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LC-MS raw dataset of Dendrobium extracts

Cite this dataset

Song, Cheng (2022). LC-MS raw dataset of Dendrobium extracts [Dataset]. Dryad.


Orbitrap mass spectrometry is one kind of high-resolution mass analyzer containing multistage fragment monitoring, a selective fragmentation mode, and a personalized data acquisition method, which is widely applied in pharmacokinetic analysis, the food industry, environmental monitoring, and proteomics. Alkaloids are an important active ingredient in Dendrobium officinale, but there are few studies on their isolation and identification. Here, a combination method for separating and detecting alkaloids and their precursors was established. The accurate mass of the components separated by HPLC were determined using an high resolution mass analyzer. The multistage fragmentation pathway of alkaloids was speculated based on a database-dependent retrieval method.

By using a SPE-HPLC-MS/MS method, the potential compounds were tentatively identified by aligning the accurate molecular weight with the METLIN and Dictionary of Natural Products databases. The chemical structures and main characteristic fragments of the potential compounds were further confirmed by retrieving the multistage mass spectra from the MassBank and METLIN databases.The Mass Frontier software was used to speculate the fragmentation pathway of the identified compounds. Seven alkaloids were separated and identified from D. officinale, which were mainly classified into five types (tropane alkaloids, tetrahydroisoquinoline alkaloids, quinolizidine alkaloids, piperidine alkaloids and spermidine alkaloids). Besides the alkaloids, forty-nine chemical substances, including guanidines, nucleotides, dipeptides, sphingolipids and nitrogen-containing glucosides, were concurrently identified. 


The LTQ-Orbitrap XL mass spectrometer were used to conduct the experiment to obtain the MS raw files. Briefly, the samples were extracted and separated by HPLC before the injection of  mass spectrometer. A three-way splitter was connected with the mass analyzer at a 0.3 mL min-1 flow rate.The detailed parameters were as follows: sheath gas at 25 arb, auxiliary gas at 3 arb, spray voltage at 4 kV, the capillary temperature at 320 °C, tube lens at 120 V, and capillary voltage at 30 V. The MS data were collected at 100 ≤ m/z ≤ 1000 in positive-ion mode. Two data acquisition methods were used in the experiments. In one method, a high-resolution scan was conducted using the Orbitrap mass analyzer to acquire the MS data at a resolution at 30,000 FWHM and the MS2 data at 15,000 FWHM. The other method is that a high-resolution scan was conducted first to acquire the MS data at a resolution at 30,000 FWHM, then the LTQ dynode was used to scan the MS2 and MS3 spectra. The collision-induced dissociation (CID) energy was set at 35%. The minimum signal threshold was 500, and the isolation width of precursor ions was 2 m/z. 

Usage notes

The Xcalibur (v.2.1) and Mass Frontier (v. 6.0) from Thermo Fisher Scientific were used for the analysis of mass spectrometry. Since Xcalibur and Mass Frontier are commercial software that was licensed alongside the hardware, If the user does not have permission to install, they can convert the raw files using the software package ProteoWizard ( The MSConvert plug-in of ProteoWizard can convert raw formats to mzML, mzXML, and TXT formats, which can be directly opened and viewed in detail.


West Anhui University