Penn Metabolomics Core

Core Description

The Penn Metabolomics Core provides expertise in targeted and untargeted metabolomics, 13C isotopic tracing, and custom method development with 2 Agilent HPLC/triple quadrupole mass spectrometers and a Thermo HPLC/Orbitrap IDX mass spectrometer. Our mission is to perform the assays and assist in the interpretation of the results. The core is available to the entire Penn research community, external research investigators, and industry.

Services:

Custom LC/MS Assay Method Development

One of our key strengths is custom LC/MS assay method development for metabolites.  There are 3 levels of method development (low, medium, and high difficulty) with a set fee for each.

Untargeted LC/MS Metabolomics

Untargeted metabolomics is performed on a Thermo Vanquish UHPLC/Orbitrap ID-X mass spectrometer to identify metabolites (MW 70-1000) for biomarker discovery.  Each sample is run through 2 separate LC/MS methods (reversed-phase C18 chromatography to retain medium polarity to non-polar metabolites and HILIC chromatography to retain highly polar metabolites). Statistical data analysis includes PCA, whisker plots, heat maps, and a database search to identify metabolites. 

¹³C Isotopic Tracing

 ¹³C isotopic tracing is available for tracing fuel-derived ¹³C into TCA cycle intermediates.

Targeted Metabolomics Assay Modules

Targeted metabolomics assays are available for the quantitative measurement of a wide variety of metabolites in cellular extracts, plasma, and tissues from an array of model organisms and human subjects. Quantitation of metabolites by liquid chromatography/mass spectrometry (two Agilent 1290 Infinity UHPLC/6495 triple quadrupole mass spectrometers) is achieved by standard calibration curves and addition of isotopically-labelled internal standards to biological samples. Our assays include the quantitation of:

• acylcarnitines (products of fatty acid oxidation)
• amino acids (products of fatty acid and amino acid oxidation)
• organic acids (TCA cycle intermediates; products of glucose and amino acid oxidation)
• R and S-2-hydroxyglutarate
• malonyl and acetyl CoA
• nucleotides
• catecholamines and metanephrines
• glycolysis/PPP
• fatty acids
• sulfatides
• psychosine
• retinoic acid
• adenosine

Acylcarnitines (57)

C2	C8	C4:1	C18:2	C22:4	C5-DC	C16-OH	C20:2-OH
C3	C10	C5:1	C20:1	C22:5	C6-OH	C16:1-OH
C4-butyryl	C12	C12:1	C20:2	C3-DC	C8-OH	C16:2-OH
C4-isobutyryl	C14	C14:1	C20:3	C4-OH butyryl	C8:1-OH	C18-OH
C5-valeryl	C16	C14:2	C20:4	C4-OH isobutyryl	C12-OH	C18:1-OH
C5-isovaleryl	C18	C16:1	C22:1	C4-DC succinyl	C14-OH	C18:2-OH
C5 2-Me-butyryl	C20	C16:2	C22:2	C4-DC Me-malonyl	C14:1-OH	C20-OH
C6	C22	C18:1	C22:3	C5-OH	C14:2-OH	C20:1-OH

 

Amino Acids (30)

Gly	Lys	His	Trp	Val	Leu	Asn	Thr	Pro	Ser
Ala	Gln	Phe	Orn	Arg	Ile	Asp	Met	Tyr	Cit
Glu	1-MeHis	3-MeHis	homoCit	ADMA	SDMA	NMMA	homoArg	kynurenine	OH-kynurenine

 

Nucleotides (30)

NAM	1-MeNAM	NMN	NAMN	NAAD	NAD	NADP	NADH
NADPH	AMP	ADP	ATP	cAMP	GMP	GDP	GTP
cGMP	CMP	CDP	CTP	TMP	TDP	TTP	UMP
UDP	UTP	IMP	IDP	ITP	ADPR

 

 

Catecholamines and Metanephrines (6)

dopamine

epinephrine

norepinephrine

3-methoxytyramine

metanephrine

normetanephrine

 

Glycolysis/Pentose-Phosphate Pathway (17)

2-phosphoglycolic acid	6-phosphogluconic acid
2-deoxyribose-5-phosphate	sedoheptulose-7-phosphate
ribose-1-phosphate/ribose-5-phosphate	xylulose-5-phosphate/ribulose-5-phosphate
adenosine-5-diphosphoglucose	glucose-6-phosphate
phosphoenolpyruvate	2-phosphoglyceric/3-phosphoglyceric acid
dihydroxyacetonephosphate	glucose-1-phosphate/fructose-1-phosphate/fructose-6-phosphate

 

Fatty Acids (6)

acetic	propopnic	butyric	isobutyric
valeryl	isovaleryl	3-methylbutyric	3-methylvaleric
octanoic	3-hydroxyoctanoic	4-methylvaleric	hexanoic
decanoic	dodecanoic

 

Organic Acids (8)

lactate

pyruvate

succinate

3-HBA

alpha-KG

malate

citrate

fumarate

 

Acyl Coenzyme As (2)

malonyl CoA

acetyl CoA

 

Protocols: Cell and Tissue Harvest Protocols

Adherent Cell Harvest for Metabolomics

Cell Suspension Harvest for Metabolomics

Tissue Collection Protocol for Targeted Metabolomics

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Service Requests

Instructions to Register and Request iLab Services

Price List (Internal, External academic and Industry Pricing)

 

Please acknowledge the Penn Metabolomics Core in your publications:

Metabolomics studies were performed by the Penn Metabolomics Core (RRID:SCR_022381) supported by the Penn Cardiovascular Institute and, in part, by NCI P30 CA016520 and NIH P30DK050306.

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Contact

Chris Petucci, Ph.D.

Director
Email: Christopher.Petucci@pennmedicine.upenn.edu
Phone: 215-898-9765
Location: Smilow TRC 9-196

 

Clarissa Shoffler, B.S.

Research Specialist
Email: Clarissa.Shoffler@Pennmedicine.upenn.edu
Location: Smilow TRC 9-196

 

Dina Abbasian, B.S.

Research Specialist
Email: Dina.Abbasian@Pennmedicine.upenn.edu
Location: Smilow TRC 9-196

 

Zoltan P. Arany, M.D., Ph.D., Faculty Core Advisor

Email: zarany@pennmedicine.upenn.edu
Location: Smilow TRC 11-106

 

Daniel Kelly, M.D., Faculty Core Advisor

Email: dankelly@pennmedicine.upenn.edu
Location: Smilow TRC 11-122