Back to HKUPP top

Human Renal Medulla Identified Proteome

 Terget Sample  Search Word  Operation
Sample 1   Sample 2   Sample 3      

Brief Overview
  This data base is the proteome which composition protein of Human renal medulla was identified by Mass spectrometer.

  Human Samples
  We got kidney from patient who can't evade Nephrectomy for kidney cancer, it donated with informed consent.
The kidney chose non-cancer part by light microscopy, and was used for this analysis.

Tissue contens
Local Sample Code
 Light Microscope 
Non-cancer pars of each sample takes the tissue of the 30mg, and it was being processed.
It had been broken by ceramic beads in Urea buffer of 1ml, and broke more by sonicator.
Next, that centrifuged at 12,000rpm and taken Supernatant.
Proteins contained in the supernatant was reduced with TCEP(Tris [2- carboxyethyl] phosphine), was alkylated with IAA(Iodoacetamid).
Then performs Tryptic Digestion, Desalted and concentrated by peptide C18 column chip type, and served as a sample for mass spectrometry.

  Protein Identify
  Peptide detection is performed by Mass spectrometer (AB Sciex Triple TOF 5600), "Wiff format" which had been result data is changed to "MGF format" by a converter, protein identify was performed in Mascot (Matrix Science).

Search parameters
Peptide Mass Tolerance
±0.1 Da
MS/MS Tolerance
±0.1 Da
Fixed modifications
Carbamidomethyl (C)
Variable modifications
Deamidated (NQ),
Gln->pyro-Glu (N-term Q),
Glu->pyro-Glu (N-term E),
Oxidation (M)

Protein identification criteria
Sequence database
Significance threshold
p < 0.024 to 0.042
Expect cut-off
Setting the same value as significant threshold
Required bold-red

  How to Use
1) Target Sample
  You can select the checkbox as Renal medulla proteome data.
You can freely combination from Sample1,2,3.
2) Search Word
  The search is determined from Protein name or Gene symbol in selected Target Sample.
Current version is possible to search only a single word.
If Search Word is blank, result will display all Gene symbol of including in Target Sample.
Next describe Setting in Operation and item, you can search from only Gene symbol or only protein name.
3) Operation
  Submit  :  This button sends condition by the Search Word and Target Sample to the server, and get search results.
Reset  :  This button is restore to initial state the Search Word and Target Sample.
Setting  :  This button is possible to change the operation settings of the search.
  - Display Results per Page-  :  number of the list to be displayed on one screen.
- Display Target Item-  :  selection of items to include in the search results.
- Search Word Target-  :  Search Word will search from each items.


Back to HKUPP top