Parallel accumulation - serial fragmentation combined with data-independent acquisition (diaPASEF)

The timsTOF Pro with diaPASEF enables deeper proteome coverage in a single 4D shotgun proteomics experiment, with highly reproducible qualitative and quantitative results – making it a near-ideal mass analyzer for proteomics.

Abstract

Data-independent acquisition (DIA) workflows have gained in popularity as they overcome the issue of stochastic selection of peptide precursors encountered in typical datadependent approaches (DDA).

The success of DIA relies on key instrumental capabilities, namely: resolution, sensitivity, accuracy and dynamic range uncompromised by a fast-spectral acquisition rate (>40 Hz) demanded by DIA. Trapped ion mobility spectrometry adds an additional dimension for separation of complex proteomics samples. In addition, the collisional cross section (CCS) term allows for unbiased alignment of precursor and fragment information. 

In this application note, we combine Parallel Accumulation Serial Fragmentation (PASEF) with a DIA approach, called  diaPASEF, to investigate its potential for the in-depth analysis of complex proteomics samples. In brief, more than 7,000 proteins could be reliably identified and quantified at a false discovery rate of 1% in each of triplicate samples consisting of a HeLa protein digest. For each injection 200 ng total peptide mass was loaded on column and 120 minute LC-MS runs were applied. Fragment ion-based quantification was very reproducible with a median coefficient of variation (COV) of 10%.