libmprc

libmprc analyzes high-resolution mass spectrometry (MS) data to interpret 16O/18O-labeled peptide spectra and quantify isotopic incorporation for differential proteomics.

Key Features:

• RAAMS algorithm: Regression Analysis Applied to Mass Spectrometry (RAAMS) interprets complex spectra from 18O-labeled peptides without requiring chemical composition information from product ion spectra.
• Handling isotope patterns: Manages isotope patterns from unlabeled 18O(0), singly labeled 18O(1), doubly labeled 18O(2), and contributions from naturally occurring 13C and 15N.
• Variable label incorporation: Accounts for variable numbers of 18O atoms incorporated by enzymatic labeling and adjusts for enzyme substrate specificity during isotope exchange.
• Correction for residual abundance: Corrects for residual 18O(0) abundance in samples processed with a two-step digestion/labeling procedure to improve label incorporation estimates.
• Distinguishing isotopic species: Differentiates between pure 18O(0) and pure 18O(2) peptides when using impure H2 18O.
• High-speed processing: Operates on centroided peak lists and processed nine chromatograms (mean 1,168 spectra each, ~6,761 isotopic clusters) at about 45 seconds per chromatogram (average ~38 ms/spectrum), enabling real-time information-dependent MS/MS on a chromatographic time scale.

Scientific Applications:

• Differential proteomics and biomarker discovery: Quantifies differential protein expression and supports identification of diagnostic and prognostic biomarkers using 16O/18O labeling.
• Information-dependent MS/MS acquisition: Enables real-time, chromatographic time-scale information-dependent MS/MS analysis by providing rapid interpretation of centroided peak lists.

Methodology:

The RAAMS algorithm applies regression analysis to centroided peak lists to infer effective 18O incorporation rates without requiring prior chemical composition from product ion spectra.