LC/MS/MS Method Package for Cell Culture Profiling Ver. 2

For LabSolutions™ LCMS Software

Simultaneous Analysis Conditions for 125 Compounds

This Method Package enables the analysis of 125 compounds in under 20 minutes per sample. Performing analysis separately for each compound group such as amino acids and vitamins makes profiling of cell culture components very laborious, but with this method package a large number of culture medium components and secreted metabolites can be analyzed simultaneously.

Compared to the previous version, several metabolites derived from amino acids, nucleic acids and the TCA cycle have been added, allowing even more comprehensive profiling information to be gathered.



 

Optimized Method for Culture Medium Analysis

Pre-set analysis conditions make full use of triple quadrupole MS capabilities for analyzing trace components such as vitamins. On the other hand, analysis conditions are adjusted so that high-concentration components such as glucose or amino acids are not saturated. It is possible to measure a variety of culture medium components from the same vial.

Note: A dilution series must be created for accurate quantification.

 


Analysis of culture supernatant 

 

Ready-to-Use Method

Analysis can be started without the need for time-consuming preparations such as optimization of MS parameters for each compound or careful consideration of LC/MS/MS analysis conditions.


Excellent Data Analysis Functionality

Using the Multiomics Analysis Package, it is easy and straightforward to compare changes in compound quantities on a bar graph, display changes over time on a line chart, etc.

It also includes easy-to-implement functions for correlation analysis, volcano plots, and more, significantly reducing the time required for bottleneck processes such as data analysis and visualization. The whole workflow from measurement to data analysis becomes smoother and more efficient.

 



 

Data obtained with the method package can be inserted on the included metabolic map. It is then simple to compare compound quantities on a bar graph or display changes over time on a line graph.



 

The data analysis software in this Method Package is 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.

List of Registered Compounds

 
Amino acids and their metabolites Group
5-Oxoproline
Alanine
Asparagine
Aspartic acid
Glutamic acid
Glutamine
N-Acetylaspartic acid
4-Aminobutyric acid
4-Hydroxyproline
Arginine
Citrulline
Ornithine
Proline
Putrescine
Argininosuccinic acid
2-Aminobutyric acid
5-Glutamylcysteine
5'-Methylthioadenosine
Cystathionine
Cysteine
Cystine
Glutathione
Homocysteine
Methionine
Methionine sulfoxide
N-Acetylcysteine
Oxidized glutathione
S-Adenosylhomocysteine
Glycine
Serine
Threonine
1-Methylhistidine
3-Methylhistidine
Histidine
Urocanic acid
2-Aminoadipic acid
Hydroxylysine
Lysine
Pipecolic acid
Saccharopine
3-Hydroxyanthranilic acid
5-Hydroxytryptophan
Anthranilic acid
Formylkynurenine
Hydroxykynurenine
Indole-3-acetic acid
Kynurenic acid
Kynurenine
Serotonin
Tryptophan
4-Hydroxyphenyllactic acid
Phenylalanine
Tyrosine
3-Hydroxyisobutyric acid
3-Methyl-2-oxovaleric acid
Isoleucine
Leucine
Valine
Alanyl-glutamine
Glycyl-glutamine
Ala, Asp and Glu MT
Ala, Asp and Glu MT
Ala, Asp and Glu MT
Ala, Asp and Glu MT
Ala, Asp and Glu MT
Ala, Asp and Glu MT
Ala, Asp and Glu MT
Arg MT
Arg MT
Arg MT
Arg MT
Arg MT
Arg MT
Arg MT
Arg MT
Cys and Met MT
Cys and Met MT
Cys and Met MT
Cys and Met MT
Cys and Met MT
Cys and Met MT
Cys and Met MT
Cys and Met MT
Cys and Met MT
Cys and Met MT
Cys and Met MT
Cys and Met MT
Cys and Met MT
Gly and Ser MT
Gly and Ser MT
Gly and Ser MT
His MT
His MT
His MT
His MT
Lys MT
Lys MT
Lys MT
Lys MT
Lys MT
Trp MT
Trp MT
Trp MT
Trp MT
Trp MT
Trp MT
Trp MT
Trp MT
Trp MT
Trp MT
Tyr MT
Tyr MT
Tyr MT
Val MT
Val MT
Val MT
Val MT
Val MT

Others Group
2-ketoglutaric acid
Acotinic acid
Citric acid
Fumaric acid
Isocitric acid
Lactic acid
Malic acid
Pyruvic acid
Succinic acid
Penicillin G
2-Aminoethanol
Glyceric acid
NAD
O-Phosphoethanolamine
Taurine
TCA Cycle
TCA Cycle
TCA Cycle
TCA Cycle
TCA Cycle
TCA Cycle
TCA Cycle
TCA Cycle
TCA Cycle
Antibiotics




 
Nucleic acids and their metabolites Group
Adenine
Adenosine
Adenosine monophosphate
Deoxyadenosine
Deoxyadenosine monophosphate
Deoxyguanosine
Deoxyguanosine monophosphate
Guanine
Guanosine
Guanosine monophosphate
Hypoxanthine
Inosine
Inosine monophosphate
Uric acid
Xanthine
Xanthosine
Xanthosine monophosphate
3-Aminoisobutyric acid
3-Aminopropanoic acid
Cytidine
Cytidine monophosphate
Cytosine
Deoxycytidine
Deoxycytidine monophosphate
Orotic acid
Thymidine
Thymidine monophosphate
Thymine
Uracil
Uridine
Uridine monophosphate
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Purine MT
Pyrimidine MT
Pyrimidine MT
Pyrimidine MT
Pyrimidine MT
Pyrimidine MT
Pyrimidine MT
Pyrimidine MT
Pyrimidine MT
Pyrimidine MT
Pyrimidine MT
Pyrimidine MT
Pyrimidine MT
Pyrimidine MT
Pyrimidine MT
Sugars Group
Gluconic acid                    
Hexose (Glucose)
Sucrose
Threonic acid



Vitamins Group
Riboflavin          
Niacinamide
Nicotinic acid
Pantothenic acid
4-Pyridoxic acid
Pyridoxal
Pyridoxalphosphate
Pyridoxine
Biotin
4-Aminobenzoic acid
Folic acid
Choline
Ascorbic acid
Cyanocobalamin
Lipoic acid
B2
B3
B3
B5
B6
B6
B6
B6
B7
B9
B9
B12
C
Vitamin-like
Vitamin-like
Internal standard Group
2-Isopropylmalic acid        
 

Remarks and Precautions

  1. LabSolutions LCMS Ver.5.97 or later is required.
  2. 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.

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