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ITMSQ: A software tool for N‐ and C‐terminal fragment ion pairs based isobaric tandem mass spectrometry quantification
Authors:Li‐Qi Xie  Lei Zhang  Ai‐Ying Nie  Guo‐Quan Yan  Jun Yao  Yang Zhang  Peng‐Yuan Yang  Hao‐Jie Lu
Affiliation:1. Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China;2. Department of Chemistry, Fudan University, Shanghai, P. R. China
Abstract:Tandem MS (MS2) quantification using the series of N‐ and C‐terminal fragment ion pairs generated from isobaric‐labelled peptides was recently considered an accurate strategy in quantitative proteomics. However, the presence of multiplexed terminal fragment ion in MS2 spectra may reduce the efficiency of peptide identification, resulting in lower identification scores or even incorrect assignments. To address this issue, we developed a quantitative software tool, denoted isobaric tandem MS quantification (ITMSQ), to improve N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantification. A spectrum splitting module was designed to separate the MS2 spectra from different samples, increasing the accuracy of both identification and quantification. ITMSQ offers a convenient interface through which parameters can be changed along with the labelling method, and the result files and all of the intermediate files can be exported. We performed an analysis of in vivo terminal amino acid labelling labelled HeLa samples and found that the numbers of quantified proteins and peptides increased by 13.64 and 27.52% after spectrum splitting, respectively. In conclusion, ITMSQ provides an accurate and reliable quantitative solutionfor N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantitative methods.
Keywords:Bioinformatics  N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantification  Quantitative software tool  Spectrum splitting
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