ITMSQ: A software tool for N- and C-terminal fragment ion pairs based isobaric tandem mass spectrometry quantification.
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 solution for N- and C-terminal fragment ion pairs based isobaric MS2 quantitative methods.
Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China.
Li-Qi
LQ
Xie
Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China.
Lei
L
Zhang
Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China.
Ai-Ying
AY
Nie
Department of Chemistry, Fudan University, Shanghai, P. R. China.
Guo-Quan
GQ
Yan
Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China.
Jun
J
Yao
Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China.
Yang
Y
Zhang
Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China.|Department of Chemistry, Fudan University, Shanghai, P. R. China.
Peng-Yuan
PY
Yang
Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China.|Department of Chemistry, Fudan University, Shanghai, P. R. China.
Hao-Jie
HJ
Lu
D006367:HeLa Cells; D006801:Humans; D007477:Ions; D013058:Mass Spectrometry / Q000295:instrumentation* / Q000379:methods; D010455:Peptides / Q000032:analysis*; D020543:Proteome / Q000032:analysis*; D012984:Software
D007477:Ions; D010455:Peptides; D020543:Proteome
Bioinformatics; N- and C-terminal fragment ion pairs based isobaric MS2 quantification; Quantitative software tool; Spectrum splitting