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Mass spectrometric proteomics

Core Facility for analysis of proteomics

Service: Protein Analysis

As a service unit of identify proteins ...

         » In SDS-PAGE-bands LINK

         » In 2DE-Gel-spots LINK


How you can analyse the mass spectrometric results, click here to get more information. LINK


For all other please contact us at pkiani@uke.de , MS@uke.de or at phone: 040-7410-51907 , -58795.




For routine protein identification the user is requested to:

- provide excised SDS-PAGE/2DE-Gel bands in locked tubes with detailed labelling (Date_Name_Samplename)
CAUTION: Please read and follow our sample preparation guidelines for gel preparation, otherwise successful results cannot be guaranteed due to contamination e.g. by keratin

- Gel-samples can be delivered at room temperature and gel can be stored in tubes in a little excess of water or dried                                                                

- Please fill our MS-request form completely (available under "Downloads")                                                                                                                                            

- Place the MS-request form together with the sample tubes into an envelope

- Put the envelope into our CF-MP Mailbox (located next to our office N27, ground floor, room 00.008)

- In addition please send us an email to "MS@uke.de"
- CAUTION: Samples will only be analyzed after an e-mail is send to inform the CF-MP about the sample delivery!


- MS/MS-data will be processed into a peaklist file (e.g. mgf or mzXML) which will be provided by us and send to the user via e-mail

- The user then needs to perform the protein identification by using Mascot (http://www.matrixscience.com/)

- For using Mascot please read the Mascot-SOP for protein identification (Analysis via LC/ESI-Q-TOF or LC/ESI-IT-MS) available under "Downloads"

Other samples as protein solution or other non-routine samples should be handed out personally to a colleague of the CF-MP.

Please send an e-mail to set up an appointment to MS@uke.de




Typical user questions that can be answered by mass spectrometric approaches

1.Protein identification of unknown proteins:

Solution: Protein identification via mass spectrometric analysis of peptides derived from tryptic digest .  (Click here to see a more detailed workflow)


2. Which protein (markers) are associated with a change in a biological system?


Solution: Differential proteomic approaches (e.g. DIGE, SILAC, iTRAQ, Lable free quantification) 




Workflow for protein identification from protein gel bands

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last update: Diana Hildebrand, 23.04.2014