This work was funded by the Xinglin Talent Program of Chengdu University of TCM (No. 030058191), the Nature Science Foundation of Sichuan (2022NSFSC1470), and the National Natural Science Foundation of China (82204765).

1. Sample preparation
<ol>
	<li>Accurately weigh 1 g of the AMS sample, and place it in a conical flask with 30 mL of 80% methanol. Transfer the mixture to an ultrasound bath sonicator for 30 min of extraction at 25 &#176;C. Centrifuge the sample at 14,000 x g for 5 min. 
	NOTE: The frequency of the ultrasound bath sonicator is 40 KHz.</li>
	<li>Prepare an injection syringe and a microporous membrane filter (0.22 &#956;m, organic only). Filter the supernatant into a 2 mL sample bottle.</l...

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B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tutorial:+Ion+activation+in+tandem+mass+spectrometry+using+ultra-high+resolution+instrumentation.">Tutorial: Ion activation in tandem mass spectrometry using ultra-high resolution instrumentation.</a> Mass Spectrometry Reviews. 39 (5-6), 680-702 (2020).</li><li>Wu, S. -. 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IT-MS and its MSn technology offer a new approach to identifying the structure of trace TCM compounds. Unlike Q-TOF-MS, which could not deeply identify the fragment ions, IT-MS with MSn technology excels due to its ability to isolate and accumulate ions. This article outlines a method for identifying trace compounds in Tibetan medicine using the IT-MS and MSn technique. The method utilizes the n value in MSn to determine the amount of fragment ion information provided. The cruc...

The qualitative analysis of trace components in traditional Chinese medicine (TCM) has become a crucial topic in research. Due to the high numbers of compounds in TCM, it is difficult to isolate them for nuclear magnetic resonance spectrometer (NMR) or X-ray diffractometer (XRD) analysis, making mass spectrometry (MS)-based methods that only require low sample volumes increasingly popular. Additionally, liquid chromatography (LC) coupled with MS has been widely used in TCM research in recent years for the improved separation of complex samples and qualitative analysis of chemical compounds1. One common method is liquid chromatography-electrospray ionization time-of-flight mass spectrometry (LC-ESI-TOF-MS), which is widely used in qualitative research on Tibetan medicine2. With this method, complex components are enriched and separated in an LC column, and the mass-to-charge ratio (m/z) of the adduct ions is observed using an MS detector. Searching tandem MS (MS/MS or MS2) databases is currently the fastest approach for confident compound annotations in small molecule analysis using quadrupole time-of-flight (Q-TOF) MS and Orbitrap MS3. However, the poor quality of databases and the presence of various isomers hinder the identification of unknown compounds. In addition, the information provided by the MS/MS database is limited4,5,6,7. It is significant to investigate the chemical compounds in each TCM using a general protocol that can be widely applied to other TCM.
IT-MS captures a wide range of ions by applying different radio frequency (RF) voltages to the ring electrodes8. IT-MS can perform time-series multiple-stage MS scans in diverse chronological orders, providing ingredient multiple-stage MS (MSn) fragmentation, where n is the number of product ion stages9. Linear IT-MS is considered the best for structure identification as it can be used for sequential MSn experiments10. Targeted ions can be isolated and accumulated in linear IT-MS1. The MSn (n &#8805; 3) in IT-MS provides more fragment information than MS/MS in Q-TOF-MS. Since IT-MS cannot lock the target ion and its fragment ions, it is a powerful tool for the structure elucidation of unknown compounds, including isomers1. MSn technology has been widely applied to the structural analysis of unknown proteins, peptides, and polysaccharides11,12. The abundance level of fragment ions in MSn provides more molecular fragment information on targeted compounds in complex samples than MS/MS in Q-TOF-MS. Hence, applying MSn technology to structural identification in TCM is essential.
Tibetan medicine is a significant component of TCM13, and these medicines are primarily derived from animals, plants, and minerals found in the plateau area14. The Tibetan medicine Abelmoschus manihot seeds (AMS) is the seed of Abelmoschus manihot (linn.) medicus. AMS is a traditional herbal medicine used to treat conditions such as atopic dermatitis, rheumatism, and leprosy. It contains chalcone, which possesses antibacterial, antifungal, anticancer, antioxidative, and anti-inflammatory effects15. In the present study, MSn procedures were improved, and a detailed method was developed to identify compound structures in the Tibetan medicine AMS using IT-MS and MSn. Certain MS parameters, including the ion mode, scanning range, and collision mode, were optimized to overcome problems in identifying trace compounds. This study aims to promote the standardized structure identification of trace compounds in TCM.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Acetonitrile</td>
			<td>Thermo Scientific</td>
			<td>CAS 75-05-8</td>
			<td>LC-MS grade</td>
		</tr>
		<tr>
			<td>Formic Acid</td>
			<td>Knowles</td>
			<td>CAS 64-18-6</td>
			<td>HPLC grade</td>
		</tr>
		<tr>
			<td>Linear ion trap mass spectrometer</td>
			<td>Thermo Scientific</td>
			<td>LTQ XL</td>
			<td></td>
		</tr>
		<tr>
			<td>liquid chromatograph</td>
			<td>Thermo Scientific</td>
			<td>U3000</td>
			<td></td>
		</tr>
		<tr>
			<td>LTQ Tune</td>
			<td>Thermo Scientific</td>
			<td>version 2.8.0</td>
			<td>MS control software</td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Thermo Scientific</td>
			<td>CAS 67-56-1</td>
			<td>LC-MS grade</td>
		</tr>
		<tr>
			<td>Pure water</td>
			<td>Thermo Scientific</td>
			<td>CAS 7732-18-5</td>
			<td>LC-MS grade</td>
		</tr>
		<tr>
			<td>Xcalibur</td>
			<td>Thermo Scientific</td>
			<td>version 2.0</td>
			<td>LC-IT-MS operational software</td>
		</tr>
	</tbody>
</table>

standardized identification of compound structure in tibetan medicine using ion trap mass spectrometry and multiple-stage fragmentation analysis

Tibetan medicines are complex and contain numerous unknown compounds, making in-depth research on their molecular structures crucial. Liquid chromatography-electrospray ionization time-of-flight mass spectrometry (LC-ESI-TOF-MS) is commonly used to extract Tibetan medicine; however, many unpredictable unknown compounds remain after using the spectrum database. The present article developed a universal method for identifying components in Tibetan medicine using ion trap mass spectrometry (IT-MS). The method includes standardized and programmed protocols for sample preparation, MS setting, LC prerun, method establishment, MS acquisition, multiple-stage MS operation, and manual data analysis. Two representative compounds in the Tibetan medicine Abelmoschus manihot seeds were identified using multiple-stage fragmentation, with a detailed analysis of typical compound structures. In addition, the article discusses aspects such as ion mode selection, mobile phase adjustment, scanning range optimization, collision energy control, collision mode switchover, fragmentation factors, and limitations of the method. The developed standardized analysis method is universal and can be applied to unknown compounds in Tibetan medicine.

Cellobiose was used as a model to verify the feasibility of MSn in positive ion mode. As shown in Figure 2A, the ESI-MS (positive ion mode) of cellobiose [C12H22O11]+ produced the protonated molecule [M+H]+ at m/z 365. The product ion scan (CID-MS/MS) of [M+H]+ at m/z 365 resulted in the second fragment ion at m/z 305 (Figure 2B), which was further analyzed using MS3 and MS<s...

Watch this Scientific Journal Video about Standardized Identification of Compound Structure in Tibetan Medicine Using Ion Trap Mass Spectrometry and Multiple-Stage Fragmentation Analysis at JoVE.com

Standardized Identification of Compound Structure in Tibetan Medicine Using Ion Trap Mass Spectrometry and Multiple-Stage Fragmentation Analysis

Here, we describe a general protocol and design that could be applied to identify trace amounts and minor constituents in the complex natural product formulations (matrixes) in Tibetan medicine.

Tibetan medicines are complex and contain numerous unknown compounds, making in-depth research on their molecular structures crucial. Liquid ...

This method can help researchers analyze the structures of Tibetan medicine compounds, especially the tree's components. It can provide insight into the qualitative study of compound's content in natural medicine. The main advantage of this technique is that the accuracy of the compound structure obtained in this case is higher than that of the database.This technique can be used in the structure analysis of metabolic intermediates in bladder or urine. To begin, the Tibetan medicine Abelmoschus manihot's seeds sample preparation. Accurately weigh one gram of AMS and place it in a conical flask containing 30 milliliters of 80%methanol.Using an ultrasound bath sonicator at 40 kilohertz, perform extraction on the mixture for 30 minutes at 25 degrees Celsius. Then, centrifuge the sample at 14, 000g for five minutes. Prepare an injection syringe and an organic 0.22 micron microporous membrane filter, and filter the supernatant into a two-milliliter sample bottle.After turning on the switch of the vacuum pump, open the main valve of the argon cylinder along with the partial pressure valve and adjust the pressure to approximately 0.3 megapascals. Then, open the nitrogen valve. Launch the mass spectrometry, or MS, control software.Click on Heated ESI Source in the software panel and set the MS parameters, including heater temperature, gas flow rates, spray voltage for positive and negative modes, and capillary temperature. Click on the Apply button to activate the ion source for liquid chromatography or LC.Prepare mobile phases A and B using 0.1%formic acid in an aqueous solution in pure acetonitrile respectively. Degas them in an ultrasound bath sonicator at 40 kilohertz for at least 15 minutes before connecting the solutions to the A and B fluid passages respectively.Prepare a 1:9 volume by volume methanol water solution, then manually fill it into the clean-out fluid bottles of the pump and injector. After launching the LC-MS control software, click Direct Control to open the LC control panel. Open the purge valve in the counterclockwise direction on the pump module.Click on More Option to open the pump setting and set the purge parameters at five milliliters per minute for three minutes. Click on Purge to start the bubble removal. Once done, close the purge valve.Then, click on Prime Syringe to rinse the syringe for three cycles, Wash Buffer Loop to rinse the loop for one cycle, and Wash Needle Externally to wash the needle for one cycle. Place the sample bottle in the sampler. Click on Instrument Setup to open the Method Editing Window and click on New to create a new LC-MS instrument method.Establish a total runtime for the method and set the pressure limit. Total flow rate, flow gradient, sample temperature, column temperature, and ready temperature delta in the Method Editing Window. For the MS method, select the General MS or MSn experiment type.Enter values of the acquisition time, polarity, mass range, divert value number, and duration. Click on Save to configure the settings as an instrument method. Click on Sequence Setup to open the sequence table, wherein enter the information about sample type, file, name, path, sample ID, instrument method, position, and injection volume.Record the sequence table by clicking Save, then implement the settings and initiate the MS acquisition. To load the MS data into the data processing software, double-click on the raw file in Explorer. In the base peak chromatogram BPI, select the maximum area under the curve or AUC by clicking and dragging the mouse.The corresponding MS spectrum will be displayed in the same window. Select a targeted ion for the next MS/MS analysis. Reopen the Method Editing Window, and in the MSn setting table, set the m/z of the targeted ion to one decimal place in the Parent Mass column.Next, select collision mode and enter the collision energy, or CE value. Set the MS/MS scan range. Click on Save to record the MS method and enter a new file name in the sequence table.Click on the Start button to initiate the MS/MS acquisition. Once the acquisition is complete, double-click on the raw file in Explorer to load the MS/MS raw file into the data processing software. Identify the strongest fragment ion in the spectrum and enter its m/z value in the MSn method list.In the MSn setting table, set the MS3 parameters, including collision mode, CE value, and scan range. Again, click Save to record the MS method and enter a new file name in the sequence table. Click Start to initiate the MS3 acquisition.As demonstrated before, double-click on the raw file in the Explorer to load the MS3 raw file into the data processing software, and repeat the steps to obtain the MS4 spectrum. To analyze the data, double-click on the raw files to open all the mass spectra from MS to MSn. Manually calculate the m/z difference values between the ion and the corresponding fragment ions.Then, manually draw the core structure according to the MS4 results and derive the original structure using functional groups or molecular segments based on the m/z difference value. Manually draw the molecular cleavage paths according to each molecular structure in MSn. The ESI-MS of model carbohydrate cellobiose produced the proteinated molecule M H at m/z 365 in positive mode.The product ion scan, or CID MS/MS resulted in a second fragment ion at m/z 305. Further, MS3 and MS4 analysis sequentially resulted in the third and fourth fragment ions at m/z 254 and m/z 185, respectively. The MS/MS analysis revealed the sequence of ion fragmentations, namely ring opening hydrolysis, CC cleavage, and dehydration.So, this method was found suitable for carbohydrates. The preliminary qualitative analysis of AMS using LC Q-TOF MS revealed the presence of numerous unknown compounds. The negative MSn analysis of the M H ion at m/z 617 produced a second fragment ion at m/z 571.The MS3 analysis of this fragment ion produced a third fragment ion at m/z 525 by the loss of hydroxyethyl as methanol corresponding to 32 dalton and hydroxyl as water, which is 18 dalton. The MS4 analysis produced fourth fragment ions at m/z 344 and 273. Manual identification of the core structure revealed the molecular structure of the compound at m/z 617 and its cleavage paths in MSn.The product ion scan of the M H ion of another unknown compound was performed, and its molecular structure and cleavage mechanism were also revealed. After the vacuum pump is turned on, wait for at least five hours to ensure sufficient vacuum degree for the experimental conditions. Statistic analysis can be used to collate the fragments having the same or similar mass-to-charge ratio.With mass spectrometry solution increasing, this technique could help researchers obtain newer compounds in natural medicines.

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747 visualizações.  Chengdu University of Traditional Chinese Medicine. Este método pode ajudar os pesquisadores a analisar as estruturas dos compostos da medicina tibetana, especialmente os componentes da árvore. Ele pode fornecer informações sobre o estudo qualitativo do conteúdo do composto na medicina natural. A principal vantagem desta técnica é que a precisão da estrutura composta obtida neste caso é superior à do banco de dados.Esta técnica pode ser utilizada na análise da estrutura de intermediários metabólicos na bexiga ou urina. Par...

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