Hi,

It will be a challenging task. QqQ analyser will be the idea choice  for femtogram level protein quantitation. Which model of ESI-q-TOF you are planning  to use for protein quantitation?

hi, an agilent micromass esi q tof

I would say it to be impossible for a q-tof system, independently of the manufacturer and level. I would consider about 50 amol as a solid LOQ for a q-tof system (and this is also for very good proteins-peptides), while going deeper is a real chance of luck and very-very-very good peptide behaviour. And this you better do via pseudoMRM. If you decide to go on with isotopic standards be careful of such low peptide/protein concentration absorbtion on tube walls. It would be not very easy to get a standard with a precise desired concentration. Anyway the best way is to enrich your sample with the protein of interest (or deplete the sample from all the noise). And to load more that femtograms, at least go up to several dozen attomols. Or use QqQ instead, people promise 0.05-0.1 attomoles sensitivity (just what you need):)). If you believe that, you can try - but only top-level QqQ from e.g. ABSciex or Agilent. 

You need to optimize the measurement  first, voltage, temperature , buffer applied, but consider that the purity of the sample is also very important. Good Luck

I recently had to chance to see a Xevo TQS QqQ (Waters) working with ionkey fluidics (150um ID colum on the chip) operating in MRM mode for protein quantitation. Pretty impressive. Very high sensitivity. If I remember right, the first calibrator of the curve was 50aM. For very high sensitivity in targeted mode, I would always go for QqQ and low scale fluidics  (keep an eye on robustness/required sample throughput)

It is going to be difficult but not impossible. Should be achievable with optimized conditions. Also, depends a lot on the type of protein you want to analyze.

in what sense it depends on the protein?

I quote VIncent. Maybe Skyline software (MacCoss Lab) might help you in picking up the best peptides/MRM transitions fro your protein. Plus, it allows different proteases as digestion options. It might be a good starting point to check the N of peptides (not too long/short etc etc) you can rely on for quantitation.