Technical Report: "Total Solution for Metabolomic Analysis of Endogenous Metabolites Using Exact Mass Database"
LC/MS/MS Method Package for Primary Metabolites
For LabSolutions™ LCMS Software
Ready-to-Use Analytical Conditions
Shimadzu Method Packages deliver conditions for efficient and simultaneous multi-component analysis. They enable the user to quickly and easily implement complex methods without costly and laborious method development by providing sample preparation protocols, LC separation conditions, and MS acquisition parameters.
Two Selectable Analysis Methods
Customers can select an appropriate analysis method from the two methods; analysis using an ion pairing reagent (55 components) and analysis using a PFPP column (97 components) according to the instrument conditions or metabolites to be analyzed.
Overlaid MRM chromatograms for 55 standards mixture by ion pair method
LC/MS/MS Method Package for Primary Metabolites Ver. 2 supports LCMS-8040/8045/8050/8060, enables high-sensitivity simultaneous multi-component analyses of primary metabolites.
Complete from Sample Preparation to Analysis
Protocols are included for the preparation of extracts from biological tissue. Saving the user time and money, even laboratories unfamiliar with extraction can follow prescribed steps for LC/MS/MS sample preparation.
Normalization of Multiple Sample Results
Due to mass differences between biological tissue samples, normalization of results must be performed when multiple samples are analyzed. This method package includes optimized analytical conditions for two internal standards to permit normalization across multiple samples.
Improved Data Analysis Functionality in Method Package
A wide variety of new data analysis functions have been added to the LC/MS/MS Method Package for Primary Metabolites. Functions such as automatically pasting data on metabolic maps, using a bar graph to compare changes in compound quantities, or graphing the changes as a function of time, for example, can be performed using simple operations. It also enables correlation analysis, volcano plots, displaying data on metabolic maps for target compounds, and other functionality. Consequently, it can significantly reduce the amount of work required for bottleneck processes such as data analysis and visualization, so that all operations from measurement to data analysis can be performed smoothly.
In this method package, we provide the data analysis software developed based on tools (gadgets) that have been released on the GARUDA™ open research platform, which is mainly managed by The Systems Biology Institute, Japan (SBI).
Data Analysis Tools Used in Method Package
A tool that combines a t-test (statistically significant difference) and a fold analysis (Example: Difference in mean value such as 2 times or 1/2) to visualize the differences between the 2 groups. The Volcano Plot gadget developed by Shimadzu is included in the package.
Tool maintained at University of Konstanz, Germany, for visualization and analysis of networks across different data sets. (GARUDA support was developed at Monash University)
Data analysis tool developed by the European Molecular Biology Laboratory that can be used for visualization of diverse metabolic pathways or data mapping and customization.
Bioinformatics tool developed by the Cytoscape Consortium, used to visualize metabolic pathways, to integrate gene expression profiles with related data, and so on. It is especially useful for analyzing networks and visualizing correlations.
Index of compounds
|List of compounds for ion pair method|
|Adenosine 3',5'-cyclic monophosphate
Guanosine 3',5'-cyclic monophosphate
|TCA cycle||Internal STDs|
|Acetyl coenzyme A
Succinyl coenzyme A
|List of compounds for PFPP column method|
|Glycolytic system||Organic acids|
|Amino acids||Nucleosides and Nucleotides|
Adenosine 3',5'-cyclic monophosphate
Cytidine 3',5'-cyclic monophosphate
Guanosine 3',5'-cyclic monophosphate
|Methylation and Transsulfuration cycle||Others|
* In this method package, customer can select an appropriate analysis method from the two methods using ion pairing reagent (57 components) and PFPP column (97 components) according to the instrument conditions or metabolites to be analyzed.
* The analysis method using ion-pairing reagents is recommended for fluctuation analysis of primary metabolites related to major metabolic pathways such as glycolysis, the pentose phosphate cycle, diphosphate and triphosphate nucleotides. While, the analysis method using PFPP columns is recommended for analysis of amino acids, organic acids (including the TCA circuit), the Methylation cycle and the Urea cycle.
Remarks and Precautions
- LabSolutions LCMS Ver.5.93 or later is required.
- Shimadzu makes no warranty regarding the accuracy of information included in the database or the usefulness of information obtained from using the database.
- It is the user's responsibility to adopt appropriate quality control tests using standard samples to confirm qualitative and quantitative information obtained with this method package.
LabSolutions and LCMS are trademarks of Shimadzu Corporation.
GARUDA is a trademark of The Systems Biology Institute.
News / Events
Shimadzu has released the LC/MS/MS Method Package for Short Chain Fatty Acids
Shimadzu has released the LC/MS/MS Method Package for Lipid Mediators Ver. 3
Shimadzu has released the LC/MS/MS Method Package for Veterinary Drugs Ver. 2
Shimadzu has released the LC/MS/MS Method Package for Bile Acids Ver. 2.
User interviews December 2020
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