M-PER, T-PER, B-PER, RIPA, and Bio-Rad 2D-rehydration buffers are commercially available and versatile total protein extraction reagents. PER reagents from Thermo differ dependent on your target host (tissue, mammalian, bacterial...Besides in-house developed buffers/mixtures can also be used for this purpose. But since the whole proteome is targeted, the detergent ingredient is needed and these all have surfactant-type additives to promote protein recovery. In general, mixtures of non-ionic and ionic detergents are the best for wide-spectrum extraction. The main bottleneck is the removal of detergent after extraction due to the MS being highly sensitive against these agents. Dramatic signal decrease caused by the ion suppression effect of the detergents may be seen. You should remove the detergent prior to MS detection by using an effective micro-proteomic workflow. There are many alternatives to do this such as adding chaotropic agents and decomposing the detergent micelles to perform ultrafiltration (e.g. FASP, S-TRAP procedures), precipitation of the proteome (acetone precipitation, TCA precipitation, look for 2D-clean up kits, etc...), IEX resin application, and most effectively acid hydrolysis of the detergent. Look for MS-compatible detergents such as The commonly used including ionic (ProteaseMAX (PM), RapiGest (RG), PPS Silent Surfactant (PPS)) and non-ionic (Octyl β-D-glucopyranoside (OG), n-Dodecyl β-D-maltoside (DDM), and Digitonin (DGT))...You may prepare a buffer system including selected MS-compatible detergent and can get rid of any surfactant contaminants by acid addition followed by centrifugation or by ethyl acetate extraction.

Good luck, İEA...

Thanks a lot doctor

Hello, there is no one clear answer as a single solution for all types of protein separation.

Tetrahydrofuran is used with aqueous mixtures to dissolve a wide range of proteinsIsopropanol which useful for dissolving very hydrophobic proteins

Acetone is used as an additive but absorbs in the range of many amino acid residues.

Methanol/Ethanol is rarely used for protein/peptide analysis (but cost-effective).

Acetonitrile is a favored mobile phase solvent that can dissolve most proteins with good performance.

Water is the most polar but should not be used alone in HPLC as it can desorb the hydrocarbon chains in the column.

Karen A. Darbinyan thanks a lot doctor