Novel targeted proteomics workflows can be highly multiplexed, allowing for parallel quantification of hundreds of proteins. This requires new approaches for the development and handling of optimized assay panels.

With the latest version of SpectroDive, Biognosys has introduced a workflow for quick set-up of optimized custom-made panels. With the panel set-up wizard, users can quickly assemble an optimized assay panel from the peptides that are most suited for quantification.

Additional features of SpectroDive include

  • MS1 support for PRM: Improved confidence in peak picking by using MS1 information
  • Live support: Analysis of MaxQuant.Live acquired data; inclusion list export in MaxQuant.Live compatible format
  • False discovery rate control: Increased confidence in peptide identification, specifically in larger panels
  • Pulsar integration: Fast and scalable library generation for assay development with Biognosys’ embedded search engine
  • Easier assay panel generation: intuitive and automated selection of the best-suited peptides for any target protein assay



Targeted proteomics is known to be the most flexible tool for the quantification of multiple candidate proteins in biological and biomedical applications. Often these assay panels are custom-made to address unique research questions. SpectroDive now supports the optimization of custom panels and subsequent data analysis.



Recently, Kelliher et al. (2018)[1] investigated the role of transcription factors in the periodic expression of genes and the subsequent production of proteins during the cell cycle. In their study, Kelliher et al. used budding yeast Saccharomyces cerevisiae as a model system and opted for targeted quantitative proteomics to understand transient protein expression patterns over the course of the cell-cycle. The researchers developed custom-made assays for 45 cell cycle proteins and were able to detect 31 unique proteins dynamically expressed during the cell cycle. To test SpectroDive’s ability to quantify the peptides of interest, Biognosys re-analyzed the published dataset.

Using SpectroDive's panel generation functionality and under default factory settings for analysis, we were able to reproduce the identical protein expression pattern over the cell cycle, reaching the same biological interpretation with a minimum amount of time and resources.


[1] Christina M. Kelliher, et al. Layers of regulation of cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae. Molecular Biology of the Cell. 2018, 29, 2644-2655.


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