timsTOF Pro for the Parallel Accumulation Serial Fragmentation (PASEF) Acquisition Method

How can we dig deeper into the proteome? Mass spectrometry (MS)-based proteomics has become influential in technology for the identification and quantification of thousands of proteins. Nevertheless, the coverage of complete proteomes of current mass spectrometers still presents some difficulty due to the reduced speed, sensitivity and resolution of existing models.

The timsTOF Pro can provide extremely high speed and high sensitivity using the Parallel Accumulation Serial Fragmentation (PASEF) acquisition process. Using low sample amounts, this can reach new depths in shotgun proteomics and phosphoproteomics.

PASEF is an ideal fit for shotgun proteomics. The timsTOF Pro is powered by PASEF and offers an impressive sequencing speed at faster than 100 Hz, without losing sensitivity or resolution. This capability is accomplished by coordinating the quadrupole isolation mass window with the elution time of the specific peptide packages from the TIMS funnel.

With the dual TIMS technology, near 100% duty cycle for high sensitivity and high-speed shotgun proteomics can now be achieved. The unique, new design permits accumulation of ions in the front section, while ions in the rear section are serially released depending on their ion mobility. This process is called Parallel Accumulation Serial Fragmentation, or PASEF.

A new design of the timsTOF means superior robustness. The new orthogonal design of the ion optics has resulted in shotgun proteomics performance now being uncompromised over large sample cohorts, as required for proteomics in clinical research.

MaxQuant/Perseus and PEAKS Studio enabled data processing uses industry leading software. It is an open-file data format that allows researchers to work directly with raw data.

MaxQuant has been altered to manage 4-dimensional features in the space covered by retention time, ion mobility, mass, and signal intensity, which give an advantage to the identification and quantification of peptides, proteins, and posttranslational modifications. Additionally, PEAKS Studio combines de novo sequencing with traditional database searches and is adjusted for processing timsTOF raw data.

We now know that the peptide mixtures are still extremely complex when analyzing them in two dimensions (retention time and m/z). Adding one more dimension should in principle get us a long way ahead. In addition to the additional dimension of separation, the timsTOF Pro gives us extremely high speed and sensitivity to get deeper into the proteome and using less sample material.

Prof. Dr. Matthias Mann, Director Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Germany.