Spectronaut was featured in a recent Nature Biotechnology paper entitled “A multicenter study benchmarks software tools for label-free proteome quantification”.
The aim of the paper was to develop a tool that will benchmark different proteomics software solutions used for analyzing data sets obtained with data independent acquisition mass spectrometry (DIA or SWATH). Specifically, the newly developed tool called LFQbench calculates metrics of precision and accuracy in label-free quantitative MS, and reports the identification performance, robustness and specificity of each software solution.
The authors evaluated five of the most widely used software methods for processing DIA/SWATH data OpenSWATH, SWATH2.0, Skyline, Spectronaut and DIA-Umpire and used Biognosys iRT Kit for retention time normalization of all of the samples.
Results show that the Spectronaut software performed very well, achieving low CVs between runs, while showing excellent sensitivity, and together with OpenSWATH also produced the lowest numbers of false identification reports. Compared to other solutions, the Spectronaut analysis was mainly carried out with software default settings. This means that Spectronaut users can get excellent results with no or little optimization. Another distinctive Spectronaut advantage is the speed of the analysis and low hardware requirements (though not reported in the paper), which we have presented in a recent technical note (download here).
While in the publication the Spectronaut version 7 was used for evaluation, Spectronaut version 9 is meanwhile available and Spectronaut version 10 will be launched in a couple of months.
Overall, the results of the paper confirmed that the DIA/SWATH workflows will get you great proteome coverage, reproducibility, and precise quantitation. As a pioneer in the field Ruedi Aebersold said it in a recent GenomeWeb interview “As soon as you are in the range of 6’000, 7’000, 8’000 proteins credibly and quickly measured, you have a terrific tool for biology and clinical research”.