Proteomics Unit, Viikki

The broad field of proteomics is an essential technology in biosciences that underpins strategically important areas in academia and biotechnology, enabling characterisation and temporal and spatial quantitation of proteins at various locations in practically all biological systems. It also affords measurement and discovery of post-translational protein modifications, protein-protein interactions and protein properties, which are amongst the most sought after applications.

We offer mass spectrometry servises to Academy and private sector. We have 5 different mass spectometers: 3 LC-MS/MS (Orbitrap Elite, Q Exactive and TripleTOF 6600) , one Single cell MS (Helios, CyTOF), one Applied Biosystems Procise 494 HT sequencer and one MALDI-TOF (Ultraflex TOF/TOF).

 

Protein digestion in-gel or in-solution using a proteolytic enzyme, usually trypsin. Peptide can be fragmentated by CID, HCD or ETD.

For protein identification Proteome Discoverer™ Software is used as the default search engine. Databases can be customised to the user´s needs.

For protein quantification we use MaxQuant or Proteome Discoverer.

Generally results are provided with 5% FDR (false discovery rate) on the peptide level.

Measures intact mass of protein or peptides in mass range 700 to 70 000 Da.

Proteins up to 70 000 Da and peptides up to 4000 Da.

Salt can be removed and sample can be concentrated with C18 or C4 ZipTip® Pipette Tips.

Minimun sample amount 1 ul. Concentration of the sample more than 20 µM or 1 µg/µl.

Mass accuracy within 50 ppm.

Results are in mass to charge ratio (m/z).

Label-free quantification determines the relative amout of proteins in two or more biological samples. Label-free quantification don´t use stable isotopes compounds to bind and label the protein.

Labelled methods are used to compare protein or peptide abundace between samples. Spiking unlabeled samples with Isotopically labeled peptides we can yeild absolute quantitation for target peptides. Labelled protein quantification approach is more costly and time-consuming. Quantification methods for labeled analysis include ICAT, TMT, iTRAQ, ICPL, IDBEST, TMT, MeCAT, SILAC and TAILS.

Protein digestion using a proteolytic enzyme, usually trypsin. Peptide fragmentation by CID, HCD or ETD.

For protein identification Proteome Discoverer™ Software is used as the default search engine. Databases can be customised to the user´s needs. For protein quantification we use MaxQuant or Proteome Discoverer.

 

Generally results are provided with 5% FDR (false discovery rate) on the peptide level.