Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF

In the ever lasting effort to boost the number of protein identified in MS-based proteomic experiments, it has become clear that Data Independent Analysis (DIA), combined with short gradients, has become a winning combination.

The steep development over the last years, have positioned DIA as an important acquisition strategy to generate record high identifications with short gradients on the Evosep One.

Join this webinar to explore how our customers have used Evosep One to generate record high IDs per minute for large-scale sample cohorts.

Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF

• Presenter: Patricia Skowronek (PhD student, DEPARTMENT OF PROTEOMICS AND SIGNAL TRANSDUCTION, MAX PLANCK INSTITUTE OF BIOCHEMISTRY)

Data-independent acquisition combined with parallel accumulation ‒ serial fragmentation (dia-PASEF) uses the correlation of the mass to charge ratio to the ion mobility separation in a Bruker timsTOF mass spectrometer.

In this webinar, I will elaborate on how to generate dia-PASEF methods with variable isolation widths and optimal isolation window placement. Additionally, I will demonstrate that these optimal methods applied to short Evosep gradients with project-specific in-depth libraries lead to a deep proteome and even deeper phosphoproteome. In only 21 min (60 per day/method), we quantify the HeLa cell proteome to a depth of more than 7,000 and the phosphoproteome to more than 10,000 distinct class I phosphosites. I will also show advanced visualization of these results in the AlphaMap and AlphaViz environment.