液相色谱与串联质谱联用(LC-MS/MS)技术是蛋白质组学研究中的常见方法.保留时间作为独立于质谱信息的参数已经被用于蛋白质的鉴定和定量工作中.在多肽鉴定领域,多肽的色谱保留时间预测与常规的二级串联质谱数据库搜索算法结合可以提高鉴定的可信度.鉴定的灵敏度也可以通过匹配多次LC-MS实验中具有相同精确质量数和保留时间的峰而提高.另一方面,由于色谱条件的微小改变即会引起保留时间的变化,因此对多次实验结果进行保留时间比对是进行非标记定量的不可或缺的步骤.另外,联合保留时间偏移和质量数信息还可以进行蛋白质翻译后修饰(post-translational modification,PTM)的鉴定.
Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has been one of the most popular approaches in proteome analysis.As an independent parameter to mass spectrometry information,peptide retention time has been utilized to facilitate protein identification and quantification.In the field of peptide identification,the prediction of the retention time combined with routine tandem mass spectrometry database searching methods could help improve the confidence of identification.The sensitivity of identification could also be improved by matching peaks with both the accurate mass and retention time in multiple aligned LC-MS runs.Meanwhile,because small changes of liquid chromatography conditions lead to variability in retention times unavoidably,retention time alignment is crucial to label-free quantification.Additionally,post-translational modifications (PTM) could be identified by combining retention time shifts and mass deviation information.
参考文献
| [1] | Guo D,Mant C T,Taneja A K,et al.J Chromatogr,1986,359:499 |
| [2] | Mant C T,Burke T W L,Black J A,et al.J Chromatogr,1988,458:193 |
| [3] | Browne C A,Bennett H P J,Solomon S.Anal Biochem,1982,124:201 |
| [4] | Meek J L.Proc Natl Acad Sci USA,1980,77:1632 |
| [5] | Meek J L,Rossetti Z L.J Chromatogr,1981,211:15 |
| [6] | Sakamoto Y,Kawakami N,Sasagawa T.J Chromatogr,1988,442:69 |
| [7] | Petritis K,Kangas L J,Ferguson P L,et al.Anal Chem,2003,75(5):1039 |
| [8] | Guo D,Mant C T,Taneja A K,et al.J Chromatogr,1986,359:518 |
| [9] | Krokhin O V,Craig R,Spicer V,et al.Mol Cell Proteomics,2004,3(9):908 |
| [10] | Kawakami T,Tateishi K,Yamano Y,et al.Proteomics,2005,5(4):856 |
| [11] | Petritis K,Kangas L J,Yan B,et al.Anal Chem,2006,78(14):5026 |
| [12] | Baczek T,Wiczling P,Marszall M,et al.J Proteome Res,2005,4(2):555 |
| [13] | Kaliszan R,Baczek T,Cimochowska A,et al.Proteomics,2005,5(2):409 |
| [14] | Salgado J C,Rapaport I,Asenjo J A.J Chromatogr A,2005,1098:44 |
| [15] | Salgado J C,Rapaport I,Asenjo J A.J Chromatogr A,2005,1075:133 |
| [16] | Salgado J C,Rapaport I,Asenjo J A.J Chromatogr A,2006,1107:120 |
| [17] | Salgado J C,Rapaport I,Asenjo J A.J Chromatogr A,2006,1107:110 |
| [18] | Old W M,Meyer-Arendt K,Aveline-Wolf L,et al.Mol Cell Proteomics,2005,4(10):1487 |
| [19] | Li X J,Yi E C,Kemp C J,et al.Mol Cell Proteomics,2005,4(9):1328 |
| [20] | Vandenbogaert M,Li-Thiao-Te S,Kaltenbach H M,et al.Proteomics,2008,8(4):650 |
| [21] | Bylund D,Danielsson R,Malmquist G,et al.J Chromatogr A,2002,961(2):237 |
| [22] | Christin C,Smilde A K,Hoefsloot H C,et al.Anal Chem,2008,80(18):7012 |
| [23] | Eilers P H.Anal Chem,2004,76(2):404 |
| [24] | Listgarten J,Neal R M,Roweis S T,et al.Bioinformatics,2007,23(2):e198 |
| [25] | Mueller L N,Rinner O,Schmidt A,et al.Proteomics,2007,7(19):3470 |
| [26] | Fischer B,Grossmann J,Roth V,et al.Bioinformatics,2006,22(14):e132 |
| [27] | Fischer B,Roth V,Buhmann J M.BMC Bioinformatics,2007,8(Suppl 10):S4 |
| [28] | Podwojski K,Fritsch A,Chamrad D C,et al.Bioinformatics,2009,25(6):758 |
| [29] | Strittmatter E F,Ferguson PL,Tang K,et al.J Am Soc Mass Spectrom,2003,14(9):980 |
| [30] | Zimmer J S,Monroe M E,Qian W J,et al.Mass Spectrom Rev,2006,25(3):450 |
| [31] | Kiebel G R,Auberry K J,Jaitly N,et al.Proteomics,2006,6(6):1783 |
| [32] | Adkins J N,Monroe M E,Auberry K J,et al.Proteomics,2005,5(13):3454 |
| [33] | Manes N P,Estep R D,Mottaz H M,et al.J Proteome Res,2008,7(3):960 |
| [34] | Monroe M E,Tolic N,Jaitly N,et al.Bioinformatics,2007,23(15):2021 |
| [35] | Jaffe J D,Mani D R,Leptos K C,et al.Mol Cell Proteomics,2006,5(10):1927 |
| [36] | Strittmatter E F,Kangas L J,Petritis K,et al.J Proteome Res,2004,3(4):760 |
| [37] | Shen Y,Kim J,Strittmatter E F,et al.Proteomics,2005,5(15):4034 |
| [38] | Pfeifer N,Leinenbach A,Huber C G,et al.J Proteome Res,2009,8(8):4109 |
| [39] | Sun W,Zhang L,Yang R,et al.Rapid Commun Mass Spectrom,2009,23(1):109 |
| [40] | Savitski M M,Nielsen M L,Zubarev R A.Mol Cell Proteomics,2006,5(5):935 |
| [41] | Dasari S,Wilmarth P A,Rustvold D L,et al.J Proteome Res,2007,6(9):3819 |
| [42] | Fu Y,Jia W,Lu Z,et al.BMC Bioinformatics,2009,10(Suppl 1):S50 |
| [43] | Kim J,Petritis K,Shen Y,et al.J Chromatogr A,2007,1172(1):9 |
| [44] | Radulovic D,Jelveh S,Ryu S,et al.Mol Cell Proteomics,2004,3(10):984 |
| [45] | Lommen A.Anal Chem,2009,81(8):3079 |
| [46] | Prakash A,Mallick P,Whiteaker J,et al.Mol Cell Proteomics,2006,5(3):423 |
| [47] | Wong J W,Sullivan M J,Cagney G.Brief Bioinform,2008,9(2):156 |
| [48] | America A H,Cordewener J H.Proteomics,2008,8(4):731 |
- 下载量()
- 访问量()
- 您的评分：
-
10%
-
20%
-
30%
-
40%
-
50%