The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics.

ABSTRACT: The combination of qualitative analysis with label-free quantification has greatly facilitated the throughput and flexibility of novel proteomic techniques. However, such methods rely heavily on robust and reproducible sample preparation procedures. Here, we benchmark a selection of in gel, on filter, and in solution digestion workflows for their application in label-free proteomics. Each procedure was associated with differing advantages and disadvantages. The in gel methods interrogated were cost effective, but were limited in throughput and digest efficiency. Filter-aided sample preparations facilitated reasonable processing times and yielded a balanced representation of membrane proteins, but led to a high signal variation in quantification experiments. Two in solution digest protocols

SUBMITTER: Vowinckel J 

PROVIDER: S-EPMC3983906 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature