Data reduction of isotope-resolved LC-MS spectra

Data reduction of isotope-resolved LC-MS spectra

MOTIVATION Data reduction of liquid chromatography-mass spectrometry (LC-MS) spectra can be a challenge due to the inherent complexity of biological samples, noise and non-flat baseline. We present a new algorithm, LCMS-2D, for reliable data reduction of LC-MS proteomics data. RESULTS LCMS-2D can reliably reduce LC-MS spectra with multiple scans to a list of elution peaks, and subsequently to...

A new protocol of analyzing isotope-coded affinity tag data from high-resolution LC-MS spectrometry

Isotope-coded affinity tags (ICAT) is a labeling technique that provides insights into quantitative molecular changes. In this paper, we propose a new protocol to identify and analyze ICAT labeled peak pairs in high-resolution LC-MS data. Our major contributions are: (1) we use isotope distance constraint, ICAT distance constraint, and LC-span constraint to identify ICAT labeled peak pairs and ...

Visualization of LC‐MS/MS proteomics data in MaxQuant

Modern software platforms enable the analysis of shotgun proteomics data in an automated fashion resulting in high quality identification and quantification results. Additional understanding of the underlying data can be gained with the help of advanced visualization tools that allow for easy navigation through large LC-MS/MS datasets potentially consisting of terabytes of raw data. The updated...

Computational Analysis of LC-MS/MS Data for Metabolite Identification

Metabolomics aims at the detection and quantitation of metabolites within a biological system. As the most direct representation of phenotypic changes, metabolomics is an important component in system biology research. Recent development on highresolution, high-accuracy mass spectrometers enables the simultaneous study of hundreds or even thousands of metabolites in one experiment. Liquid chrom...

Data reduction strategies, uncertainty assessment and resolution of LA–(MC–)ICP–MS isotope data