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MB Sample ID: SA034006

Local Sample ID:19071
Subject ID:SU000637
Subject Type:Bladder Cancer Tissues
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

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Subject:

Subject ID:SU000637
Subject Type:Bladder Cancer Tissues
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
19071SA034006FL007468CancerDiagonsis
19071SA034006FL007468Former SmokerSmoking Status

Collection:

Collection ID:CO000631
Collection Summary:Witten-Herdecke University;The University of Texas Southwestern Medical Center; Baylor College of Medicin
Sample Type:Bladder tissue

Treatment:

Treatment ID:TR000651
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP000644
Sampleprep Summary:All the tissues and urine samples used for this study were stored in -140oC. 50 mg of tissue was used for the extraction. For cell lines, 3 x106 cell pellets were thawed at 4 °C and subjected to three freeze-thaw cycles, freezing in liquid nitrogen and thawing on ice, to rupture the cell membranes. The extraction step start with 750 µL ice-cold methanol:water (4:1) containing 20 µL spiked internal standards was added to each cell pellet or tissue sample. Ice-cold chloroform and water was added in a 3:1 ratio for a final proportion of 1:4:3:1 water:methanol:chloroform:water. The organic (methanol and chloroform) and aqueous layers dried and re suspended with 50:50 methonal: water. The extract was deproteinized using a 3-kDa molecular filter (Amicon Ultracel-3K Membrane; Millipore Corporation, Billerica, MA) and the filtrate was dried under vacuum (Genevac EZ-2plus; Gardiner, Stone Ridge, NY). Prior to mass spectrometry, the dried extracts were resuspended in identical volumes of injection solvent composed of 1:1 water:methanol and subjected to liquid chromatography-mass spectrometry. 50 ul of urine was used for sample preparation. Internal standard was spiked into raw sample. Then it was processed through Amicon 3k filter. After that, 50 ul of urine sample was diluted with 450 solvent ( methanol water =50:50 v/v) and subjected to LC/MS analysis. The injection volume was 10 ul.

Combined analysis:

Analysis ID AN000939 AN000940 AN000941 AN000942 AN000943
Analysis type MS MS MS MS MS
Chromatography type HILIC HILIC HILIC HILIC HILIC
Chromatography system Unspecified Unspecified Unspecified Unspecified Unspecified
Column Waters XBridge Amide (100 x 4.6mm,3.5um) Waters XBridge Amide (100 x 4.6mm,3.5um) Waters XBridge Amide (100 x 4.6mm,3.5um) Waters XBridge Amide (100 x 4.6mm,3.5um) Phenomenex Luna NH2 (150 x 2.1mm,3um)
MS Type ESI ESI ESI ESI ESI
MS instrument type Triple quadrupole Triple quadrupole Triple quadrupole Triple quadrupole Triple quadrupole
MS instrument name Agilent 6495 QQQ Agilent 6495 QQQ Agilent 6495 QQQ Agilent 6495 QQQ Agilent 6495 QQQ
Ion Mode POSITIVE NEGATIVE POSITIVE POSITIVE POSITIVE
Units Peak intensity Peak intensity Peak intensity Peak intensity Peak intensity

Chromatography:

Chromatography ID:CH000670
Instrument Name:Unspecified
Column Name:Waters XBridge Amide (100 x 4.6mm,3.5um)
Chromatography Type:HILIC
  
Chromatography ID:CH000671
Instrument Name:Unspecified
Column Name:Phenomenex Luna NH2 (150 x 2.1mm,3um)
Chromatography Type:HILIC

MS:

MS ID:MS000835
Analysis ID:AN000939
Instrument Name:Agilent 6495 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000836
Analysis ID:AN000940
Instrument Name:Agilent 6495 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:NEGATIVE
  
MS ID:MS000837
Analysis ID:AN000941
Instrument Name:Agilent 6495 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000838
Analysis ID:AN000942
Instrument Name:Agilent 6495 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000839
Analysis ID:AN000943
Instrument Name:Agilent 6495 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
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