I know pricing should not be difficult
Unfortunately, it's a bit tricky if to charge accurately for the work we perform.
All samples are a bit different and take different amounts of time to work on . Almost all of the variability (in your results & in the pricing) is due to the protein extraction and sample prep. All samples are a bit different and require different amount of time to prepare. LC-MS runs are charged per hour.
We can give you an estimate and you can cut down the costs by doing a lot of the work yourself and using shorter LC-MS gradients.
Doing the protein extraction yourself is not that difficult
We use S-traps from Protifi.com as they work with a wide variety of samples and we can semi automate the digestion using our Tecan A200
Essentially Follow these steps and stop After Step 4
You should also do a BCA at this point as knowing the protein concentration is very beneficial. But if you can estimate accurately using past knowledge, this works too
The entire protocol is here
and there are some great troubleshooting tips at the bottom and here
You can do the whole protocol your self and save even more money , plus it's fun
The above protocol is for 100-300 ug of starting protein. If you have less you can use this protocol
but steps 1-4 are essentially the same
This protocol works well too
There are also specific protocols for things like Urine or Plasma here
If you don't want to use S-traps we recommend these