Isotope pattern vector based tandem mass spectral data calibration for improved peptide and protein identification

Abstract

Tandem mass spectra contain noisy peaks which make peak picking for peptide identification difficult. Moreover, all spectral peaks can be shifted due to systematic measurement errors. In this paper, a novel use of an isotope pattern vector (IPV) is proposed for denoising and systematic measurement error prediction. By matching the experimental IPVs with the theoretical IPVs of candidate fragment ions, true ionic peaks can be identified. Furthermore, these identified experimental IPVs and their corresponding theoretical IPVs are used in an optimization process to predict the systematic measurement error associated with the target spectrum. In return, the subsequent spectral data calibration based on the predicted systematic measurement error enhances the data quality. We show that such an integrated denoising and calibration process leads to significantly improved peptide and protein identification. Different from the commonly employed chemical calibration methods, our IPV-based method is a purely computational method for individual spectra analysis and globally optimizes the use of spectral data.

Features-Based Deisotoping Method for Tandem Mass Spectra

“…Since the fundamental data used for peptide identification in tandem mass spectra (MS/MS) is the m / z values, charge states of fragment ions, their detection can directly influence the subsequent analysis of mass spectra including the peptide identification and quantification [2]. However, there are two difficulties during the process of detecting fragment ions: first, in some cases many real fragment ions have very low intensity that they can be removed as noise peaks by accident [3]. Numerous noisy peaks in tandem mass spectra can cause either false negative or false positive fragment ions.…”

Automatic annotation and visualization tool for mass spectrometry based glycomics

“…Isotope matching is a novel strategy to define the confidence of a signal peak according to the mass‐to‐charge ratio ( m/z ) and abundance distribution of its molecule isotopic cluster. It has significantly improved the identification of large molecules such as peptides and proteins . With the resolution power of MALDI‐TOF MS (>15,000), isotope peaks of different molecules can overlap each other.…”