LC/MS/MS Method Package for Primary Metabolites Ver. 2

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.


Area ratio comparison between two tissues focused on methylation cycle

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

 
 
 

Supporting LCMS-8040/8045/8050/8060

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

Volcano Plot
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.

VANTED
Tool maintained at University of Konstanz, Germany, for visualization and analysis of networks across different data sets. (GARUDA support was developed at Monash University)

iPath
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.

Cytoscape
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
Glycolytic system Nucleotides
2,3-Bisphosphoglyceric acid
3-Phosphoglyceric acid
(2-Phosphoglyceric acid)
Dihydroxyacetone phosphate
Fructose 1,6-bisphosphate
Glucose 1-phosphate
Glucose 6-phosphate
Glycerol 3-phosphate
Phosphoenolpyruvic acid
Pyruvic acid
Adenosine 3',5'-cyclic monophosphate
Adenosine diphosphate
Adenosine monophosphate
Adenosine triphosphate
Cytidine diphosphate
Cytidine monophosphate
Cytidine triphosphate
Guanosine 3',5'-cyclic monophosphate
Guanosine diphosphate
Guanosine monophosphate
Guanosine triphosphate
Thymidine diphosphate
Thymidine monophosphate
Thymidine triphosphate
Uridine diphosphate
Uridine monophosphate
Uridine triphosphate
Co-enzyme Pentose-phosphate pathway
NAD
NADH
NADP
NADPH
6-Phosphogluconic acid
Erythrose 4-phosphate
Ribose 5-phosphate
Ribulose 5-phosphate
Sedoheptulose 7-phosphate
TCA cycle Internal STDs
Acetyl coenzyme A
Succinyl coenzyme A
2-Morpholinoethanesulfonic acid
Methionine sulfone
Amino acids  
Alanine
Arginine
Asparagine
Aspartic acid
Cysteine
Glutamic acid
Glutamine
Glycine
Histidine
Lysine
Methionine
Phenylalanine
Serine
Threonine
Tryptophan
Tyrosine
List of compounds for PFPP column method
Glycolytic system Organic acids
Lactic acid
Pyruvic acid
4-Aminobutyric acid
Adenylsuccinic acid
Argininosuccinic acid
Cholic acid
Creatine
Nicotinic acid
Ophthalmic acid
Orotic acid
Pantothenic acid
Taurocholic acid
Uric acid
TCA cycle
2-Ketoglutaric acid
Aconitic acid
Citric acid
Fumaric acid
Isocitric acid
Malic acid
Succinic acid
Amino acids Nucleosides and Nucleotides
4-Hydroxyproline
Alanine
Arginine
Asparagine
Aspartic acid
Asymmetric dimethylarginine
Citrulline
Cystine
Dimethylglycine
Glutamic acid
Glutamine
Glycine
Histidine
Homocystine
Isoleucine
Leucine
Lysine
Methionine sulfoxide
Ornitine
Phenylalanine
Proline
Serine
Symmetric dimethylarginine
Threonine
Tryptophan
Tyrosine
Valine
Adenine
Cytosine
Guanine
Thymine
Uracil
Xanthine
Adenosine
Cytidine
Guanosine
Inosine
Thymidine
Uridine
Adenosine 3',5'-cyclic monophosphate
Adenosine monophosphate
Cytidine 3',5'-cyclic monophosphate
Cytidine monophosphate
Guanosine 3',5'-cyclic monophosphate
Guanosine monophosphate
Thymidine monophosphate
Co-enzymes
FAD
FMN
NAD
Methylation and Transsulfuration cycle Others
Cystathionine
Cysteine
Homocysteine
Methionine
2-Aminobutyric acid
Acetylcarnitine
Acetylcholine
Allantoin
Carnitine
Carnosine
Choline
Citicoline
Creatinine
Cysteamine
Dopa
Dopamine
Epinephrine
Histamine
Hypoxanthine
Kynurenine
Niacinamide
Norepinephrine
Serotonin
5-Glutamylcysteine
Glutathione
Oxidized glutathione
S-Adenosylhomocysteine
S-Adenosylmethionine
Internal STDs
2-Morpholinoethanesulfonic acid
Methionine sulfone

* 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

  1. LabSolutions LCMS Ver.5.93 or later is required.
  2. Shimadzu makes no warranty regarding the accuracy of information included in the database or the usefulness of information obtained from using the database.
  3. 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.

Application
Simultaneous Analysis of 97 Primary Metabolites By PFPP: Pentafluorophenylpropyl Column
Simultaneous Analysis of Hydrophilic Metabolites Using Triple Quadrupole LC/MS/MS

For Research Use Only. Not for use in diagnostic procedures.

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