Shinyscreen integrates MetFrag, a widely used tool for in silico fragmentation and candidate structure ranking . A local CSV database version is typically employed to rank candidate structures based on MS2 information, with the current default use set to PubChemLite , . The local runs are much better option for large datasets, however the configuration can be complicated for databases with advanced scoring terms such as PubChemLite, and especially for data processing, with many MS2 inputs. Shinyscreen provides a MetFrag configuration interface (Figure ) that hides a lot of the complexity and runs several MetFrag instances in background to speed up the analysis. The integration is streamlined through an automated configuration interface, hiding the complexity of MetFrag setup. Shinyscreen has been primarily tested with local databases, such as PubChemLite, which is downloaded from Zenodo (RRID:SCR_004129) within the Docker image. PubChemLite includes additional fields, such as annotation count, patent count, and PubMed (RRID:SCR_004846) count, which can be utilized by MetFrag as additional scoring terms to aid in the ranking of candidate structures. The results are aggregated into summary tables, allowing users to efficiently review candidate structures and their associated scores for all the MS2 spectra that passed the quality control criteria. Finally, the object returned by a prescreen call contains the extracted data, associations between MS1 and MS2, as well as other data generated by Shinyscreen during the execution of the pipeline organised in multiple related tables. This is the most low-level of all the outputs, but offers the largest degree of flexibility in terms of further processing.