As the advancement of Mass Spectrometry, Proteomics are catching up with Genomics and are able to identify around 90% of total proteins theoretically present in human tissues, as reported in "A draft map of the human proteome" Nature. 2014 May 29;509(7502):575-81, a paper Omics Technologies scientists are involved. However, due to the fundamental laws of physics, the most advanced Proteomics specialized mass spectrometers are still far from analyzing all proteins in a complex sample in one run, a standard next generation sequencing techniques routinely reach. The fundamental way to improve the success of a proteomics study is to fractionate a complex samples into smaller and smaller fractions and try to analyze them with an advanced mass spectrometer one by one. Here is an example acquired in our daily work:
As you can see here, as the number of fractions increases, the total coverage and depth as well as the quality (FDR) of the data improves dramatically. There are several reasons behind this, but to make it simple, by fractionating a complex sample into smaller pieces, you are not only reducing the complexicity of each piece dramatically, but also improving the ionization of low abundance analytes which were previously masked by high abundance analytes or even by just noise. You will have a much better chance to see something novel and interesting, which are the key to your success. You won't be able to find these low abundance peptides/proteins when you analyze your unfractionated samples using even the most advanced mass spectrometer, or analyzing your well-fractionated samples using a low end mass spectrometer.
In Omics Technologies, we encourage you to take full advantage of our world's most advanced mass spectrometers, and to do that, you need to try to maximize the fractions, within your budget, to generate a guaranteed publishable data in every run and make every penny count.