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Formate

Formate is a crucial one-carbon compound that plays a pivotal role in various biological processes.
It is an anion derived from formic acid, and can serve as a metabolic intermediate, a cofactor, and a signaling molecule.
Formate is involved in cellular respiration, DNA synthesis, and folate metabolism, among other functions.
Understandng the role of formate in health and disease is an active area of research, with applications in fields like energy production, cancer biology, and neuroscience.
Leveraging AI-driven tools like PubCompare.ai can help researchers optimize their formaete-related projects, locating the most reproducible and effective research methods from the literature, preprints, and patents.

Most cited protocols related to «Formate»

The liquid chromatography system consisted of an Agilent 1290 system (Agilent Technologies Inc.) with a pump (G4220A), a column oven (G1316C), and an autosampler (G4226A). For hydrophilic metabolite analysis, mobile phase A was 10 mM ammonium formate with 0.125 % formic acid in water; mobile phase B was 95:5 acetonitrile:water (v/v) with 10 mM ammonium formate and 0.125 % formic acid. An Acquity UPLC BEH Amide column (150×2.1 mm; 1.7 µm) coupled to a VanGuard BEH Amide pre-column (5×2.1 mm; 1.7 µm) (Waters; Milford, MA, USA) was used. The gradient was 0 min, 100% B; 2 min, 100% B; 7.7 min, 70% B; 9.5 min, 40% B; 10.3 min, 30% B; 12.8 min, 100% B; 16.8 min, 100% B. The column flow rate was 0.4 mL/min, autosampler temperature was 4 °C, injection volume was 2 µL, and column temperature was 45 °C. For lipid analysis, mobile phase A was 60:40 acetonitrile:water (v/v) with 10 mM ammonium formate and 0.1% formic acid; mobile phase B was 90:10 isopropanol:acetonitrile (v/v) with 10 mM ammonium formate and 0.1% formic acid.
The lipidomic LC method utilized an Acquity UPLC charged-surface hybrid (CSH) C18 column (100×2.1 mm; 1.7 µm) coupled to an Acquity CSH C18 VanGuard pre-column (5×2.1 mm; 1.7 µm) (Waters; Milford, MA, USA). The gradient was 0 min, 15% B; 2 min, 30% B; 2.5 min, 48% B; 11 min, 82% B, 11.5 min, 99% B; 12 min, 99% B; 12.1 min, 15% B; 15 min, 15% B. The column flow rate was 0.6 mL/min, autosampler temperature was 4 °C, injection volume was 3 µL in positive mode and 5 µL in negative mode, and column temperature was 65 °C.
Mass spectrometry was performed on an AB Sciex TripleTOF 5600+ system (Q-TOF) equipped with a DuoSpray ion source. All analyses were performed at the high sensitivity mode for both TOF MS and product ion scan. The mass calibration was automatically performed every 10 injections using an APCI positive/negative calibration solution via a calibration delivery system (CDS). For hydrophilic interaction chromatography analysis, SWATH (sequential window acquisition of all theoretical mass spectra) acquisition with positive ion mode was used as the data independent acquisition system. The SWATH parameters were MS1 accumulation time, 50 ms; MS2 accumulation time, 30 ms; collision energy, 45 V; collision energy spread, 15 V; cycle time, 640 ms; Q1 window, 25 Da; mass range, m/z 50–500. The other parameters were curtain gas, 35; ion source gas 1, 50; ion source gas 2, 50; temperature, 300 °C; ion spray voltage floating, 4.5 kV; declustering potential, 100 V; RF transmission, m/z 40: 33%, m/z 120: 33%, and m/z 390: 34%. For lipid analysis, six different methods were used; DDA (data-dependent acquisition) with positive ion mode, DDA with negative ion mode, SWATH acquisition (Q1 window, 21 Da) with positive ion mode, SWATH acquisition (Q1 window, 21 Da) with negative ion mode, SWATH acquisition (Q1 window, 65 Da) with positive ion mode, and SWATH acquisition (Q1 window, 65 Da). The common parameters in both SWATH/DDA and positive/negative ion mode were collision energy, 45 V; collision energy spread, 15 V; mass range, m/z 100–1250; curtain gas, 35; ion source gas 1, 60; ion source gas 2, 60; temperature, 350 °C; declustering potential, 80 V; RF transmission, m/z 80: 50%, m/z 200: 50%. The ion spray voltage floating of positive/negative ion mode were +5.5/–4.5 kV, respectively. The DDA parameters in both positive and negative ion modes were MS1 accumulation time, 100 ms; MS2 accumulation time, 50 ms; cycle time, 650 ms; dependent product ion scan number, 10; intensity threshold, 500; exclusion time of precursor ion, 5 s; mass tolerance, 20 mDa; ignore peaks, within 6 Da; dynamic background subtraction, TRUE. The SWATH parameters of 21/65 Da Q1 window were MS1 accumulation time, 100/50 ms; MS2 accumulation time, 10/30 ms; cycle time, 731/640 ms; Q1 window, 21/65 Da.
Publication 2015
The liquid chromatography system consisted of an Agilent 1290 system (Agilent Technologies Inc.) with a pump (G4220A), a column oven (G1316C), and an autosampler (G4226A). For hydrophilic metabolite analysis, mobile phase A was 10 mM ammonium formate with 0.125 % formic acid in water; mobile phase B was 95:5 acetonitrile:water (v/v) with 10 mM ammonium formate and 0.125 % formic acid. An Acquity UPLC BEH Amide column (150×2.1 mm; 1.7 µm) coupled to a VanGuard BEH Amide pre-column (5×2.1 mm; 1.7 µm) (Waters; Milford, MA, USA) was used. The gradient was 0 min, 100% B; 2 min, 100% B; 7.7 min, 70% B; 9.5 min, 40% B; 10.3 min, 30% B; 12.8 min, 100% B; 16.8 min, 100% B. The column flow rate was 0.4 mL/min, autosampler temperature was 4 °C, injection volume was 2 µL, and column temperature was 45 °C. For lipid analysis, mobile phase A was 60:40 acetonitrile:water (v/v) with 10 mM ammonium formate and 0.1% formic acid; mobile phase B was 90:10 isopropanol:acetonitrile (v/v) with 10 mM ammonium formate and 0.1% formic acid.
The lipidomic LC method utilized an Acquity UPLC charged-surface hybrid (CSH) C18 column (100×2.1 mm; 1.7 µm) coupled to an Acquity CSH C18 VanGuard pre-column (5×2.1 mm; 1.7 µm) (Waters; Milford, MA, USA). The gradient was 0 min, 15% B; 2 min, 30% B; 2.5 min, 48% B; 11 min, 82% B, 11.5 min, 99% B; 12 min, 99% B; 12.1 min, 15% B; 15 min, 15% B. The column flow rate was 0.6 mL/min, autosampler temperature was 4 °C, injection volume was 3 µL in positive mode and 5 µL in negative mode, and column temperature was 65 °C.
Mass spectrometry was performed on an AB Sciex TripleTOF 5600+ system (Q-TOF) equipped with a DuoSpray ion source. All analyses were performed at the high sensitivity mode for both TOF MS and product ion scan. The mass calibration was automatically performed every 10 injections using an APCI positive/negative calibration solution via a calibration delivery system (CDS). For hydrophilic interaction chromatography analysis, SWATH (sequential window acquisition of all theoretical mass spectra) acquisition with positive ion mode was used as the data independent acquisition system. The SWATH parameters were MS1 accumulation time, 50 ms; MS2 accumulation time, 30 ms; collision energy, 45 V; collision energy spread, 15 V; cycle time, 640 ms; Q1 window, 25 Da; mass range, m/z 50–500. The other parameters were curtain gas, 35; ion source gas 1, 50; ion source gas 2, 50; temperature, 300 °C; ion spray voltage floating, 4.5 kV; declustering potential, 100 V; RF transmission, m/z 40: 33%, m/z 120: 33%, and m/z 390: 34%. For lipid analysis, six different methods were used; DDA (data-dependent acquisition) with positive ion mode, DDA with negative ion mode, SWATH acquisition (Q1 window, 21 Da) with positive ion mode, SWATH acquisition (Q1 window, 21 Da) with negative ion mode, SWATH acquisition (Q1 window, 65 Da) with positive ion mode, and SWATH acquisition (Q1 window, 65 Da). The common parameters in both SWATH/DDA and positive/negative ion mode were collision energy, 45 V; collision energy spread, 15 V; mass range, m/z 100–1250; curtain gas, 35; ion source gas 1, 60; ion source gas 2, 60; temperature, 350 °C; declustering potential, 80 V; RF transmission, m/z 80: 50%, m/z 200: 50%. The ion spray voltage floating of positive/negative ion mode were +5.5/–4.5 kV, respectively. The DDA parameters in both positive and negative ion modes were MS1 accumulation time, 100 ms; MS2 accumulation time, 50 ms; cycle time, 650 ms; dependent product ion scan number, 10; intensity threshold, 500; exclusion time of precursor ion, 5 s; mass tolerance, 20 mDa; ignore peaks, within 6 Da; dynamic background subtraction, TRUE. The SWATH parameters of 21/65 Da Q1 window were MS1 accumulation time, 100/50 ms; MS2 accumulation time, 10/30 ms; cycle time, 731/640 ms; Q1 window, 21/65 Da.
Publication 2015
PEG precipitation: Self-assembly reaction mixtures at 20 mm MgCl2 were mixed 1:1 (v/v) with precipitation buffer containing 15 % PEG 8000 (w/v) (Ph.Eur.), 5 mm Tris, 1 mm EDTA, and 505 mm NaCl (all chemicals from Carl Roth, Karlsruhe, Germany). The solution was mixed by tube inversion and spinned at 16 000 g, at room temperature (RT) for 25 min using a microcentrifuge (Eppendorf 5420, Hamburg, Germany). The supernatant was removed using a pipette. The pellet was dissolved in target buffer as indicated for each set of experiments and incubated for approximately 20 h at RT or 30 °C.
DNA object self-assembly: Structures were designed using caDNAno v0.2.19 (link) DNA scaffold strands of 7249, 7560, 7704, and 8064 bases length derived from the genome of bacteriophage M13 were used for assembly reactions.2b (link) Staple oligonucleotide strands were prepared by solid-phase chemical synthesis (Eurofins MWG, Ebersberg, Germany, HPSF grade). Production of DNA objects was accomplished in one-pot reaction mixtures containing scaffold DNA at a concentration of 20 nm (default) or 50 nm (pointer in Figure S1, RR in Figures 3 and S8, 24 hb, 42 hb, 100 hb), staple DNA oligonucleotides at 200 nm each, and 5 mm TRIS, 1 mm EDTA, 20 mm MgCl2, and 5 mm NaCl (pH 8). The reaction mixtures were subjected to a thermal annealing protocol using TETRAD (Biorad) thermal cycling devices. The mixtures were first incubated at 65 °C for 15 min and then annealed from 60 to 40 °C in steps of 1 °C per 2–3 h. The reaction products were stored at RT.
Agarose gel electrophoresis: Electrophoresis of the folded DNA objects was carried out in 2 % agarose gels containing electrophoresis buffer (1 mm EDTA, 44.5 mm Tris base, 44.5 mm boric acid, and 11 mm MgCl2, pH 8.4). The samples were electrophoresed for two hours at 70–90 V in a water-cooled gel box filled with electrophoresis buffer. The gels typically contained ethidium bromide at a concentration of 1 μm. The agarose gels were scanned using a Typhoon 9500 FLA laser scanner (GE Healthcare) at a resolution of 50 μm/px (ethidium bromide: excitation at 535 nm, emission> 575 nm; fluorescein: excitation at 473 nm, emission 520–540 nm) to give 16-bit tif image files, which we analyzed using ImageJ64 V1.47 (U.S. National Institutes of Health). Cross-sectional lane intensity profiles were computed by averaging over grayscale values within a 20–75 pixel wide box drawn over the lane of interest. After linear background correction, the regions of interest were quantified by integrating the area under the peaks. Yields were estimated by comparing the intensity of bands of interest for treated versus untreated samples.
Negative-staining TEM: Samples were adsorbed on glow-discharged formvar-supported carbon-coated Cu400 TEM grids (Science Services, Munich) and stained using a 2 % aqueous uranyl formate solution containing 25 mm sodium hydroxide. Imaging was performed using a Philips CM100 EM operated at 100 kV. Images were acquired using an AMT 4 Megapixel CCD camera. Micrograph scale bars were calibrated by imaging 2D catalase crystals and using the lattice constants as length reference. Imaging was performed at ×28 500 magnification.
Publication 2014
Profiles of endogenous, polar metabolites and lipids were obtained using LC-MS. The polar metabolite profiling methods were developed using reference standards of each metabolite to determine chromatographic retention times and MS multiple reaction monitoring transitions, declustering potentials and collision energies (See Supplemental Data Tables 1-3 for LC-MS parameters for each method).
Negative ionization mode data were acquired using an ACQUITY UPLC (Waters) coupled to a 5500 QTRAP triple quadrupole mass spectrometer (AB SCIEX) running a modified version of the hydrophilic interaction chromatography (HILIC) method described by Bajad et al. (20 (link)). Plasma samples (30 μL) were extracted using 120 μL of 80% methanol (VWR) containing 0.05 ng/μL inosine-15N4, 0.05 ng/μL thymine-d4, and 0.1 ng/μL glycocholate-d4 as internal standards (Cambridge Isotope Laboratories). The samples were centrifuged (10 min, 9,000 × g, 4°C) and the supernatants (10 μL) were injected directly onto a 150 × 2.0 mm Luna NH2 column (Phenomenex) that was eluted at a flow rate of 400 μL/min with initial conditions of 10% mobile phase A (20 mM ammonium acetate and 20 mM ammonium hydroxide (Sigma-Aldrich) in water (VWR)) and 90% mobile phase B (10 mM ammonium hydroxide in 75:25 v/v acetonitrile/methanol (VWR)) followed by a 10 min linear gradient to 100% mobile phase A. The ion spray voltage was −4.5 kV and the source temperature was 500°C.
Positive ionization mode data were acquired as in Wang et al. with a modification to the MS acquisition in which all multiple reaction monitoring transitions were scheduled in a single method file (3 (link)). Briefly, the LC-MS system consisted of a 4000 QTRAP triple quadrupole mass spectrometer (AB SCIEX) coupled to an 1100 Series pump (Agilent) and an HTS PAL autosampler (Leap Technologies). Plasma samples (10 μL) were extracted using nine volumes of 74.9:24.9:0.2 (v/v/v) acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (0.2 ng/μL valine-d8, Isotec; and 0.2 ng/μL phenylalanine-d8 (Cambridge Isotope Laboratories)). The samples were centrifuged (10 min, 9,000 × g, 4°C) and the supernatants (10 μL) were injected onto a 150 × 2.1 mm Atlantis HILIC column (Waters). The column was eluted isocratically at a flow rate of 250 μL/min with 5% mobile phase A (10 mM ammonium formate and 0.1% formic acid in water) for 1 minute followed by a linear gradient to 40% mobile phase B (acetonitrile with 0.1% formic acid) over 10 minutes. The ion spray voltage was 4.5 kV and the source temperature was 450°C.
Lipids were profiled as described in Rhee et al. (21 (link)). Briefly, plasma samples (10 μL) were extracted for lipid analyses with 190 μL of isopropanol containing 0.25 ng/μL 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids). After centrifugation, supernatants (10 μL) were injected directly onto a 150 × 3.0 mm Prosphere HP C4 column (Grace). The column was eluted isocratically with 80% mobile phase A (95:5:0.1 vol/vol/vol 10mM ammonium acetate/methanol/acetic acid) for 2 minutes followed by a linear gradient to 80% mobile-phase B (99.9:0.1 vol/vol methanol/acetic acid) over 1 minute, a linear gradient to 100% mobile phase B over 12 minutes, then 10 minutes at 100% mobile-phase B. MS analyses were carried out using electrospray ionization and Q1 scans in the positive ion mode. Ion spray voltage was 5.0 kV and source temperature was 400°C.
Prior to each set of analyses, LC-MS system sensitivity and chromatography quality were checked by analyzing reference samples: synthetic mixtures of reference metabolites (Sigma) and a lipid extract prepared from a pooled human plasma stock (Bioreclamation). During the application of each method, internal standard peak areas were monitored for quality control. Moreover, reference pooled plasma samples (which were not blinded to the laboratory, unlike the QC pooled plasma samples in the blinded duplicates pilot) were included in each set of analyses, with samples inserted at the beginning and after sets of approximately twenty study samples. The reproducibility of each metabolite in the pooled plasma samples was determined to confirm the overall quality of the analyses (See Supplemental Data Tables 4-6). MultiQuant 1.2 software (AB SCIEX) was used for automated peak integration and metabolite peaks were manually reviewed for quality of integration and compared against a known standard to confirm identity. Metabolites with a signal to noise ratio <10 were considered unquantifiable. For these analyses, metabolite signals were retained as measured LC-MS peak areas, which are proportional to metabolite concentration and are appropriate for metabolite clustering and correlative analyses.
Publication 2013
Conventional, gnotobiotic or mice reconstituted with human or murine gut flora were infected with 109 viable CFU of C. jejuni strains ATCC 43431, 81–176, B2 or mutant strains B2ΔfdhD and B2Δcj0952c deficient in the formate dehydrogenase subunit D or the formic acid receptor gene, respectively [37] (link), by gavage in a total volume of 0.3 mL PBS on three consecutive days.
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Publication 2011
Formate Dehydrogenase formic acid Gastrointestinal Microbiome Genes Homo sapiens Mus Protein Subunits Strains Tube Feeding

Most recents protocols related to «Formate»

Liquid ethyl formate (EF, purity: 97%) was purchased from Sigma Aldrich Co. (St. Louis, MO, USA). For efficacy trials, liquid EF was applied on a filter paper (90 mm dia., Whatman, Inc., Buckinghamshire, UK) for vaporization. For the scaled up (1.0 m3) trials, the liquid EF was vaporized using a prototype EF vaporizer (Safefume Inc., Daegu, Republic of Korea) and EF gas was propelled into the fumigation chamber using nitrogen gas from a cylinder [39 (link)].
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Publication 2024
Formate quantification using gas chromatography-mass spectrometry (GC-MS) was performed as previously described by ref. 34 . Media samples from CML CD34+ cells (40 μL) were added in 20 μl of 50 μM internal standard sodium 13C,2H-formate (m + 2), 10 μl of 1 M sodium hydroxide, 5 μl of benzyl alcohol and 50 μl of pyridine. While vortexing, derivatisation of formate was commenced by the addition of 20 μl of methyl chloroformate. 200 μl of water and 100 μl of methyl tertiary butyl ether were then added, and the samples were vortexed for 20 s and centrifuged at 10,000 g for 5 min. The resulting apolar phase containing the formate derivative (benzyl formate) was transferred to a GC-vial and capped. Formate standards and blank samples (water) were prepared in the same manner and analysed with the experimental samples. Derivatized formate samples were analysed with an Agilent 7890B GC system coupled to a 7000 triple quadrupole MS system34 . MassHunter Quantitative analysis software (Agilent Technologies) was used to extract and process the peak areas for m + 0, m + 1, m + 2 formate. After correction for background signals, quantification was performed by comparing the peak area of formate (m/z of 136) and of m + 1 formate (m/z of 137) against that of m + 2-formate (m/z of 138).
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Publication 2024

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Publication 2024
Tissue sections were washed in 50 mM ammonium formate for 30 seconds to enhance ganglioside signal as previously described[2 (link)]. The wash was applied over slides sitting tissue side up on a flat surface to prevent tissue displacement and the slide was gently tilted to allow runoff at 30 seconds. Slides were then placed in a desiccator for 10 minutes/until all moisture was visibly evaporated off the slide, prior to matrix application.
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Publication Preprint 2024
In 500 mL methanol, choline chloride (1 mol) and sodium cyanide (1 mol) were refluxed for 6 h under air condition. By ion exchange, Choline formate was obtained by evaporating the methanol solution under reduced pressure and filtering the sodium salts (NaCl, extra NaCN). A red-liquid was formed.
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Publication 2024

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Ammonium formate is a chemical compound that is commonly used in various laboratory applications. It is a crystalline solid that is soluble in water and other polar solvents. Ammonium formate serves as a buffer in analytical techniques and is also used as a mobile phase additive in liquid chromatography.
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Formic acid is a colorless, pungent-smelling liquid chemical compound. It is the simplest carboxylic acid, with the chemical formula HCOOH. Formic acid is widely used in various industrial and laboratory applications.
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Acetonitrile is a colorless, volatile, flammable liquid. It is a commonly used solvent in various analytical and chemical applications, including liquid chromatography, gas chromatography, and other laboratory procedures. Acetonitrile is known for its high polarity and ability to dissolve a wide range of organic compounds.
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Methanol is a clear, colorless, and flammable liquid that is widely used in various industrial and laboratory applications. It serves as a solvent, fuel, and chemical intermediate. Methanol has a simple chemical formula of CH3OH and a boiling point of 64.7°C. It is a versatile compound that is widely used in the production of other chemicals, as well as in the fuel industry.
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Formic acid is a clear, colorless liquid chemical compound used in various industrial and laboratory applications. It is the simplest carboxylic acid, with the chemical formula HCOOH. Formic acid has a pungent odor and is highly corrosive. It is commonly used as a preservative, pH adjuster, and analytical reagent in laboratory settings.
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Ammonium formate is a chemical compound commonly used as a mobile phase additive in liquid chromatography-mass spectrometry (LC-MS) applications. It serves as a volatile buffer to improve the ionization and separation of analytes during mass spectrometric analysis.
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Acetonitrile is a highly polar, aprotic organic solvent commonly used in analytical and synthetic chemistry applications. It has a low boiling point and is miscible with water and many organic solvents. Acetonitrile is a versatile solvent that can be utilized in various laboratory procedures, such as HPLC, GC, and extraction processes.
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Methanol is a colorless, volatile, and flammable liquid chemical compound. It is commonly used as a solvent, fuel, and feedstock in various industrial processes.
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Ammonium acetate is a chemical compound with the formula CH3COONH4. It is a colorless, crystalline solid that is soluble in water and alcohol. Ammonium acetate is commonly used in various laboratory applications, such as pH adjustment, buffer preparation, and as a mobile phase component in chromatography.
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The Milli-Q system is a water purification system designed to produce high-quality ultrapure water. It utilizes a multi-stage filtration process to remove impurities, ions, and organic matter from the input water, resulting in water that meets the strict standards required for various laboratory applications.

More about "Formate"

Formate is a crucial one-carbon compound that plays a pivotal role in various biological processes.
It is an anion derived from formic acid (also known as methanoic acid), and can serve as a metabolic intermediate, a cofactor, and a signaling molecule.
Formate is involved in cellular respiration, DNA synthesis, and folate metabolism, among other functions.
Ammonium formate is a salt of formic acid and ammonium, which can be used as a buffer or eluent in liquid chromatography.
Formic acid, on the other hand, is the simplest carboxylic acid and can be used as a solvent, preservative, or in the production of other chemicals like acetonitrile and methanol.
Acetonitrile is a commonly used solvent in high-performance liquid chromatography (HPLC) and other analytical techniques, often in combination with formic acid or ammonium formate as modifiers.
Methanol is another important one-carbon compound that can be used in various applications, including as a fuel, solvent, or in the production of other chemicals.
Ammonium acetate is a salt of acetic acid and ammonium, which can also be used as a buffer or eluent in liquid chromatography, similar to ammonium formate.
Understanding the role of formate in health and disease is an active area of research, with applications in fields like energy production, cancer biology, and neuroscience.
Leveraging AI-driven tools like PubCompare.ai can help researchers optimize their formate-related projects, locating the most reproducible and effective research methods from the literature, preprints, and patents.
Milli-Q systems are used to produce ultrapure water, which is essential for many analytical techniques, including those involving formate and related compounds.
By understanding the key properties and applications of formate and related compounds, researchers can enhance their formate-related projects and develop more effective and reproducible methods, ultimately advancing our knowledge and understanding of this important one-carbon compound.