4D Proteomics enabled Maxquant demonstrates unprecedented depth of coverage.

The recent adoption of trapped ion mobility into the sensitive and ultra-high resolution Bruker TOF platform, has created a remarkably powerful instrument. The timsTOF Pro directly provides an accurate measure of the collisional cross-sectional (CCS) area of every molecule being analysed and can drastically boost proteome coverage, quantification accuracy and dynamic range of analysed samples.

In a remarkable achievement, Prof. Jürgen Cox at the Max Plank Institute has continued to develop Maxquant, his freely available proteomics analysis software, over a 12-year period, whilst remaining ahead of the pack in the fast-paced mass spectrometry field. His recent publication in Molecular & Cellular Proteomics, which outlines arguably his biggest update since its release in 2008, now provides full support for the timsTOF Pro’s ion mobility data.

Using IonOpticks Aurora Series columns, he demonstrates the unprecedented identification depth of single shot HeLa runs and additionally, the quantitative precision using ground-truth seeded samples. Also, they clearly demonstrate that by making match-between-runs CCS-aware, this greatly reduces the missing value problem that plagues most other data dependant-based approaches.

Read the full paper
MaxQuant software for ion mobility enhanced shotgun proteomics.
Mol Cell Proteomics. 2020 Mar 10.
doi: https://doi.org/10.1074/mcp.TIR119.001720.
Prianichnikov N, Koch H, Koch S, Lubeck M, Heilig R, Brehmer S, Fischer R, Cox J.

Commentary by Andrew Webb, PhD.

About the author
Andrew has over 15 years’ experience in the field of chromatography and mass spectrometry. He is the lead innovator and inventor at IonOpticks, working closely with the team to test, refine and develop cutting edge techniques to support higher quality outputs and analytics from MS instruments. Andrew is also the Lab Head of the Walter and Eliza Hall Institute of Medical Research’s Proteomics Research Laboratory.