Y.A.D.A.

Y.A.D.A. deconvolutes high-resolution mass spectrometry (MS/MS) spectra to remove isotopic peaks and charge states, link precursor monoisotopic peaks to tandem spectra, and account for co-fragmenting ion species to improve peptide identification in proteomics.

Key Features:

• Deisotoping and Decharging: Removes isotopic peaks and charge states from high-resolution mass spectra to identify peptide monoisotopic peaks.
• Linking Precursor Information: Associates precursor monoisotopic peak information with corresponding tandem (MS/MS) spectra to ensure correct precursor–fragment relationships.
• Handling Multiplexed Spectra: Accounts for co-fragmenting ion species in multiplexed spectra to improve accuracy of spectral interpretation.

Scientific Applications:

• Large-scale middle-down proteomics: Supports analysis of larger peptide fragments typical of middle-down workflows to provide broader protein sequence and structural information.
• Protein and post-translational modification identification: Facilitates identification of proteins and detection of post-translational modifications through improved precursor and fragment matching.

Methodology:

Performs deisotoping and decharging of high-resolution MS/MS spectra, links precursor monoisotopic peaks to tandem spectra, accounts for co-fragmenting ion species, and integrates with ProLuCID for peptide identification and DTASelect for data analysis.