DOI: 10.5061/dryad.v6wwpzgzq
title: LC-MS raw dataset of Dendrobium extracts

description: 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. 
description: 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<sup>-1</sup> 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 ≤ <em>m</em>/<em>z</em> ≤ 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 MS<sup>2</sup> 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 MS<sup>2</sup> and MS<sup>3</sup> 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 <em>m</em>/<em>z.</em> 
description: 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
 (http://proteowizard.sourceforge.net/). 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.