timsTOF Pro

timsTOF Pro - High sensitivity proteomics and phosphoproteomics

For most MS-based shotgun proteomics applications large sample amounts are needed to get deep proteome coverage and to identify the biologically relevant proteins. With the timsTOF Pro, a new depth in shotgun proteomics and phosphoproteomics can be achieved, due to the power of trapped ion mobility spectrometry and parallel accumulation serial fragmentation technologies even with low sample amounts.

New proteome coverage depths using low sample amounts
Same depth by using 1/10 of a common sample amount: Number of identified unique peptides and protein groups using only 200 ng of HeLa digest within a 90 min gradient.

In shotgun proteomics, sample amounts around 1 µg - 4 µg of a peptide mixture is loaded onto a column for further analysis in the mass spectrometer. This leads to extremely high costs in sample preparation, especially when analyzing a large cohort of samples. Moreover, in clinical proteomics the sample material that can be used is limited. With the timsTOF Pro, only small sample amounts (< 200 ng) are needed for deep shotgun proteomics. Using a 90 min gradient length more than 5,400 protein groups can be identified.

Deep proteome coverage with short gradients
Deep proteome coverage with short gradients (30 min, 60 min and 90 min) using 100 ng of HeLa digest

In a large number of shotgun proteomics experiments hundreds of samples needs to be measured. To avoid measurement time over months, short gradient measurements are required. The timsTOF Pro provides an extremely high speed without a loss in sensitivity making high-throughput measurements with a high proteome coverage possible.

High number of phosphopeptide identifications
Deep phosphoproteomics analysis: (A) Mobility distribution of phosphopeptide features in a 90 min gradient run. (B) Number of phosphopeptide IDs using 200 ng of a phosphopeptide mixture.

The analysis of phosphopeptides also profits from the TIMS separation provided in the timsTOF mass spectrometer. By using only 200 ng of a phosphopeptide mixture more than 14,000 unique phosphopeptides can be identified via a 90 min gradient.

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