In our experience, it cannot be removed because of its amphiphilc properties. We therefore recommend to avoid it in the first place.
Common sources: Triton-X or NP-40, deionizers, parafilm, plastics, handcreams.
I find that you can change the NP-40 for other switterionic detergent such as CHAPS, ASB14, etc, otherwise use methanol chloroform precipitation. I hope this help
My suggestion would be to try 'Filter-Aided Sample Preparation' (FASP).
This approach allows you solubilize your protein of interest with detergent. The detergent will then be removed by washing it out on a standard filter device before mass spec analysis.
http://www.nature.com/nmeth/journal/v6/n5/pdf/nmeth.1322.pdf
FASP is a good solution.
In general, try avoid detergent if you are going to use a mass spec.
But if you have to, you can use SDS and do a cleanup step with concentrated UREA (8 M), or a mix of ACN and 8M urea (20:80).
The only problem with urea is the high risk of carbamylation. But you can account it for your protein identification as a volatile modification.
If you really want to keep your protein with detergents, then there are detergents removal columns, but I have no experience with them.
I agree with all above presented opinion but do not forget that these peaks maybe also useful in the mass calibration system.
You could remove PEG with a simple chromatography with a 2D chromatography column (e.g. by Gilson)
check out this paper
https://www.dropbox.com/s/7r9b7w95guhycb1/2007%20Removal%20of%20PEG%20using%20titanium.pdf
I have had some good luck by using Zip Tips to remove PEG and related surfactants from proteins. There's a nice tutorial on the Hopkins site that you might want to view: The URL (below) is enormous, so you can also find it by Googling "remove peg zip tips".
http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CCgQFjAA&url=http%3A%2F%2Fwww.hopkinsmedicine.org%2Fpharmacology_molecular_sciences%2Fgrad_program%2Fcurrent_students%2Fcurriculums%2Fcourses%2F330_804%2520Mass%2520Spec%2520Course%2FMS2012_Lecture4_Basic_sample_preparation_Woods_handout.pdf&ei=JIssU5TtI4fwkQezq4HYBA&usg=AFQjCNEEe1Ghy7EQjq0DORuhVTtL1oM26g&sig2=OQr8kF3j-kiDD5_wl3l2HA&bvm=bv.62922401,d.eW0
Here's a shorter URL to a relevant site:
http://qb3.berkeley.edu/qb3/msf/guidelines.cfm
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