Key Parameters of the
Benchmark Datasets
In total 9 datasets:
- 8* were published 1, 2, 3, 4, 5-6, 7-8
- Gradient lengths between 90 and 180 minutes
- 7 ILQ datasets (TMT, TMTpro)
- 2 datasets with MS2 quantification
- 5 datasets withMS3 quantification
- 10 – 24 fractions
- 2 non-ILQ datasets
*Not published: reacquisition of dataset #8 with MS2 instead of MS3 quantification
With advanced deep learning models for indexed retention time (iRT) and fragmentation prediction, SpectroMine achieves unsurpassed proteome coverage.
We tested a range of software products using harmonized search space settings, protein inference, and False Discovery Rate (FDR) control. The results for datasets with and without isobaric labeling demonstrate that SpectroMine provides the most identifications and fastest processing times for a wide range of DDA experiments (see Figure).
SpectroMine lets you take full advantage of the latest instrumentation from all major vendors, including FAIMS Pro and PASEF ion mobility technologies, delivering state-of-the-art identification performance and short processing times.
At the same time, SpectroMine provides an intuitive interface to ensure data integrity and enables the sharing of data. FDR is rigorously controlled at peptide-spectrum match (PSM), peptide and protein levels, and a wide range of quality control visualizations are also available. To keep your results organized, they are saved in search archives, giving you full access to annotated raw data, and making it easy to share with anyone through the free SpectroMine Viewer.
