It is estimated that around 100,000 proteins expressed in a cell at a time point, however only 10,000 could be identified in a proteomics experiment. You can see that 90% of the proteins are not detectable due to a lot of reasons, like low abndance, trypsin resitent, too big or too small, too hydrophobic or hydrophilic, etc. You can always check if your protein(s) has (have) been identified before by MS in publications from Nextprot. This will give you a rough idea that how likely your will identifty your protein.
What is the detection limit
The detection limit of proteins from SDS-PAGE gel bands through the use of LC-MS/MS is in the femtomole amounts or on a weight basis in the low nanogram range (1-5 ng). This is also very similar to the detection limit of proteins stained with silver and sypro ruby stains. Colloidal coomassie stains typically have detection limits between 10 and 20 ng and coomassie brilliant blue has a detection limit near 50 ng. The detection limits of these stains will be dependent on many variables such as the thickness of the gel and the width of the lanes. While the detection limit of protein staining is on a weight basis, the detection limit of protein with the mass spectrometer is on a molar basis, therefore the higher the molecular weight, at the same mass, the higher the detection limit will be for the mass spectrometer. (For example 1.0 ng of a 20 kDa protein is 50 fm, while 1.0 ng of a 200 kDa protein is only 5 fm. Both proteins will have similar stain intensities, but there is 10 times less protein on a molar basis from the 200 kDa protein.)
Multiple Proteins in a single band?
It is very common for gel bands to contain several and sometimes dozens of proteins. These proteins will result in a band on the gel that is detectable but there may not be any single protein in the band.
Please ship your samples
To: Daniel Fiegys
Attention: Zhibin Ning
Roger Guindon Hall,451 Smyth Road
Ottawa, ON, Canada, K1H 8M5
University of Ottawa, Health Sciences Campus
DIRECTOR: Dr Daniel Figeys
Professor, Department of Biochemistry, Microbiology and Immunology
Canada Research Chair Proteomics and Systems Biology
Phone: 613 562-5800 ext. 8674