MaSS-Simulator is capable of simulating MS/MS spectra for LC-MS/MS based proteomics experiments. Our recently introduced MaSS-Simulator is capable of simulating highly accurate MS/MS spectra for LC-MS/MS based proteomics experiments. It provides great degree of control over the simulation by providing multiple configurable parameters. MaSS-Simulator offers a platform to assess and mark the limitations of MS-proteomics algorithms by testing them against a curated set of data and whole range of parameters. A complete evaluation report of an algorithm using all possible parametric verifications will provide a much deeper insight to the performance of of a given algorithm. Such evaluation will solve the reproducibility issues that are frequently faced in proteomics algorithm development. Testing of tools using such curated data set for which parameters (e.g. peptide coverage, S/N ratio etc.) can be carefully explored will rigorously evaluate the proteomics algorithms. In general, one can vary (to a practical degree) the size of the peptide, the coverage, the S/N ratios of the spectra and addition of PTM’s in the simulated spectra created for benchmarking. Such benchmarks when available for algorithms will inform proteomics practitioners which tool will work specifically for their data. Further, such reproducible evaluation of proteomics algorithms will enable method developers to endorse algorithms with confidence and reliability. Such an approach will also be helpful for the users, who can evaluate their dataset and cross-reference its properties with the algorithm’s evaluation report to conclude if the given algorithm will serve their purpose or if it will be able to achieve the required level of performance.

Status

The method development for this work is complete