19 1 2007 2 Chinese Bulletin of Life Sciences Vol. 19, No. 1 Feb., 2007 1004-0374(2007)01-0097-07 410081 Q51; R73 A Separation and identification progress in cancer comparative proteomics LI Xuanwen, CHEN Ping, ZHANG Lijun, LIANG Songping* (The Laboratory of Protein Chemistry and Proteomics, College of Life Sciences, Hunan Normal University, Changsha 410081, China) Abstract: With the human genome sequence now determined, the field of cancer research is moving beyond genomics to proteomics. The comparative strategies involving in the cancer proteomic research have been developed, including cancer sample preparation, proteins or peptides separation, protein identification, bioinformatics, protein quantification and so on. All these will accelerate the identification of cancer markers that could be important in early detection, diagnosis and monitoring efficacy of treatment, and also the development of protein-based, cancer-specific targets, which have a great effect on cancer medicine. In this review, we focused on the sample separation and identification progress in cancer comparative proteomics. Key words: cancer; comparative proteomics; two-dimensional electrophoresis; liquid chromatography; quantification proteomics [1-2] DNA RNA Medline 1997 2006-03-03 2006-06-26 973 (2001 CB5120) (1980 ) (1946 ) * E-mail: liangsp@hunnu.edu.cn
98 0.12% 0.17% Medline 16% [3] 1 1.1 30 (two dimensional electrophoresis, 2DE) (isoform) [4] [5] 3 MALDI-TOF ESI-Q- TOF PCR Sypro Ruby 2DE 2DE (fluorescence two-dimensional differential gel electrophoresis, DIGE) (Cy2 Cy3 Cy5) 50 µg 3, [6-7] 8 mol/l urea, 2 mol/l Thiourea, 65 mmol/l DTT, 0.5% Pharmalytes ph 3 10, 0.5 mmol/l PMSF, 4 % w/v CHAPS, 1% NP-40 / (4 1) 0.1 mol/l [8] 1.2 (liquid isoelectric focusing) (chromatofocusing) (non-porous silica reverse-phase high-performance liquid chromatography, NPS-RP-
99 HPLC) (electrospray ionization time-of-flight mass spectrometry, ESI-TOF- MS) (matrix-assisted laser desorption/ionization time of flight mass spectrometry, MALDI-TOF MS) Lubman MALDI-TOF-MS 12 000 75 000 37 [9] 22 [10] Yates (shotgun) MudPIT (multidi-mensional protein identification technology) 2 2.1 [11] 1000 5000 bottom-up FT-MS top-down [12] (biomarker) (surface-enhanced laser desorption/ionization time of flight mass spectrometry, SELDI-TOF-MS) MALDI-TOF MS ( ) [13] MALDI-TOF 10 000 (imaging mass spectromety) MALDI 2 000 200000 500 1000 [14-15] 2.2
100 ( Sypro Ruby) ( DIGE) ( ) [16] (score) (unique peptides) (coverage) PAI (protein abundance index) (spectrum count) (extracted ion current, XIC) Andersen [17] empai (exponentially modified PAI) [18] LCMS [19] [16] (in vivo labeling) (in vitro labeling) 2.2.1 Oda [20] ( 15 N 14 N ) 2DE MS (MS/MS) Ong Mann [16] SILAC (stable isotope labeling by amino acids in cell culture) Gronborg [21] SILAC [21] Krijgsveld [22] ( ) Ishihama [23] (culture-derived isotope tags, CDIT) 122 2.2.2 N C Gygi [24] Cys ICAT (isotope-coded affinity tags) Cys ICAT ICAT ICAT [25] (cleavable ICAT, cicat) Sebastiano [26] Cys ICAI [16,27] Stewart [28] (cisplatin) ICAT 121 ICAT 500 (<7 )
101 Cys Lys Trp [29-30] ICAT ICAT ICAT Cys N Lys NIT (N-terminal isotope-encoded tagging) [31] 4 itraq (isobaric tags for relative and absolute quantitation) [32] MS/MS Keshamouni [33] itraq TGF-β - 51 Gerber [34] absolute quantification (AQUA) C C [35] ; (enzymatic labeling) 18 O 16 O C Zang [36] LCM 16 O/ 18 O 1 76 2.3 [37] (de novo sequencing) icat itraq ABI (Applied Biosystem) ProQuant ProteinProspector Matthias Mann MSquant (differentially expressed protein database, DEPD) [38] (http://protchem. hunnu.edu.cn:8080/depd/index.jsp) 150 3 000 3
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