Summary of study ST000093

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000085. The data can be accessed directly via it's Project DOI: 10.21228/M8JS3X This work is supported by NIH grant, U2C- DK119886.

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Study IDST000093
Study TitleMetabolomics Analysis of Frontal Fibrosing Alopecia
Study TypeUnaffected and Affected patient scalp biopsies
Study SummaryScarring alopecia consists of a collection of disorders characterized by destruction of hair follicles, replacement with fibrous scar tissue, and irreversible hair loss. Alopecia affects men and women worldwide and can be a significant source of psychological stress and depression for affected individuals. The purpose of this study was to explore metabolic profiles in scalp tissue samples from normal control subjects (n=6) and in matched samples obtained from affected (n=12) and unaffected (n=12) areas of the scalp in patients with lymphocytic Frontal Fibrosing Alopecia (FFA). Frontal fibrosing alopecia results from destruction of hair follicles by an inflammatory lymphocytic infiltrate that is localized around the upper portion of the hair follicle.
Institute
Case Western Reserve University
DepartmentDermatology
LaboratoryKarnik Lab
Last NameKarnik
First NamePratima
Emailpsk11@case.edu
Phone216-368-0209
Submit Date2014-07-24
Num Groups3 groups-Paired unaffected and affected (n=12),Normals(n=6)
Total SubjectsPatients (N=12), Normals (N=6)
Study CommentsAffected scalp biopsies were obtained from frontal scalp, Unaffected from occipital scalp. Normal scalp biopsies were obtained from the occipital scalp.
Raw Data AvailableNo
Analysis Type DetailGC/LC-MS
Release Date2014-07-26
Release Version1
Pratima Karnik Pratima Karnik
https://dx.doi.org/10.21228/M8JS3X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000085
Project DOI:doi: 10.21228/M8JS3X
Project Title:Mitochondrial Dysfunction in Frontal Fibrosing Alopecia
Project Summary:The goal of this study was to characterize metabolic drift associated with lymphocytic frontal fibrosing alopecia (FFA), comparing same-patient affected/unaffected area tissues as well as control patient tissue.
Institute:Case Western Reserve University
Department:Dermatology
Laboratory:Karnik Laboratory
Last Name:Karnik
First Name:Pratima
Email:psk11@case.edu
Phone:216-368-0209
Funding Source:NIAMS grant R01 AR056245 and NIH Common Fund grant (Metabolomics) R01 AR056245S1 grants to Pratima Karnik

Subject:

Subject ID:SU000112
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:postmenopausal women
Gender:Female
Species Group:Human

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id condition location
SA005255Patient_138_FFA_AFFA affected frontal scalp
SA005256Patient_144_FFA_AFFA affected frontal scalp
SA005257Patient_143_FFA_AFFA affected frontal scalp
SA005258Patient_146_FFA_AFFA affected frontal scalp
SA005259Patient_147_FFA_AFFA affected frontal scalp
SA005260Patient_150_FFA_AFFA affected frontal scalp
SA005261Patient_149_FFA_AFFA affected frontal scalp
SA005262Patient_142_FFA_AFFA affected frontal scalp
SA005263Patient_145_FFA_AFFA affected frontal scalp
SA005264Patient_140_FFA_AFFA affected frontal scalp
SA005265Patient_139_FFA_AFFA affected frontal scalp
SA005266Patient_141_FFA_AFFA affected frontal scalp
SA005267Patient_150_FFA_UFFA unaffected occipital scalp
SA005268Patient_142_FFA_UFFA unaffected occipital scalp
SA005269Patient_138_FFA_UFFA unaffected occipital scalp
SA005270Patient_149_FFA_UFFA unaffected occipital scalp
SA005271Patient_139_FFA_UFFA unaffected occipital scalp
SA005272Patient_147_FFA_UFFA unaffected occipital scalp
SA005273Patient_143_FF_UFFA unaffected occipital scalp
SA005274Patient_146_FFA_UFFA unaffected occipital scalp
SA005275Patient_144_FFA_UFFA unaffected occipital scalp
SA005276Patient_141_FFA_UFFA unaffected occipital scalp
SA005277Patient_140_FFA_UFFA unaffected occipital scalp
SA005278Patient_145_FFA_UFFA unaffected occipital scalp
SA005279Patient_GN048_NormalScalp biopsy normal NA
SA005280Patient_DN338_NormalScalp biopsy normal NA
SA005281Patient_LN339_NormalScalp biopsy normal NA
SA005282Patient_TN089_NormalScalp biopsy normal NA
SA005283Patient_PN200_NormalScalp biopsy normal NA
SA005284Patient_KN336_NormalScalp biopsy normal NA
Showing results 1 to 30 of 30

Collection:

Collection ID:CO000095
Sample Type:4 mm Scalp biopsies

Treatment:

Treatment ID:TR000113
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP000108
Sampleprep Summary:Metabolon’s standard solvent extraction method. The sample preparation process was carried out using the automated MicroLab STAR® system from Hamilton Company. Recovery standards were added prior to the first step in the extraction process for QC purposes. Sample preparation was conducted using a proprietary series of organic and aqueous extractions to remove the protein fraction while allowing maximum recovery of small molecules. The resulting extract was divided into two fractions; one for analysis by LC and one for analysis by GC. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. Each sample was then frozen and dried under vacuum. Samples were then prepared for the appropriate instrument, either LC/MS or GC/MS.
Sampleprep Protocol Filename:Metabolon_Methods_CASE-03-11VW.docx
Sample Derivatization:50?L for GC/MS analysis using equal parts bistrimethyl-silyl-trifluoroacetamide and solvent mixture

Combined analysis:

Analysis ID AN000147 AN000148 AN000149
Analysis type MS MS MS
Chromatography type GC GC GC
Chromatography system
Column GCMS-5% phenyldimethyl silicone column, 2.1 mm 100 mm Waters BEH C18 1.7 um particle columns GCMS-5% phenyldimethyl silicone column, 2.1 mm 100 mm Waters BEH C18 1.7 um particle columns GCMS-5% phenyldimethyl silicone column, 2.1 mm 100 mm Waters BEH C18 1.7 um particle columns
MS Type EI ESI ESI
MS instrument type Single quadrupole Single quadrupole Single quadrupole
MS instrument name Thermo Trace DSQ Thermo LTQ Thermo LTQ
Ion Mode POSITIVE POSITIVE NEGATIVE
Units Unspecified Unspecified Unspecified

Chromatography:

Chromatography ID:CH000105
Chromatography Summary:GC/MS and LC/MS/MS platforms
Chromatography Comments:HPLC-3 ?m particle 2.1 mm 100 mm Aquasil C18 (ThermoFisher) column.LTQ mass spectrometer (Thermo Fisher Scientific, Inc., Waltham, MA),Thermo-Finnigan Trace DSQ MS (Thermo Fisher Scientific, Inc.)
Column Name:GCMS-5% phenyldimethyl silicone column, 2.1 mm 100 mm Waters BEH C18 1.7 um particle columns
Column Temperature:40 C
Solvent A:HPLC-0.1% formic acid in water
Solvent B:HPLC-0.1% formic acid in methanol (0% B for 4 min, 0?50% B in 2 min, 50?80% B in 5 min, 80?100% B in 1 min, and 100% for 2 min).
Chromatography Type:GC

MS:

MS ID:MS000123
Analysis ID:AN000147
Instrument Name:Thermo Trace DSQ
Instrument Type:Single quadrupole
MS Type:EI
MS Comments:For GC/MS analysis, samples were analyzed on a Thermo-Finnigan Trace DSQ fast-scanning single-quadrupole mass spectrometer using electron impact ionization.
Ion Mode:POSITIVE
Capillary Temperature:60°C to 340°C
  
MS ID:MS000124
Analysis ID:AN000148
Instrument Name:Thermo LTQ
Instrument Type:Single quadrupole
MS Type:ESI
MS Comments:The LC/MS portion of the platform was based on a Waters ACQUITY UPLC and a Thermo-Finnigan LTQ mass spectrometer, which consisted of an electrospray ionization (ESI) source and linear ion-trap (LIT) mass analyzer.
Ion Mode:POSITIVE
Capillary Temperature:60°C to 340°C
  
MS ID:MS000125
Analysis ID:AN000149
Instrument Name:Thermo LTQ
Instrument Type:Single quadrupole
MS Type:ESI
MS Comments:The LC/MS portion of the platform was based on a Waters ACQUITY UPLC and a Thermo-Finnigan LTQ mass spectrometer, which consisted of an electrospray ionization (ESI) source and linear ion-trap (LIT) mass analyzer.
Ion Mode:NEGATIVE
Capillary Temperature:60°C to 340°C
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