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For LabSolutions LCMS
LC/MS/MS Method Package for Cell Culture Profiling Ver. 2
LC/M
S/MS M
ethod Package for Cell C
ulture Pro�ling Ver. 2
C146-E408
List of Registered Compounds
Cautions
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 con�rm qualitative and quantitative information obtained with this method package.
© Shimadzu Corporation, 2020First Edition: February 2020 3655-02005-ODPIT
Amino acids and their metabolites Group5-OxoprolineAlanineAsparagineAspartic acidGlutamic acidGlutamineN-Acetylaspartic acid4-Aminobutyric acid4-HydroxyprolineArginineCitrullineOrnithineProlinePutrescineArgininosuccinic acid2-Aminobutyric acid5-Glutamylcysteine5'-MethylthioadenosineCystathionineCysteineCystineGlutathioneHomocysteineMethionineMethionine sulfoxideN-AcetylcysteineOxidized glutathioneS-AdenosylhomocysteineGlycineSerineThreonine1-Methylhistidine3-MethylhistidineHistidineUrocanic acid2-Aminoadipic acidHydroxylysineLysinePipecolic acidSaccharopine3-Hydroxyanthranilic acid5-HydroxytryptophanAnthranilic acidFormylkynurenineHydroxykynurenineIndole-3-acetic acidKynurenic acid
Ala, Asp and Glu MTAla, Asp and Glu MTAla, Asp and Glu MTAla, Asp and Glu MTAla, Asp and Glu MTAla, Asp and Glu MTAla, Asp and Glu MTArg MTArg MTArg MTArg MTArg MTArg MTArg MTArg MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTGly and Ser MTGly and Ser MTGly and Ser MTHis MTHis MTHis MTHis MTLys MTLys MTLys MTLys MTLys MTTrp MTTrp MTTrp MTTrp MTTrp MTTrp MTTrp MT
Nucleic acids and their metabolites GroupAdenineAdenosineAdenosine monophosphateDeoxyadenosineDeoxyadenosine monophosphateDeoxyguanosineDeoxyguanosine monophosphateGuanineGuanosineGuanosine monophosphateHypoxanthineInosineInosine monophosphateUric acidXanthineXanthosineXanthosine monophosphate3-Aminoisobutyric acid3-Aminopropanoic acidCytidineCytidine monophosphateCytosineDeoxycytidineDeoxycytidine monophosphateOrotic acidThymidineThymidine monophosphateThymineUracilUridineUridine monophosphate
Purine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTpurine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MT
Others Group2-ketoglutaric acidAcotinic acidCitric acidFumaric acidIsocitric acidLactic acidMalic acidPyruvic acidSuccinic acidPenicillin G2-AminoethanolGlyceric acidNADO-PhosphoethanolamineTaurine
TCA CycleTCA CycleTCA CycleTCA CycleTCA CycleTCA CycleTCA CycleTCA CycleTCA CycleAntibiotics—————
Amino acids and their metabolites GroupKynurenineSerotoninTryptophan4-Hydroxyphenyllactic acidPhenylalanineTyrosine3-Hydroxyisobutyric acid3-Methyl-2-oxovaleric acidIsoleucineLeucineValineAlanyl-glutamineGlycyl-glutamine
Trp MTTrp MTTrp MTTyr MTTyr MTTyr MTVal MTVal MTVal MTVal MTVal MT——
Vitamins GroupRibo�avinNiacinamideNicotinic acidPantothenic acid4-Pyridoxic acidPyridoxalPyridoxalphosphatePyridoxineBiotin4-Aminobenzoic acidFolic acidCholineAscorbic acidCyanocobalaminLipoic acid
B2B3B3B5B6B6B6B6B7B9B9B12CVitamin-likeVitamin-like
Sugars GroupGluconic acidHexose (Glucose)SucroseThreonic acid
————
Internal standard Group2-Isopropylmalic acid
*MT: metabolism
—
LabSolutions and LCMS are trademarks of Shimadzu Corporation.
GARUDA is a trademark of The Systems Biology Institute.
Analysis of culture supernatant
Guanosine KynurenineRibo�avinXanthine
0.00
0.50
1.00
1.50
2.00
(x1,000,000)
Tryp
toph
an
Phen
ylal
anin
e
Hex
ose
(Glu
cose
)
Thre
onin
e His
tidin
eA
rgin
inos
ucci
nic
acid
Oro
tic a
cid
Arg
inin
e
Cho
line
Urid
ine
Val
ine
Pant
othe
nic
acid
Cyt
idin
eTy
rosi
ne
Isol
euci
neLe
ucin
e
Met
hion
ine
5-O
xopr
olin
e
Putr
esci
ne
Asp
artic
aci
d
min1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0
1-M
ethy
lhis
tidin
e
4.5 5.0 5.5 6.0
0
250
500
750
1000
1250
1500
1750
2000
5.5 6.0 6.5 7.0
0
2500
5000
7500
10000
3.5 4.0 4.5 5.0
0
500
1000
1500
2000
2500
3000
3500
2.5 3.0 3.5 4.0
0
1000
2000
3000
4000
5000
6000
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.
Simultaneous Analysis Conditions for 125 Compounds
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.
Optimized Method for Culture Medium Analysis
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.
Ready-to-Use Method
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.
Excellent Data Analysis Functionality
Volcano plot display Visualization of compounds
showing changes on the volcano plot
Visual representation of
related compounds
Display of changes over time
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).
http://www.garuda-alliance.org/
VANTEDSupports data analysis of biological processes through metabolic pro�ling and visualization of enzyme activity on metabolic maps. Tool maintained at University of Konstanz, Germany, for visualization and analysis of networks across different data sets. GARUDA support was developed at Monash University.
iPathData analysis tool developed by the European Molecular Biology Laboratory that can be used for visualization of diverse metabolic pathways or data mapping and customization.
CytoscapeBioinformatics tool developed by the Cytoscape Consortium, used to visualize metabolic pathways, integrate gene expression pro�les with related data, etc. It is especially useful for analyzing networks and visualizing correlations.
Data Analysis Tools in the Method Package
Volcano PlotA tool that combines a t-test (for statistically signi�cant differences) and a fold analysis (e.g. twice or half the mean value) to visualize the differences between the two groups. The Volcano Plot gadget developed by Shimadzu is included in the package.
Tools for Data Analysis
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.
Data Analysis Example
Time-series measurement data
Select �les
A blank map for Cell Culture Profiling Ver. 2 is included with
the method package installer
Analysis of culture supernatant
Guanosine KynurenineRibo�avinXanthine
0.00
0.50
1.00
1.50
2.00
(x1,000,000)
Tryp
toph
an
Phen
ylal
anin
e
Hex
ose
(Glu
cose
)
Thre
onin
e His
tidin
eA
rgin
inos
ucci
nic
acid
Oro
tic a
cid
Arg
inin
e
Cho
line
Urid
ine
Val
ine
Pant
othe
nic
acid
Cyt
idin
eTy
rosi
ne
Isol
euci
neLe
ucin
e
Met
hion
ine
5-O
xopr
olin
e
Putr
esci
ne
Asp
artic
aci
d
min1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0
1-M
ethy
lhis
tidin
e
4.5 5.0 5.5 6.0
0
250
500
750
1000
1250
1500
1750
2000
5.5 6.0 6.5 7.0
0
2500
5000
7500
10000
3.5 4.0 4.5 5.0
0
500
1000
1500
2000
2500
3000
3500
2.5 3.0 3.5 4.0
0
1000
2000
3000
4000
5000
6000
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.
Simultaneous Analysis Conditions for 125 Compounds
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.
Optimized Method for Culture Medium Analysis
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.
Ready-to-Use Method
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.
Excellent Data Analysis Functionality
Volcano plot display Visualization of compounds
showing changes on the volcano plot
Visual representation of
related compounds
Display of changes over time
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).
http://www.garuda-alliance.org/
VANTEDSupports data analysis of biological processes through metabolic pro�ling and visualization of enzyme activity on metabolic maps. Tool maintained at University of Konstanz, Germany, for visualization and analysis of networks across different data sets. GARUDA support was developed at Monash University.
iPathData analysis tool developed by the European Molecular Biology Laboratory that can be used for visualization of diverse metabolic pathways or data mapping and customization.
CytoscapeBioinformatics tool developed by the Cytoscape Consortium, used to visualize metabolic pathways, integrate gene expression pro�les with related data, etc. It is especially useful for analyzing networks and visualizing correlations.
Data Analysis Tools in the Method Package
Volcano PlotA tool that combines a t-test (for statistically signi�cant differences) and a fold analysis (e.g. twice or half the mean value) to visualize the differences between the two groups. The Volcano Plot gadget developed by Shimadzu is included in the package.
Tools for Data Analysis
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.
Data Analysis Example
Time-series measurement data
Select �les
A blank map for Cell Culture Profiling Ver. 2 is included with
the method package installer
For LabSolutions LCMS
LC/MS/MS Method Package for Cell Culture Profiling Ver. 2
LC/M
S/MS M
ethod Package for Cell C
ulture Pro�ling Ver. 2
C146-E408
List of Registered Compounds
Cautions
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 con�rm qualitative and quantitative information obtained with this method package.
© Shimadzu Corporation, 2020First Edition: February 2020 3655-02005-ODPIT
Amino acids and their metabolites Group5-OxoprolineAlanineAsparagineAspartic acidGlutamic acidGlutamineN-Acetylaspartic acid4-Aminobutyric acid4-HydroxyprolineArginineCitrullineOrnithineProlinePutrescineArgininosuccinic acid2-Aminobutyric acid5-Glutamylcysteine5'-MethylthioadenosineCystathionineCysteineCystineGlutathioneHomocysteineMethionineMethionine sulfoxideN-AcetylcysteineOxidized glutathioneS-AdenosylhomocysteineGlycineSerineThreonine1-Methylhistidine3-MethylhistidineHistidineUrocanic acid2-Aminoadipic acidHydroxylysineLysinePipecolic acidSaccharopine3-Hydroxyanthranilic acid5-HydroxytryptophanAnthranilic acidFormylkynurenineHydroxykynurenineIndole-3-acetic acidKynurenic acid
Ala, Asp and Glu MTAla, Asp and Glu MTAla, Asp and Glu MTAla, Asp and Glu MTAla, Asp and Glu MTAla, Asp and Glu MTAla, Asp and Glu MTArg MTArg MTArg MTArg MTArg MTArg MTArg MTArg MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTCys and Met MTGly and Ser MTGly and Ser MTGly and Ser MTHis MTHis MTHis MTHis MTLys MTLys MTLys MTLys MTLys MTTrp MTTrp MTTrp MTTrp MTTrp MTTrp MTTrp MT
Nucleic acids and their metabolites GroupAdenineAdenosineAdenosine monophosphateDeoxyadenosineDeoxyadenosine monophosphateDeoxyguanosineDeoxyguanosine monophosphateGuanineGuanosineGuanosine monophosphateHypoxanthineInosineInosine monophosphateUric acidXanthineXanthosineXanthosine monophosphate3-Aminoisobutyric acid3-Aminopropanoic acidCytidineCytidine monophosphateCytosineDeoxycytidineDeoxycytidine monophosphateOrotic acidThymidineThymidine monophosphateThymineUracilUridineUridine monophosphate
Purine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTPurine MTpurine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MTPyrimidine MT
Others Group2-ketoglutaric acidAcotinic acidCitric acidFumaric acidIsocitric acidLactic acidMalic acidPyruvic acidSuccinic acidPenicillin G2-AminoethanolGlyceric acidNADO-PhosphoethanolamineTaurine
TCA CycleTCA CycleTCA CycleTCA CycleTCA CycleTCA CycleTCA CycleTCA CycleTCA CycleAntibiotics—————
Amino acids and their metabolites GroupKynurenineSerotoninTryptophan4-Hydroxyphenyllactic acidPhenylalanineTyrosine3-Hydroxyisobutyric acid3-Methyl-2-oxovaleric acidIsoleucineLeucineValineAlanyl-glutamineGlycyl-glutamine
Trp MTTrp MTTrp MTTyr MTTyr MTTyr MTVal MTVal MTVal MTVal MTVal MT——
Vitamins GroupRibo�avinNiacinamideNicotinic acidPantothenic acid4-Pyridoxic acidPyridoxalPyridoxalphosphatePyridoxineBiotin4-Aminobenzoic acidFolic acidCholineAscorbic acidCyanocobalaminLipoic acid
B2B3B3B5B6B6B6B6B7B9B9B12CVitamin-likeVitamin-like
Sugars GroupGluconic acidHexose (Glucose)SucroseThreonic acid
————
Internal standard Group2-Isopropylmalic acid
*MT: metabolism
—
LabSolutions and LCMS are trademarks of Shimadzu Corporation.
GARUDA is a trademark of The Systems Biology Institute.