Bekker-Jensen D B, Bernhardt O M, Hogrebe A, Martinez-Val A, Verbeke L, Gandhi T, Kelstrup C D, Reiter L, Jesper V, and Olsen J V. Nature Communications
In this article, we present a novel phosphoproteomics workflow combining data independent acquisition (DIA), short LC-MS/MS methods, and an accurate site localization algorithm implemented in Spectronaut. This procedure outperforms state-of-the-art DDA phosphoproteomics approaches in all benchmarked aspects including throughput, sensitivity, identification performance, phosphosite discovery capabilities, and localization accuracy. Our DIA approach provided a higher number of known regulated sites than DDA, showing the potential of applying our pipeline to real biological studies.
Huang T, Bruderer R, Muntel J, Xuan Y, Vitek O, and Reiter L. Molecular & Cellular Proteomics
In this publication, we report a novel statistical procedure that takes advantage of the two independent quantitative spaces available in DIA data, i.e., MS1 and MS2, for the detection of differentially abundant proteins. The use of these two levels improves precision and reduces the effect of the interferences. This new approach was applied to six sets of controlled mixtures, showing a consistent improvement in the ability to find differential changes at the protein level.
Muntel J, Gandhi T, Verbeke L, Bernhardt OM, Treiber T, Bruderer R, and Reiter L. Molecular Omics
In this study we showed how improvements in chromatography and data analysis can push the proteome coverage in human tissue beyond 10,000 proteins, spanning six orders of magnitude in dynamic range. Such remarkable coverage was achieved using Hybrid Libraries, a novel approach that combines the depth of resource libraries with the high precision of directDIA. Thousands of these proteins could be linked to the hallmarks of testis cancer.
Bruderer R, Muntel J, Müller S, Bernhardt OM, Gandhi T, Cominetti O, Macron C, Carayol J, Rinner O, Astrup A, Saris WHM, Hager J, Valsesia A, Dayon L, and Reiter L. Molecular & Cellular Proteomics
We have established a robust capillary-flow DIA platform capable of measuring a large number of clinical samples in a fast and reproducible manner. The platform allowed the acquisition of 31 plasma proteomes per day, and a total of 1508 samples from the dietary intervention study DiOGenes measured on a single column. Our workflow revealed distinct biological reactions to weight loss and maintenance, and the comparison to independent studies showed the robustness for potential biomarker discovery.
Muntel J, Kirkpatrick J, Bruderer R, Huang T, Vitek O, Ori A, and Reiter L. Journal of Proteome Research
Here we compare the performance of the two most popular quantitative workflows employed in discovery proteomics, label-free DIA, and isobaric-labeled TMT 10-plex. Workflows were tested on the same spike-in samples, with matched instrument time and reciprocal assessment in two facilities. Both workflows delivered high proteome coverage with low missing values at the protein level. While TMT performed slightly better in coverage and quantitative precision, DIA showed higher scalability and quantitative accuracy.