ProMEX protein mass spectral library

ProMEX protein mass spectral library provides a curated MS/MS mass spectral library of tryptic peptides for plant proteomics to enable protein identification and functional interpretation of cell type-specific and sub-cellular proteomes.

Key Features:

• Mass spectral content: Contains experimental MS/MS spectra of tryptic peptides for protein identification.
• Instrumentation: Spectra were generated using liquid chromatography coupled to ion trap mass spectrometry (LC-ITMS).
• Species coverage: Includes data from Arabidopsis thaliana, Medicago truncatula, Chlamydomonas reinhardtii, Lotus japonicus, Lotus corniculatus, Phaseolus vulgaris, Lycopersicon esculentum, Solanum tuberosum, Nicotiana tabacum, Glycine max, Zea mays, Bradyrhizobium japonicum, and Sinorhizobium meliloti.
• Cell type and sub-cellular specificity: Provides experimental MS/MS-based information for cell type-specific and sub-cellular proteomes.
• Integration across molecular levels: Links spectral data to metabolites, pathways, and transcripts for multi-omic context.
• Protein-level linking: Each peptide spectrum is linked at the protein level to relevant external databases.
• Pathway mapping: Spectral sequence information is connected to metabolic and signaling pathways and visualized through pathway maps.
• Spectral matching application: Enables identification of proteins in uncharacterized samples by comparison of observed spectra against the annotated library.

Scientific Applications:

• Protein identification: Identification of proteins in uncharacterized plant samples by MS/MS spectral matching to the library.
• Cell-type proteomics: Analysis of cell type-specific proteomes using experimentally derived spectra.
• Sub-cellular proteomics: Characterization of sub-cellular proteomes through annotated spectral references.
• Pathway and functional interpretation: Mapping peptides to metabolic and signaling pathways to support functional annotation and interpretation.
• Comparative proteomics: Comparative analysis of proteomes across the listed plant and symbiotic bacterial species.

Methodology:

Experimental MS/MS spectra generated by LC-ITMS are annotated and linked at the protein level to external databases and connected to metabolic and signaling pathways, enabling spectrum-to-protein matching and pathway visualization.