We have isolated extracellular vesicles (EVs) from plasma samples and are preparing them for LC-MS/MS-based proteomics at a core facility. However, I am uncertain whether EV lysis is necessary before trypsin digestion. The literature is inconsistent: some studies report lysis with SDS, while others do not mention lysis at all. What is the general consensus on this? If lysis is required, what detergent would be suitable without interfering with mass spectrometry?
Extracellular vesicle (EV) lysis is recommended before trypsin digestion for comprehensive proteomics, typically using detergents like SDS, which should be removed using methods like cyclodextrins or SP3 beads. Suitable detergents include SDS and sodium deoxycholate, with careful removal to avoid interference in mass spectrometry.
Thank you for your response! I've also come across studies using the S-Trap kit for detergent cleanup.
Would you mind sharing a protocol for SDS-based EV lysis, including details on SDS concentration, incubation time, and any other key parameters? I’d really appreciate it.
Certainly detergent based lysis is necessary. Choose SDS concentration based on MS tolerance level. Talk to company's tech department what is the maximum amount of SDS you can use. Alternatively you can rupture your EV by sonication.
Good luck.
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