture. The MS data were collected at 5 min intervals, and the reaction time (treact) was calculated as the time between the reagent mixing and the data acquisition. For each reaction, the intensities of the free hydrazine (IH) and the corresponding hydrazone conjugate (IHC) were tabulated and the reaction rate constant (k1) was determined as the slope of the primary linear fit to the integrated rate equation ln R = −k1treact, where R = IH/(IH + IHC). It was presumed that the relative ion intensities represent the true solution concentrations, [H] and [HC], and that the reaction follows firstorder kinetics. The latter was proven by sufficient linearity (R2 > 0.99) observed for the primary linear fits. The second-order rate constant (k2) was then obtained from the slope of the secondary linear fit k1 vs [CC], which is essentially k2 = k1/ [CC] at any concentration. All linear fittings were performed with OriginPro 15.0 software (Origin Lab, Northampton, MA). Finally, the relative second-order rate constants (krel) for different CCs were calculated as krel = k2,CC/k2,ref, where k2,ref is the rate constant observed for acetophenone, which was the slowest among the all CCs studied. Enzyme Reaction. For the DERA-catalyzed aldol reaction to cleave DR (deoxyribose), 1 mL of substrate (6 mM) in 50 mM ammonium acetate (pH 7.1) was mixed with 50.6 μL of DERA enzyme (1.1 mg mL−1 in 50 mM sodium phosphate solution). This mixture was then incubated for 60 min at room temperature. After this, 10 μL of the reaction mixture was mixed with 100 μL of methanol, which essentially quenches the enzymatic reaction, and then 90 μL of DMAEH (1 mM in water) was added and the mixture was further incubated for 15 min before the analysis. The control experiment was conducted in the absence of enzyme. Mass Spectrometry. All experiments were performed using a 12-T Bruker solariX XR Fourier transform ion cyclotron resonance (FT-ICR) instrument (Bruker Daltonics, Bremen, Germany), coupled with an Apollo-II ESI source. The samples were injected into the ion source at a flow rate of 2 μL min−1 with dry nitrogen serving as a nebulizing (4 L min−1) and drying gas (80 °C, 1 bar). The ESI-generated positive ions were accumulated for 0.08 s in the hexapole ion trap and subsequently transferred to a dynamically harmonized ICR cell

method. Figure 5 shows a representative ESI-MS spectrum of the DMAEH bioconjugates of the DERA-catalyzed retro−aldol reaction products of DR, glyceraldehyde and acetaldehyde. Indeed, both the substrate and the two aldehyde products can be efficiently detected directly from the reaction mixture. The results indicate that the developed ESI-MS method is suitable for the simultaneous detection and further quantitation of substrates and products of enzyme-catalyzed reactions (here demonstrated for the DERA enzyme) and also holds a vast potential for ESI-MS-based enzyme kinetics assays, especially in the case of small molecules that are difficult to detect with conventional API techniques.

Figure 5. ESI-MS spectrum of the DMAEH bioconjugates of the DERA-catalyzed retro−aldol reaction products of deoxyribose (m/z 220.1649), glyceraldehyde (m/z 176.1389), and acetaldehyde (m/z 130.1336). The unlabeled peaks are impurities coming from the enzyme preparation. For details, see Experimental Section.



CONCLUSIONS We have developed a bioconjugation method for small carbonyl compounds based on DMAEH to form the corresponding hydrazone conjugates. This methodology allows successful measurements of small aldehydes, ketones, or sugars by using electrospray ionization mass spectrometry and can be utilized in diverse applications such as measuring small volatile organic compounds or following enzymatic reactions.



EXPERIMENTAL SECTION Chemicals. Formaldehyde (37% aqueous solution), acetaldehyde (≥99.5%), propionaldehyde (≥98.0%), benzaldehyde (≥99.5%), butyraldehyde (≥99.5%), isobutyraldehyde (≥99.0%), valeraldehyde (≥97.0%), isovaleraldehyde (≥97.0%), pyruvaldehyde (40% aqueous solution), DLlactaldehyde (≥95.0%), 2-hexanone (≥99.5%), acetophenone (≥99.5%), butanone (≥99.9%), 2-pentanone (≥99.5%), 2deoxy- D -ribose (≥97.0%), 2-deoxyribose-5-phosphate (≥95.0%), 2,4-dinitrophenylhydrazine (97.0%), o-(2,3,4,5,6pentafluorobenzyl)-hydroxylamine (≥99.0% hydrochloride salt), and 2-(dimethylamino)ethylhydrazine (≥97.0% dihydrochloride salt) were purchased from Sigma-Aldrich (St. Louis, MO). 4-Hydrazinobenzoic acid (98.0%) and 4-methoxyphenylhydrazine (98.0%, hydrochloride salt) were purchased from Acros Organics (New Jersey). Acetone (100%) was purchased from VMR (Fontenay-sous-Bois, France); 3-pentanone (≥99.0%) was from Merck (Darmstadt, Germany). The recombinant DERA enzyme was expressed in E. coli as described below in more details. All solvents (HPLC grade) were obtained from Sigma-Aldrich and used without further purification. The DERA substrates were prepared in 50 mM ammonium acetate (pH 7.1), while carbonyl compounds were 13451

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(Paracell) for trapping, excitation, and detection. The ion flight time was set to 0.25 ms. One hundred (1 M word) timedomain transients at m/z 40−1500 were summed for each spectrum, zero-filled once, and full-sine apodized prior fast Fourier transform and magnitude calculation. The mass spectra were externally calibrated using ESI-L Tuning Mix (Agilent Technologies, Santa Clara, CA). The data acquisition was performed using Bruker ftmsControl 2.1 software, and the data postprocessing and analysis were accomplished with Bruker DataAnalysis 4.4 SR1 software.



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ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acsomega.9b01691. ESI FT-ICR mass spectra of hydrazone conjugates between DMAEH and aldehydes, ketones, or sugars; the pseudo-first-order (ln R vs time) and second-order plots (k1 vs [CC]) of the hydrazone conjugation reactions; the proposed reaction mechanisms for hydrazone conjugate formation of formaldehyde and pyruvaldehyde (PDF)



AUTHOR INFORMATION

Corresponding Author

*E-mail: juha.rouvinen@uef.fi. ORCID

Juha Rouvinen: 0000-0003-1843-5718 Notes

The authors declare no competing financial interest.



ACKNOWLEDGMENTS The FT-ICR facility is supported by Biocenter Finland, Biocenter Kuopio and the European Regional Development Fund (project number A70135). We thank Arja Kiema and Kirsi Kiiveri for technical assistance (VTT). This work received support from the Academy of Finland through SAENGBIOCAT project (Decision Numbers 287241 and 288677).



REFERENCES

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