What is the MMDB?

The Mulberry Metabolome Database (MMDB) is a comprehensively, freely, and user-friendly available electronic database containing detailed information (structure, MS data, and so on) about all metabolites identified in the mulberry species. It is intended to be used for applications in metabolomics, traditional medicines, biomarker discovery and general education.

Now, the database (version 1.0) contains 124 metabolites and 812 metabolite features of mulberry species.


Workflow of metabolite profiling and related data analysis in mulberry species.


A widely-targeted metabolomics approach based on high-performance liquid chromatography mass spectrometer (HPLC-MS/MS) was carried out in this study. By application of a segmented Full-MS/MS scan strategy, metabolites with mass range from m/z 100 to 1,000 were high-sensitivity detected in 18 LC/MS/MS runs. About 4900 chromatographic peaks with signal/noise (s/n) >10 were manually checked out (data not shown). To produce a matrix containing fewer biased and redundant data, redundancies that caused by isotopes, in-source fragmentation, K+, Na+, and NH4+ adduct, and dimerization was removed by using an in-house-developed software written in Perl. In addition, we believed that transitions derived from the same metabolites would have high-correlation among different samples. Thus, a pre-experiment contains 50 mulberry varieties were then carried out to figure out the potential redundancy. More than 650 metabolites with high-correlation coefficients (over 0.8) and the same retention time (± 0.1min) were considered as redundancy. Finally, a MS2 spectral tag (MS2T) library contains 936 distinct metabolite features (almost non-redundant) were obtained and reported as recommended previously. The data matrix was then used for metabolite identification/annotation and semi-quantification.

Metabolite identification/annotation was based on the accurate m/z, the retention time (RT) and the fragmentation patterns delivered by a Q Exactive LC-MS/MS system. In this study, 35 commercially available standards were purchased and identified using the same profiling conditions as the extracts, including amino acids, flavonoids, alkaloids, and vitamins. Eighty-eight metabolite features were putatively identified by query the MS/MS spectral data taken from the literature or to search the databases (MassBank, KNApSAcK, HMDB, and METLIN). It is noteworthy that 35.5% (44/123) of these metabolites features were classified as flavonoids, which was identified based on the fragmentation pattern (delivered by MS/MS spectra). For instance, m1903 (RT 7.35min, m/z 595.1652, error -0.84 ppm) and m1963 (RT 6.81min, m/z 611.1590, error -2.78 ppm) were identified as kaempferol O-rhamnosyl-O-hexoside (m/z 287.0539, 153.0179, and 121.0282 are the diagnostic fragment ions of Kaempferol, the natural loss of hexoside (162 Da, 449.1071 → 287.0539) and rhamnoside (146 Da, 595.1650 → 449.1071) are revealed in the mass spectrum) and quercetin O-rhamnosyl-O-hexoside (m/z 303.0494, 257.0434, 229.0491, and 153.0180 are the diagnostic fragment ions of Quercetin). Based on this strategy, the data matrix with 124 annotated metabolites has been constructed and used for the following studies.


Mulberry Metabolomics Reporting Checklist


AspectInformationFill in
Type of metabolome analysistargeted metabolite analysisFALSE
 non-targeted metabolite class scale profilingFALSE
 non-targeted metabolome scale profilingTRUE
 non-targeted finger printing of mass featuresFALSE
Type of quantificationabsolute or quantificationQuantification
Type of reference sampleschemcially definedFALSE
 biologically definedMore than 50 divergent samples were mixed as the reference sample
Type of replicationanalytical (same analytical sample preparation)1
 technological (same biological preparation)0
 biological (same experimental condition)2
 full experiment2
Type of technologyreference publicationPlant Cell reference style
Sample preparationmethod of sample preparationChemically non-modified|derivatized (70% methanol)
 method of chromatography/separation 
 method of ionizationESI
 method of detectionspecify detection type (MS) and instrumentation (Thermo Scientific™ Q Exactive™ hybrid quadrupole-Orbitrap mass spectrometer)
Metabolitemetabolite namem****
 metabolite sum formulaThe formula were calculated by Qualitative Analysis B.04.00
 metabolite structure and public source of metabolite identifierMassbank_database、METLIN-Scripps Center for Metabolomics and Spectrometry and Human Metabolome Database
Identificationidentification processmanually supervized
 by authentic mass isotopomer added to one or all biological sample(s)FALSE
 by authentic reference compound within a co-processed reference mixtureTRUE
 by authentic reference compound previously mapped to the analytical systemTRUE
 reference libraryMassbank_database、METLIN-Scripps Center for Metabolomics and Spectrometry and Human Metabolome Database
 type of mass spectrum Thermo Scientific™ Q Exactive™ hybrid quadrupole-Orbitrap mass spectrometer
 by match of molecular mass (single mass fragment)The molecular mass were correct to 0.0001
 by match of fragmentsMatch the main fragments
 by match of fragmentation patternSpecify set of mass fragment
 by match of mass spectrum to reference libraryMatch the molecular mass and the main fragments
 type of retention indexFALSE
 by match of retention time (index) to reference libraryFALSE
Quantificationtype of quantificationRelative quantification
Validity testingRecovery testing (chemical analog)FALSE
 Recovery testing (internally added mass isotopomer)FALSE
 Recovery testing (mixture of most divergent samples from the experiment)FALSE
 Test for linear range FALSE
 Limit of quantification (LOQ)FALSE
 Limit of detection (LOD)FALSE

Mulberry Varieties Reporting Checklist


IDName
ml001M. alba var. Taiwansijiguosang
ml002M. alba var. Taiwanlongguosang
ml003M. alba var. Taiwandaguosang
ml004M. alba var. Baiyuwang
ml005M. alba var. 8632
ml006M. alba var. Wittiorum
ml007M. alba var. Jinqiang No.82
ml008M. alba var. Jinqiang No.63
ml009M. alba var. Gui 23
ml010M. alba var. Emeihuasang
ml011M. alba var. Ichibei 34
ml012M. alba var. Langzhongdayesang
ml013M. alba var. 603133
ml014M. alba var. Yusang
ml015M. alba var. Banqiao No.6
ml016M. alba var. 607138
ml017M. alba var. Huai 30-2
ml018M. alba var. Lesangdahongpi 30
ml019M. alba var. Tuosang 25
ml020M. alba var. Heyebai 36
ml021M. alba var. Jiadingsang 29
ml022M. alba var. Yidashoumusang 31
ml023M. alba var. Wupisang
ml024M. alba var. Jimengsang
ml025M. alba var. Shidian No.6
ml026M. alba var. Dejiang No.13
ml027M. alba var. Gui 14
ml028M. alba var. Huosang
ml029M. alba var. Baojing No.7
ml030M. alba var. Pisang No.2
ml031M. alba var. Mangshi No.10
ml032M. alba var. Tortuosa
ml033M. alba var. Shanxitiansang
ml034M. alba var. Shenglidaye
ml035M. alba var. Xinjiansang No.4
ml036M. alba var. Lizhuang 5
ml037M. alba var. Changyajingsang 17
ml038M. alba var. Dayezaoshengsang
ml039M. alba var. Nongsang 14
ml040M. alba var. Xiang No.0
ml041M. alba var. Yun 3
ml042M. alba var. Shin-Ichinose
ml043M. alba var. Huanglusang 13
ml044M. alba var. Pendula 1
ml045M. alba var. Tongxiangqing 3
ml047M. alba var. Shansang 305
ml050M. alba var. Laevigata
ml051M. alba var. Hanguodabaizhengzhu
ml052M. alba var. Hongguo No.2
ml053M. alba var. Kanwa
ml054M. alba var. Yun No.3
ml055M. alba var. Shin-ichibei
ml056M. alba var. Shiping
ml057M. alba var. 6071
ml058M. alba var. Ribengailiangshizi
ml060M. alba var. Gongnongjingsang
ml061M. alba var. 6031
ml062M. alba var. Cathayana
ml063M. alba var. Shengnan
ml064M. alba var. Ichibei
ml065M. alba var. Shimiansang
ml066M. alba var. Yidashoumusang
ml067M. alba var. Zhuangelou
ml068M. alba var. Kuisang
ml069M. alba var. Nongsang No.8
ml070M. alba var. Gailiangshufan
ml071M. alba var. Shanxitiansang
ml072M. alba var. Baokan 61
ml073M. nigra
ml076M. alba var. Hongguo No.1
ml079M. alba var. Jianpuzhai
ml088M. alba var. pendula
ml089M. alba var. Agentingsang
ml091M. alba var. Yunguo No.1
ml092M. alba var. Yun 1
ml093M. alba var. Yun 2
ml094M. alba var. Yun 3
ml095M. alba var. Yun 4
ml096M. alba var. Yun 5
ml097M. alba var. Yun 6
ml098M. alba var. Yun 7
ml100M. alba var. Yun 9
ml103M. alba var. Yun 12
ml104M. alba var. Yun 13
ml105M. alba var. Yun 14
ml110M. alba var. Yun 19
ml111M. alba var. Zhenzhubai
ml112M. alba var. Mongolica
ml114M. alba var. Shuangtouheyebai
ml115M. alba var. Zu 83122
ml116M. alba var. Meiguosang
chuanM. notabilis