Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison

Abstract

Here, we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison (). Mass spectra under investigation can be either provided manually by the user (table format) or automatically retrieved from online repositories supporting access to spectral data via the universal spectrum identifier (USI), or requested from other resources and services implementing a newly designed REST interface. As a proof of principle, we implemented such an interface in ProteomicsDB thereby allowing the retrieval of spectra acquired within the ProteomeTools project or real-time prediction of tandem mass spectra from the deep learning framework Prosit. Annotated mirror spectrum plots can be exported from the USE as editable scalable high-quality vector graphics. The USE was designed and implemented with minimal external dependencies allowing local usage and integration into other web sites ().

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

“…The public availability and direct access to mass spectra data create the opportunity for scientists to directly assess whether, e.g., a novel peptide evidence, PTM, or amino acid variant (SAAV) are supported by a good-quality and well-annotated mass spectrum ( 19 , 37 ). PSI and PX partners have recently created a novel mechanism to uniquely resolve each mass spectrum in public proteomics resources.…”

iProX in 2021: connecting proteomics data sharing with big data

“…The ability to refer to specific spectra of high importance and cite data in published manuscripts was done by implementing a new standardized Universal Spectrum Identifier (USI) proposed by PX ( 14 , 15 ). The USI is a multi-part key separated by colon characters; for example, mzspec:PXD006512:CNHPP_HCC_LC_profiling_L006_P_F1:scan:64442:VADALTNAVAHVDDMPNALSALSDLHAHK/3.…”

ProteomicsDB: toward a FAIR open-source resource for life-science research

“…The second example of a vastly improved visualization is the spectrum viewer (Figure 5 ) that is a modified version of the Universal Spectrum Explorer ( 23 ). It is accessible by selecting a specific peptide of interest in either the Peptide MS/MS or Reference Peptides view that show a table with the observed or synthetic/predicted reference peptides for the selected protein.…”