As mentioned by others, a whole proteome analysis helps you compare the levels of individual proteins under the two conditions you are studying - cells subjected or not subjected to mechanical stress. How deep the information that you get, i.e. regarding only abundant proteins or delving down into less abundant proteins and recognition of different types of covalent modification, depends on the mass spectrometer, the protocol used for the analysis and the program for identification of the proteins. You would carry out a phosphoproteomic analysis if you have some reason to think that the cells you are studying respond to mechanical stress by phosphorylation or de-phosphorylation of some key proteins, changing how the protein functions. You can base your reason on finding higher activity of a specific kinase that you have been studying, or from reading in the literature that a kinase (or a phosphatase) was important in regulation in another type of cell subjected to mechanical stress. Knowing which proteins were phosphorylated (or de-phosphorylated) only gives you clues regarding the cells' response to mechanical stress. You would need additional experiments to understand the relation of the change in phosphorylation status to the cell's response to mechanical stress. For example, the phosphoproteomic analysis might identify a protein that becomes phosphorylated when the cells are mechanically stressed. You might then engineer a mutation of the residue that gets phosphorylated, to prevent the modification, and ask if you still see the whole cell's response to mechanical stress. Bear in mind, also that phosphorylation is one of many types of covalent modifications that are important in the regulation of cell function. 

Why are phosphorylated protein analysis more worthwhile though?

Its hard to say what is better... depends on your interest.

Total proteins will give you information on changed protein transcription/translation and is well suited for long term observation, i.e., gives you information how the cell changes in reaction to the mechanic stress. (1 hour to days)

Phospho-proteins is especially valuable to monitor immedeate processes (minutes to several hours) and give you information how cellular signaling changes in reaction to the stress. The altered signaling will in part lead to altered protein production, which you can see wiht total protein.

Best

Christian

Try both if you have easy access to MS system.

I guess your final purpose is to be able to alter the cells response to mechanical stress.  There are more tools to change kinase activity (=phosphorylation) than to change protein expression (total proteome), therefore, phospho-profiling is more useful and unique with MS approach.

I will say don't limit yourself only to phosphorylation; Keep yourself open to other modifications as well; Go for SILAC based proteomic analysis initially, if you get some good hits pertaining to altered Kinases or phosphatase; Carry out Phosphoproteomic Analysis. 

While doing whole proteome analysis, you may find some other interesting hits which may suggest the role of other PTMs as well, which also you can check.

hi joel you seem to know a great deal about proteomic analyses. In general, why or what are the factors a researcher might do proteome analysis vs phosphoproteome analysis?

As mentioned by others, a whole proteome analysis helps you compare the levels of individual proteins under the two conditions you are studying - cells subjected or not subjected to mechanical stress. How deep the information that you get, i.e. regarding only abundant proteins or delving down into less abundant proteins and recognition of different types of covalent modification, depends on the mass spectrometer, the protocol used for the analysis and the program for identification of the proteins. You would carry out a phosphoproteomic analysis if you have some reason to think that the cells you are studying respond to mechanical stress by phosphorylation or de-phosphorylation of some key proteins, changing how the protein functions. You can base your reason on finding higher activity of a specific kinase that you have been studying, or from reading in the literature that a kinase (or a phosphatase) was important in regulation in another type of cell subjected to mechanical stress. Knowing which proteins were phosphorylated (or de-phosphorylated) only gives you clues regarding the cells' response to mechanical stress. You would need additional experiments to understand the relation of the change in phosphorylation status to the cell's response to mechanical stress. For example, the phosphoproteomic analysis might identify a protein that becomes phosphorylated when the cells are mechanically stressed. You might then engineer a mutation of the residue that gets phosphorylated, to prevent the modification, and ask if you still see the whole cell's response to mechanical stress. Bear in mind, also that phosphorylation is one of many types of covalent modifications that are important in the regulation of cell function.