S‑Trap, an Ultrafast Sample-Preparation Approach for Shotgun Proteomics

The
success of shotgun proteomic analysis depends largely on how
samples are prepared. Current approaches (such as those that are gel-,
solution-, or filter-based), although being extensively employed in
the field, are time-consuming and less effective with respect to the
repetitive sample processing, recovery, and overall yield. As an alternative,
the suspension trapping (S-Trap) filter has been commercially available
very recently in the format of a single or 96-well filter plate. In
contrast to the conventional filter-aided sample preparation (FASP)
approach, which utilizes a molecular weight cut-off (MWCO) membrane
as the filter and requires hours of processing before digestion-ready
proteins can be obtained, the S-Trap employs a three-dimensional porous
material as filter media and traps particulate protein suspensions
with the subsequent depletion of interfering substances and in-filter
digestion. Due to the large (submicron) pore size, each centrifugation
cycle of the S-Trap filter only takes 1 min, which significantly reduces
the total processing time from approximately 3 h by FASP to less than
15 min, suggesting an ultrafast sample-preparation approach for shotgun
proteomics. Here, we comprehensively evaluate the performance of the
individual S-Trap filter and 96-well filter plate in the context of
global protein identification and quantitation using whole-cell lysate
and clinically relevant sputum samples.