蛋白质组学研究中傅立叶变换离子回旋共振质谱数据采集方法的比较

Comparison of Acquisition Methods for Linear Quadrupole Ion Trap-Fourier Transform Cyclotron Resonance Mass Spectrometer in Shotgun Proteomics

探讨了线性离子阱-傅立叶变换离子回旋共振质谱(LTQ-FT)的数据采集模式对蛋白质组鉴定结果的影响,比较和分析了针对不同复杂程度样本的最佳采集模式。对于α-乳清蛋白4种标准蛋白质酶切肽段混合物的简单体系,在傅立叶变换离子回旋共振腔中选3个最强母离子进行选择离子监测扫描后,再实施二级碎裂的方法(SIM3)得到的肽段覆盖率,分别是直接选10个最强母离子进行二级碎裂(FT10)方法得到的肽段覆盖率的1.5～1.9倍。另外,对酵母蛋白酶切肽段混合物的复杂体系鉴定时,只采集双电荷和三电荷母离子进行二级扫描的方法(FT10_23)比单电荷、双电荷和三电荷都采集的方法(FT10_123)得到的图谱鉴定成功率提高64.1%。实验还对不同数据采集模式下图谱的特点进行了考察。本研究表明,针对不同复杂程度的样本,应采取不同的质谱数据采集方法。

Mass spectrometers with high accuracy and high resolution,such as FT-ICR have been widely used in proteomic studies in recent years.To compare the effectiveness of various data acquisition methods in shotgun proteomics,we used a linear quadrupole ion trap-Fourier transform ion cyclotron resonance（LTQ-FT） mass spectrometer to analyze two peptide mixtures with different complexity by different acquisition strategies.For the peptide mixture of four standard proteins,sequence coverage obtained by selected ion monitoring scans（SIM3） was 1.51 to 1.9 fold than that by survey MS scans（FT10）.For the peptide mixture of yeast proteins,the strategy of only acquiring double and triple charged ions（FT_23） got 64.1% more MS/MS spectra identifications than that of total acquisition of single,double and triple charge ions（FT_123）.Finally,the features of the spectrum obtained with different acquisition mode were also compared.In conclusion,optimal acquisition methods are needed for the samples with different complexity.