1.建立基于富集指数的蛋白质组学数据分析方法研究分泌蛋白质组—小鼠树突状肉瘤细胞分泌蛋白质组 2.正常人尿蛋白质组动态变化过程中稳定表达蛋白质组作为潜在的生物标志物资源
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摘要
细胞产生的分泌蛋白是一类功能上非常重要的蛋白。真正的分泌蛋白样品是很难得到,它经常被细胞内蛋白质或环境中的蛋白质所污染。
我们建立了一种依靠蛋白质组学数据分析判断分泌蛋白质样品是否合格及分辨真正的分泌蛋白质的方法。阳性鉴定的谱图数用于蛋白质半定量。分别对分泌蛋白质样品和胞内可溶性蛋白质样品进行质谱分析,选择高丰度的分泌蛋白质作为标志蛋白,求它们在两个样品中谱图数的百分比,计算样品富集指数(theenrichment index of sample,EIS),以此评价分泌蛋白质样品的质量。用合格谱图数的百分比计算每个蛋白质在两个样品中的权重,定义分泌蛋白富集指数(theenrichment index for protein,EIP)为:在两种样品中相应蛋白的权重比值。用EIP值鉴定分泌蛋白质,同时参考信号肽预测和swiss-prot解释。
新方法能够鉴定“非经典分泌途径”产生的分泌蛋白,也可以排除来源于死细胞的带有信号肽的污染蛋白。谱图数计量方法的优点在于对设备测试要求不高、没有同位素污染和使用方便。
对于无血清条件培养基中体外培养的小鼠树突状肉瘤细胞(dendritic cellsarcoma,DCS),采用SCX-RP-MS/MS策略分析了培养基中的DCS产生的分泌蛋白质组。两个分泌蛋白质样品的EIS分别为75.4和84.65。共得到141个阳性鉴定的蛋白,73个认为是分泌蛋白质。33个蛋白质是信号肽预测和swiss-prot解释均为阳性的,10个蛋白质是信号肽预测阳性或swiss-prot解释阳性的,30个蛋白质是信号肽预测和swiss-prot解释均为阴性的,还有待于进一步验证。
对于新发现的30个潜在的、swiss-prot解释和信号肽预测都是阴性的蛋白质,我们用“非经典途径”分泌蛋白质的预测服务器(SecretomeP server和ProP server)进行了分析,其中分别有12个蛋白质(占40%)和15个蛋白质(占50%)的蛋白质是阳性鉴定,其中有5个蛋白质是两种方法都被鉴定的。我们还和其他细胞产生的exosome的结果进行了比较,有11个蛋白质在exosome中存在。相比小鼠树突状细胞DC1系产生的exosome的结果,有6个蛋白质是相同的。这些数据证明,这30个蛋白质也很有可能是DCS细胞产生的分泌蛋白质。
尿液作为人体的一种正常体液,其中包含的蛋白质成分反映了肾脏及泌尿生殖道的生理和病理状态。尿蛋白质组研究已经取得了很多成果。但是,尿蛋白质组的动态研究还未很好地开展,尚不能得到不同尿样和不同时刻尿的蛋白质组数据。因此在不同尿样的比较分析中,尤其是正常尿液和病理尿液的比较中,很难断定差异蛋白质源于尿样本身,还是尿蛋白质的正常变化。
本文用1DLC策略和谱图数半定量的方法分析了正常人汇集尿样和个体尿样中蛋白质组的动态变化。五种汇集尿样是由六名健康的志愿者(三男三女)提供,分别收集了志愿者即日内的五种尿样,即:晨尿、清晨第二次尿、水利尿、随机尿和24小时尿,汇集后进行分析。另外,收集志愿者第0天和第7天的晨尿,用于研究跨天、个体间、性别间的尿差异。分析了汇集尿样分析的利弊。
研究表明,尿蛋白质组在不同种类尿样中,50%以上的蛋白质可以被共同鉴定,其中40%以上的蛋白质的谱图数变化小于2倍。基于六名志愿者的小样本数据,同一个体跨天的晨尿之间差异小于同性别不同个体间尿蛋白质组差异,异性个体之间的稳定性最差。其中部分在尿中稳定表达的蛋白质被报道与疾病相关。我们提供了不同条件下,尿样中稳定存在的蛋白质成分,在这些蛋白质中,任何定性和定量的显著性改变,都很有可能成为潜在的疾病诊断的生物标志物。
Secretory proteins are important for organisms to maintain the normal biological processes. They are important sources for discovering the candidate tumour biomarkers with clinical significance. However, secretory protein samples are usually polluted by cytosolic proteins from dead cells or other proteins from the environment.
We propose that a good secretory protein sample should be enriched with known secretory proteins, and a secretory protein should be enriched in the secretory protein sample compare to soluble cell lysate. A method based on enrichment index for both quality control of the sample and identification of secretory proteins was developed. Positive identifications of the proteins were subjected to quantification by spectral count. Enrichment index of the sample (EIS) and the enrichment index for protein (EIP) were set up by comparing proteins identified from secretory protein sample and soluble cell lysate sample. The quality of secretory protein sample can be evaluated with EIS. EIP was used to identify the secretory proteins.
This method can identify novel secretory proteins from unconventional pathways. It can also exclude the contaminating proteins with signal peptide from dead cells. The method is simple to perform. No complicated procedures were used other than common LC-MS/MS. There was no isotopes pollution in whole operation.
We analyzed the secretory proteins of mouse dendritic cell sarcoma (DCS) cell line cultured in protein-free media with insulin. The sample's EISs were 75.4 and 84.65. 141 proteins were detected, of which 73 proteins were significantly enriched and identified as secretory proteins in this study. In these 73 proteins, 33 proteins were both swiss-prot annotated and signal peptide predicted as secretory proteins. 10 proteins were identified by either signal peptide prediction or swiss-prot annotation, 30 proteins were previously unidentified as secretory proteins.
The 30 novel potential secretory proteins were analyzed by SecretomeP server and ProP server which can predict the mammalian secretory protein targeted to the non-classical secretory pathway. 11 (36.7%) and 15 (50%) were predicted as secretory proteins by SecretomeP and ProP, respectively. 5 proteins were positive by both methods. Compared with the protein component of exosome in other studies, 11 proteins were in exosome in other studies. Six proteins were found in exosome from mice dendritic cells line DC1. These references provided supporting evidences for these 30 proteins as secretory proteins.
Human urinary proteome analysis was a convenient approach to clarify the disease processes affecting the kidney and the urogenital tract. Many potential biomarkers have been identified by differential urinary proteome analyses. However, the urinary proteome variation has not been very well studied; it is hard to conclude whether those potential biomarkers come from differences of biological states studied or just from normal proteome variation.
In this paper 1DLC/MS and spectral count as the semi-quantitative analysis were used to study human urinary proteome variation by pooled and individual urine samples. Five types of pooled urinary samples (first morning void, second morning void, excessive water drinking void, random void and 24 hour void) collected in one day from six volunteers (three males and three females) were used to analyze the urinary proteome overall intra-day variations. Six pair first morning urine collected on day 0 and day 7 from above six volunteers were utilized to study inter-day, inter-individual and inter-gender variations. We also discussed the advantages and disadvantages of pooling the samples.
The intra-day, inter-day, inter-individual, inter-gender variation results showed 50% of proteins were found in various samples and more than 40% of these proteins whose spectral count variation was less than two times. Based on the proteomics data of urine from six volunteers, the intra-day variation is less than the inter-individual variation. Inter-gender stability is the worst. Some of them have been reported as potential disease biomarkers. The data presented herein should provide a pool of stable urinary proteins at different conditions. Any significant qualitative and quantitative changes of those stable proteins may have greater chances to serve as potential urinary biomarkers.
我们建立了一种依靠蛋白质组学数据分析判断分泌蛋白质样品是否合格及分辨真正的分泌蛋白质的方法。阳性鉴定的谱图数用于蛋白质半定量。分别对分泌蛋白质样品和胞内可溶性蛋白质样品进行质谱分析,选择高丰度的分泌蛋白质作为标志蛋白,求它们在两个样品中谱图数的百分比,计算样品富集指数(theenrichment index of sample,EIS),以此评价分泌蛋白质样品的质量。用合格谱图数的百分比计算每个蛋白质在两个样品中的权重,定义分泌蛋白富集指数(theenrichment index for protein,EIP)为:在两种样品中相应蛋白的权重比值。用EIP值鉴定分泌蛋白质,同时参考信号肽预测和swiss-prot解释。
新方法能够鉴定“非经典分泌途径”产生的分泌蛋白,也可以排除来源于死细胞的带有信号肽的污染蛋白。谱图数计量方法的优点在于对设备测试要求不高、没有同位素污染和使用方便。
对于无血清条件培养基中体外培养的小鼠树突状肉瘤细胞(dendritic cellsarcoma,DCS),采用SCX-RP-MS/MS策略分析了培养基中的DCS产生的分泌蛋白质组。两个分泌蛋白质样品的EIS分别为75.4和84.65。共得到141个阳性鉴定的蛋白,73个认为是分泌蛋白质。33个蛋白质是信号肽预测和swiss-prot解释均为阳性的,10个蛋白质是信号肽预测阳性或swiss-prot解释阳性的,30个蛋白质是信号肽预测和swiss-prot解释均为阴性的,还有待于进一步验证。
对于新发现的30个潜在的、swiss-prot解释和信号肽预测都是阴性的蛋白质,我们用“非经典途径”分泌蛋白质的预测服务器(SecretomeP server和ProP server)进行了分析,其中分别有12个蛋白质(占40%)和15个蛋白质(占50%)的蛋白质是阳性鉴定,其中有5个蛋白质是两种方法都被鉴定的。我们还和其他细胞产生的exosome的结果进行了比较,有11个蛋白质在exosome中存在。相比小鼠树突状细胞DC1系产生的exosome的结果,有6个蛋白质是相同的。这些数据证明,这30个蛋白质也很有可能是DCS细胞产生的分泌蛋白质。
尿液作为人体的一种正常体液,其中包含的蛋白质成分反映了肾脏及泌尿生殖道的生理和病理状态。尿蛋白质组研究已经取得了很多成果。但是,尿蛋白质组的动态研究还未很好地开展,尚不能得到不同尿样和不同时刻尿的蛋白质组数据。因此在不同尿样的比较分析中,尤其是正常尿液和病理尿液的比较中,很难断定差异蛋白质源于尿样本身,还是尿蛋白质的正常变化。
本文用1DLC策略和谱图数半定量的方法分析了正常人汇集尿样和个体尿样中蛋白质组的动态变化。五种汇集尿样是由六名健康的志愿者(三男三女)提供,分别收集了志愿者即日内的五种尿样,即:晨尿、清晨第二次尿、水利尿、随机尿和24小时尿,汇集后进行分析。另外,收集志愿者第0天和第7天的晨尿,用于研究跨天、个体间、性别间的尿差异。分析了汇集尿样分析的利弊。
研究表明,尿蛋白质组在不同种类尿样中,50%以上的蛋白质可以被共同鉴定,其中40%以上的蛋白质的谱图数变化小于2倍。基于六名志愿者的小样本数据,同一个体跨天的晨尿之间差异小于同性别不同个体间尿蛋白质组差异,异性个体之间的稳定性最差。其中部分在尿中稳定表达的蛋白质被报道与疾病相关。我们提供了不同条件下,尿样中稳定存在的蛋白质成分,在这些蛋白质中,任何定性和定量的显著性改变,都很有可能成为潜在的疾病诊断的生物标志物。
Secretory proteins are important for organisms to maintain the normal biological processes. They are important sources for discovering the candidate tumour biomarkers with clinical significance. However, secretory protein samples are usually polluted by cytosolic proteins from dead cells or other proteins from the environment.
We propose that a good secretory protein sample should be enriched with known secretory proteins, and a secretory protein should be enriched in the secretory protein sample compare to soluble cell lysate. A method based on enrichment index for both quality control of the sample and identification of secretory proteins was developed. Positive identifications of the proteins were subjected to quantification by spectral count. Enrichment index of the sample (EIS) and the enrichment index for protein (EIP) were set up by comparing proteins identified from secretory protein sample and soluble cell lysate sample. The quality of secretory protein sample can be evaluated with EIS. EIP was used to identify the secretory proteins.
This method can identify novel secretory proteins from unconventional pathways. It can also exclude the contaminating proteins with signal peptide from dead cells. The method is simple to perform. No complicated procedures were used other than common LC-MS/MS. There was no isotopes pollution in whole operation.
We analyzed the secretory proteins of mouse dendritic cell sarcoma (DCS) cell line cultured in protein-free media with insulin. The sample's EISs were 75.4 and 84.65. 141 proteins were detected, of which 73 proteins were significantly enriched and identified as secretory proteins in this study. In these 73 proteins, 33 proteins were both swiss-prot annotated and signal peptide predicted as secretory proteins. 10 proteins were identified by either signal peptide prediction or swiss-prot annotation, 30 proteins were previously unidentified as secretory proteins.
The 30 novel potential secretory proteins were analyzed by SecretomeP server and ProP server which can predict the mammalian secretory protein targeted to the non-classical secretory pathway. 11 (36.7%) and 15 (50%) were predicted as secretory proteins by SecretomeP and ProP, respectively. 5 proteins were positive by both methods. Compared with the protein component of exosome in other studies, 11 proteins were in exosome in other studies. Six proteins were found in exosome from mice dendritic cells line DC1. These references provided supporting evidences for these 30 proteins as secretory proteins.
Human urinary proteome analysis was a convenient approach to clarify the disease processes affecting the kidney and the urogenital tract. Many potential biomarkers have been identified by differential urinary proteome analyses. However, the urinary proteome variation has not been very well studied; it is hard to conclude whether those potential biomarkers come from differences of biological states studied or just from normal proteome variation.
In this paper 1DLC/MS and spectral count as the semi-quantitative analysis were used to study human urinary proteome variation by pooled and individual urine samples. Five types of pooled urinary samples (first morning void, second morning void, excessive water drinking void, random void and 24 hour void) collected in one day from six volunteers (three males and three females) were used to analyze the urinary proteome overall intra-day variations. Six pair first morning urine collected on day 0 and day 7 from above six volunteers were utilized to study inter-day, inter-individual and inter-gender variations. We also discussed the advantages and disadvantages of pooling the samples.
The intra-day, inter-day, inter-individual, inter-gender variation results showed 50% of proteins were found in various samples and more than 40% of these proteins whose spectral count variation was less than two times. Based on the proteomics data of urine from six volunteers, the intra-day variation is less than the inter-individual variation. Inter-gender stability is the worst. Some of them have been reported as potential disease biomarkers. The data presented herein should provide a pool of stable urinary proteins at different conditions. Any significant qualitative and quantitative changes of those stable proteins may have greater chances to serve as potential urinary biomarkers.
引文
1. Wilkins MR, Sanchez JC, Gooley AA, et al. (1995) Progress with proteome projects: why all proteins expressed by a gonome should be identified and how to do it. Biotech &Genetic Engineering Rev, 13, 19-50.
2. Florens, L., Liu, X., Wang. Y. et al. (2004) Proteomics approach reveals novel proteins on the surface of malaria-infected erythrocytes, Mol Biochem Parasitol 135, 1-11.
3. Knudsen, G. M., Medzihradszky, K. F., Lim, K. C. Hansell, E. & McKerrow, J. H. (2005) Proteomic analysis of Schistosoma mansoni cercarial secretions, Mol Cell Proteomics, 4, 1862-75.
4. Trost, M., Wehmhoner, D., Karst, U. et al. (2005) Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species, Proteomics, 5, 1544-57.
5. Volmer, M. W., Stuhler, K., Zapatka, M. et al. (2005) Differential proteome analysis of conditioned media to detect Smad4 regulated secreted biomarkers in colon cancer, Proteomics, 5, 2587-601.
6. Xiao, T., Ying, W, Li, L. et al. (2005) An approach to studying lung cancer-related proteins in human blood, Mol Cell Proteomics, 4, 1480-6.
7. Kobayashi, Y, Yamamoto, K., Saido, T. et al. (1990) Identification of calcium-activated neutral protease as a processing enzyme of human interleukin 1 alpha, Proc Natl Acad Sci U S A, 87, 5548-52.
8. Chen, X., Cushman, S. W., Pannell, L. K. & Hess, S. (2005) Quantitative proteomic analysis of the secretory proteins from rat adipose cells using a 2D liquid chromatography-MS/MS approach, J Proteome Res, 4, 570-7.
9. Mbeunkui, F., Fodstad, O. & Pannell, L. K. (2006) Secretory protein enrichment and analysis: an optimized approach applied on cancer cell lines using 2D LC-MS/MS, J Proteome Res, 5, 899-906.
10. Pellitteri-Hahn, M. C, Warren, M. C, Didier, D. N. et al. (2006) Improved mass spectrometric proteomic profiling of the secretome of rat vascular endothelial cells, J Proteome Res, 5, 2861-4.
11. Tjalsma, H., Stover, A. G, Driks, A. et al. (2000) Conserved serine and histidine residues are critical for activity of the ER-type signal peptidase SipW of Bacillus subtilis, J Biol Chem, 275, 25102-8.
12. Glaser, P., Frangeul, L., Buchrieser, C. et al. (2001) Comparative genomics of Listeria species, Science, 294, 849-52.
13. Nielsen, H., Brunak, S. & von Heijne, G. (1999) Machine learning approaches for the prediction of signal peptides and other protein sorting signals, Protein Eng, 12, 3-9.
14. Lamonica, J. M., Wagner, M., Eschenbrenner, M. et al. (2005) Comparative secretome analyses of three Bacillus anthracis strains with variant plasmid contents, Infect Immun, 73, 3646-58.
15. Menne, K. M., Hermjakob, H. & Apweiler, R. (2000) A comparison of signal sequence prediction methods using a test set of signal peptides, Bioinformatics. 16, 741-2.
16. Zhou, S., Liu, Y., Weng, J. et al. (2005) Expression profiles of mouse dendritic cell sarcoma are similar to those of hematopoietic stem cells or progenitors by clustering and principal component analyses, Biochem Biophys Res Commun, 331, 194-202.
17. Monda, L., Warnke, R. & Rosai, J. (1986) A primary lymph node malignancy with features suggestive of dendritic reticulum cell differentiation. A report of 4 cases, Am J Pathol, 122, 562-72.
18. Shia, J., Chen, W., Tang, L. H. et al. (2006) Extranodal follicular dendritic cell sarcoma: clinical, pathologic, and histogenetic characteristics of an underrecognized disease entity, Virchows Arch, 449, 148-58.
19. Delahunty, C. & Yates, J. R., 3rd (2005) Protein identification using 2D-LC-MS/MS, Methods, 35, 248-55.
20. Washburn, M. P., Wolters, D. & Yates, J. R., 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology, Nat Biotechnol, 19, 242-7.
21. Sun, W., Li, F., Wang, J., Zheng, D. & Gao, Y. (2004) AMASS: software for automatically validating the quality of MS/MS spectrum from SEQUEST results, Mol Cell Proteomics, 3, 1194-9.
22. Bendtsen, J. D., Nielsen, H., von Heijne, G. & Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0, J Mol Biol, 340, 783-95.
23. Chang, H. C, Samaniego, F., Nair, B. C, Buonaguro, L. & Ensoli, B. (1997) HIV-1 Tat protein exits from cells via a leaderless secretory pathway and binds to extracellular matrix-associated heparan sulfate proteoglycans through its basic region, Aids, 11, 1421-31.
24. Watanabe, N. & Kobayashi, Y. (1994) Selective release of a processed form of interleukin 1 alpha, Cytokine, 6, 597-601.
25. Hamon, Y, Luciani, M. F., Becq, F. et al. (1997) Interleukin-1 beta secretion is impaired by inhibitors of the Atp binding cassette transporter, ABC1, Blood, 90,2911-5.
26. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, J Mol Biol, 305, 567-80.
27. Wang, P., Mariman, E., Keijer, J. et al. (2004) Profiling of the secreted proteins during 3T3-L1 adipocyte differentiation leads to the identification of novel adipokines, Cell Mol Life Sci, 61, 2405-17.
28. Bendtsen, J. D., Jensen, L. J., Blom, N., Von Heijne, G. & Brunak, S. (2004) Feature-based prediction of non-classical and leaderless protein secretion, Protein Eng Des Sel, 17, 349-56.
29. Duckert, P., Brunak, S. & Blom, N. (2004) Prediction of proprotein convertase cleavage sites, Protein Eng Des Sel, 17, 107-12.
30. Lancaster, G. I. & Febbraio, M. A. (2005) Exosome-dependent trafficking of HSP70: a novel secretory pathway for cellular stress proteins, J Biol Chem, 280, 23349-55.
31. Clayton, A., Turkes. A.. Dewitt, S. et al. (2004) Adhesion and signaling by B cell-derived exosomes: the role of integrins, Faseb J, 18, 977-9.
32. Liegeois, S., Benedetto, A., Garnier, J. M., Schwab, Y. & Labouesse. M. (2006) The VO-ATPase mediates apical secretion of exosomes containing Hedgehog-related proteins in Caenorhabditis elegans, J Cell Biol, 173, 949-61.
33. Hardy, K. M., Hoffman, E. A., Gonzalez, P., McKay, B. S. & Stamer. W. D. (2005) Extracellular trafficking of myocilin in human trabecular meshwork cells, J Biol Chem, 280, 28917-26.
34. Foster, L. J., De Hoog, C. L. & Mann, M. (2003) Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors, Proc Natl Acad Sci U S A, 100, 5813-8.
35. Fevrier, B., Vilette, D., Laude, H. & Raposo, G (2005) Exosomes: a bubble ride for prions?, Traffic, 6, 10-7.
36. Bard, M. P., Hegmans, J. P., Hemmes, A. et al. (2004) Proteomic analysis of exosomes isolated from human malignant pleural effusions, Am J Respir Cell Mol Biol, 31,114-21.
37. van Niel, G, Raposo, G, Candalh, C. et al. (2001) Intestinal epithelial cells secrete exosome-like vesicles, Gastroenterology, 121, 337-49.
38. Morciano, M., Burre, J., Corvey, C. et al. (2005) Immunoisolation of two synaptic vesicle pools from synaptosomes: a proteomics analysis, J Neurochem, 95, 1732-45.
39. Barile, M., Pisitkun, T., Yu, M. J. et al. (2005) Large scale protein identification in intracellular aquaporin-2 vesicles from renal inner medullary collecting duct, Mol Cell Proteomics, 4, 1095-106.
40. Brunner, Y, Coute, Y, Iezzi, M. et al. (2007) Proteomic analysis of insulin secretory granules, Mol Cell Proteomics.
41. Casey, T. M., Meade, J. L. & Hewitt, E. W. (2007) Organelle Proteomics: Identification of the Exocytic Machinery Associated with the Natural Killer Cell Secretory Lysosome, Mol Cell Proteomics, 6, 767-780.
42. Segura, E., Amigorena, S. & Thery, C. (2005) Mature dendritic cells secrete exosomes with strong ability to induce antigen-specific effector immune responses, Blood Cells Mol Dis, 35, 89-93.
43. Segura, E., Nicco, C, Lombard, B. et al. (2005) ICAM-1 on exosomes from mature dendritic cells is critical for efficient naive T-cell priming, Blood, 106, 216-23.
44. Vipond, C, Suker, J., Jones, C. et al. (2006) Proteomic analysis of a meningococcal outer membrane vesicle vaccine prepared from the group B strain NZ98/254, Proteomics, 6, 3400-13.
45. Silver, R. B. & Pappas, G. D. (2005) Secretion without membrane fusion: porocytosis, Anat Rec B New Anat, 282, 18-37.
46. Thery, C, Regnault, A., Garin, J. et al. (1999) Molecular characterization of dendritic cell-derived exosomes. Selective accumulation of the heat shock protein hsc73, J Cell Biol, 147, 599-610.
47. Sahaf, B. & Rosen, A. (2000) Secretion of 10-kDa and 12-kDa thioredoxin species from blood monocvtes and transformed leukocytes,Antioxid Redox Signal,2,717-26.
48.高进,刘玉琴,段德义,李存玺(1997)《小鼠树突状肉瘤细胞系的建立和鉴定及其与转移相关特性的研究》中国肿瘤生物治疗杂志4(4):310-312。
49.刘玉琴,顾蓓,高进,段德义,赵雪梅(2000)《转移性癌细胞体外水解酶表达及影响因素的作用》中国医学科学院学报22(2):149-153。
50.ABOUFARHA,K.M.,MENHEERE,P.P.,NIEMAN,F.H.,ARENDS,J.W.&JANKNEGT,R.A.(1992) Value of serum laminin P1 as a diagnostic and monitoring parameter in transitional cell carcinoma of the bladder,Urol Int,49,130-6.
51.GOLDBERG,I.,DAVIDSON,B.,LERNER-GEVA,L.et al.(1998) Expression of extracellular matrix proteins in cervical squamous cell carcinoma—a clinicopathological study,J Clin Pathol,51,781-5.
52.AUSTYN,J.M.(1993) The dendritic cell system and anti-tumour immunity,In Vivo,7,193-201.
53.CAVANAGH,L.L.,SAAL,R.J.,GRIMMETT,K.L.& THOMAS,R.(1998)Proliferation in monocyte-derived dendritic cell cultures is caused by progenitor cells capable of myeloid differentiation,Blood,92,1598-607.
54.OKI,M.,ANDO,K.,HAG[HARA,M.et al.(2001) Efficient lentiviral transduction of human cord blood CD34(+) ceils followed by their expansion and differentiation into dendritic cells,Exp Hematol,29,1210-7.
55.LIN,C.L.,SURI,R.M.,RAHDON,R.A.,AUSTYN,J.M.& ROAKE,J.A.(1998)Dendritic cell chemotaxis and transendothelial migration are induced by distinct chemokines and are regulated on maturation,Eur J Immunol,28,4114-22.
56.JOHNSTONE,R.M.,ADAM,M.,HAMMOND,J.R.,ORR,L.& TURBIDE,C.(1987)Vesicle formation during reticulocyte maturation.Association of plasma membrane activities with released vesicles(exosomes),J Biol Chem,262,9412-20.
57.THERY,C.,BOUSSAC,M.,VERON,P.et al.(2001) Proteomic analysis of dendritic cell-derived exosomes:a secreted subcellular compartment distinct from apoptotic vesicles,J Immunol,166,7309-18.
58.RITTLING,S.R.& CHAMBERS,A.F.(2004) Role of osteopontin in tumour progression,Br J Cancer,90,1877-81.
1. Washburn, M. P., Wolters, D., and Yates, J. R., 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19, 242-247.
2. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17, 994-999.
3. Zhou, H., Ranish, J. A., Watts, J. D., and Aebersold, R. (2002) Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat Biotechnol 20, 512-515.
4. Unlu, M., Morgan, M E., and Minden, J. S. (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18, 2071-2077.
5. States, D. J., Omenn, G. S., Blackwell, T. W., Fermin, D., Eng, J., Speicher, D. W., and Hanash, S. M. (2006) Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol 24, 333-338.
6. Thongboonkerd, V, McLeish, K. R., Arthur, J. M., and Klein, J. B. (2002) Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int 62, 1461-1469.
7. Pieper, R., Gatlin, C. L., McGrath, A. M., Makusky, A. J., Mondal, M., Seonarain, M., Field, E., Schatz, C. R., Estock, M. A., Ahmed, N., Anderson, N. G, and Steiner, S. (2004) Characterization of the human urinary proteome: a method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots. Proteomics 4, 1159-1174.
8.Oh, J., Pyo, J. H., Jo, E. H., Hwang, S. I., Kang, S. C, Jung, J. H., Park, E. K., Kim, S. Y, Choi, J. Y, and Lim, J. (2004) Establishment of a near-standard two-dimensional human urine proteomic map. Proteomics 4, 3485-3497.
9. Khan, A., and Packer, N. H. (2006) Simple urinary sample preparation for proteomic analysis. J Proteome Res 5, 2824-2838.
10. Spahr, C. S., Davis, M. T., McGinley, M. D, Robinson, J. H., Bures, E. J., Beierle, J., Mort, J., Courchesne, P. L., Chen, K., Wahl, R. C, Yu, W., Luethy, R., and Patterson, S. D. (2001) Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest. Proteomics 1, 93-107.
11. Davis, M. T., Spahr, C. S., McGinley, M. D., Robinson, J. H., Bures, E. J., Beierle, J., Mort, J., Yu, W., Luethy, R., and Patterson, S. D. (2001) Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. II. Limitations of complex mixture analyses. Proteomics 1, 108-117.
12. Sun, W., Li, R, Wu, S., Wang, X., Zheng, D., Wang, J., and Gao, Y. (2005) Human urine proteome analysis by three separation approaches. Proteomics 5, 4994-5001.
13. Castagna, A., Cecconi, D., Sennels, L., Rappsilber, J., Guerrier, L., Fortis, R, Boschetti, E., Lomas, L., and Righetti, P. G. (2005) Exploring the hidden human urinary proteome via ligand library beads. J Proteome Res 4, 1917-1930.
14. Adachi, J., Kumar, C, Zhang, Y, Olsen, J. V., and Mann, M. (2006) The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol 7, R80.
15. Wang, L., Li, R, Sun, W., Wu, S., Wang, X., Zhang, L., Zheng, D., Wang, J., and Gao, Y (2006) Concanavalin A-captured glycoproteins in healthy human urine. Mol Cell Proteomics 5, 560-562.
16. Vlahou. A., Schellhammer, P. F., Mendrinos, S., Patel, K., Kondylis, R I.. Gong. L. Nasim, S., and Wright Jr, G. L., Jr. (2001) Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. Am J Pathol 158, 1491-1502.
17. Rogers, M. A., Clarke, P., Noble, J., Munro, N. P., Paul, A., Selby, P. J.. and Banks, R. E. (2003) Proteomic profiling of urinary proteins in renal cancer by surface enhanced laser desorption ionization and neural-network analysis: identification of key issues affecting potential clinical utility. Cancer Res 63, 6971-6983.
18. Schaub, S., Rush, D., Wilkins, J., Gibson, I. W., Weiler, T., Sangster, K., Nicolle, L, Karpinski, M., Jeffery, J., and Nickerson, P. (2004) Proteomic-based detection of urine proteins associated with acute renal allograft rejection. J Am Soc Nephrol 15, 219-227.
19. Cutillas, P. R., Norden, A. G, Cramer, R., Burlingame, A. L., and Unwin, R. J. (2003) Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome. Clin Sci (Lond) 104, 483-490.
20. Pang, J. X., Ginanni, N., Dongre, A. R., Hefta, S. A., and Opitek, G. J. (2002) Biomarker discovery in urine by proteomics. J Proteome Res 1, 161-169.
21. Tantipaiboonwong, P., Sinchaikul, S., Sriyam, S., Phutrakul, S., and Chen, S. T. (2005) Different techniques for urinary protein analysis of normal and lung cancer patients. Proteomics 5, 1140-1149.
22. Nedelkov, D. (2005) Population proteomics: addressing protein diversity in humans. Expert Rev Proteomics 2, 315-324.
23. Nedelkov, D., Kiernan, U. A., Niederkofler, E. E., Tubbs, K. A., and Nelson, R. W. (2006) Population proteomics: the concept, attributes, and potential for cancer biomarker research. Mol Cell Proteomics 5, 1811-1818.
24. Hu, Y., Malone, J. P., Fagan, A. M, Townsend, R. R., and Holtzman, D. M. (2005) Comparative proteomic analysis of intra- and interindividual variation in human cerebrospinal fluid. Mol Cell Proteomics 4, 2000-2009.
25. Molloy, M. P., Brzezinski, E. E., Hang, J., McDowell, M. T., and VanBogelen, R. A. (2003) Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 3, 1912-1919.
26. Zhang, X., Guo, Y., Song, Y, Sun, W., Yu, C, Zhao, X., Wang, H., Jiang, H., Li, Y, Qian, X., Jiang, Y, and He, F. (2006) Proteomic analysis of individual variation in normal livers of human beings using difference gel electrophoresis. Proteomics 6, 5260-5268.
27. Thongboonkerd, V., Chutipongtanate, S., and Kanlaya, R. (2006) Systematic evaluation of sample preparation methods for gel-based human urinary proteomics: quantity, quality, and variability. J Proteome Res 5, 183-191.
28. Russo, L. M., Bakris, G. L., and Comper, W. D. (2002) Renal handling of albumin: a critical review of basic concepts and perspective. Am J Kidney Dis 39, 899-919.
29. Zhou, H., Yuen, P. S., Pisitkun, T., Gonzales, P. A., Yasuda, H., Dear, J. W., Gross, P., Knepper, M. A., and Star, R. A. (2006) Collection, storage, preservation, and normalization of human urinary exosomes for biomarker discovery. Kidney Int 69, 1471-1476.
30. Bradford, M. M (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72, 248-254.
31. Sun, W., Gao, S., Wang, L., Chen, Y, Wu, S., Wang, X., Zheng, D., and Gao, Y. (2006) Microwave-assisted protein preparation and enzymatic digestion in proteomics. Mol Cell Proteomics 5, 769-776.
32. Kersey, P. J., Duarte, J., Williams. A., Karavidopoulou, Y, Birney, E., and Apweiler, R. (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics 4, 1985-1988.
33. Wolters, D. A., Washburn, M. P., and Yates, J. R., 3rd (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 73, 5683-5690.
34. Peng, J, Elias, J. E., Thoreen, C. C, Licklider, L. J., and Gygi, S. P. (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res 2, 43-50.
35. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., and Yates, J. R., 3rd (1999) Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 17, 676-682.
36. Sun, W., Wu, S., Wang, X., Zheng, D., and Gao, Y. (2004) A systematical analysis of tryptic peptide identification with reverse phase liquid chromatography and electrospray ion trap mass spectrometry. Genomics Proteomics Bioinformatics 2, 174-183.
37. Sun, W., Wu, S., Wang, X., Zheng, D., and Gao, Y. (2005) An analysis of protein abundance suppression in data dependent liquid chromatography and tandem mass spectrometry with tryptic peptide mixtures of five known proteins. Eur J Mass Spectrom (Chichester, Eng) 11, 575-580.
38. Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G., Mendoza, A., Sevinsky, J. R., Resing, K. A., and Ahn, N. G. (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4, 1487-1502.
39. Clarke, W., Silverman, B. C., Zhang, Z., Chan, D. W., Klein, A. S., and Molmenti, E. P. (2003) Characterization of renal allograft rejection by urinary proteomic analysis. Ann Surg 237, 660-664; discussion 664-665.
40. Voshol, H., Brendlen, N., Muller, D., Inverardi, B., Augustin, A., Pally, C., Wieczorek, G., Morris, R. E., Raulf, F., and van Oostrum, J. (2005) Evaluation of biomarker discovery approaches to detect protein biomarkers of acute renal aliograft rejection. J Proteome Res 4, 1192-1199.
41. Hirawa, N., Uehara, Y., Ikeda, T., Gomi, T., Hamano, K., Totsuka, Y., Yamakado, M., Takagi, M., Eguchi, N., Oda, H., Seiki, K., Nakajima, H., and Urade, Y. (2001) Urinary prostaglandin D synthase (beta-trace) excretion increases in the early stage of diabetes mellitus. Nephron 87, 321-327.
42. Hirawa, N., Uehara, Y., Yamakado, M., Toya, Y., Gomi, T., Ikeda, T., Eguchi, Y., Takagi, M., Oda, H., Seiki, K., Urade, Y, and Umemura, S. (2002) Lipocalin-type prostaglandin d synthase in essential hypertension. Hypertension 39, 449-454.
43. Jain, S., Rajput, A., Kumar, Y, Uppuluri, N., Arvind, A. S., and Tatu, U. (2005) Proteomic analysis of urinary protein markers for accurate prediction of diabetic kidney disorder. J Assoc Physicians India 53, 513-520.
44. Jung, K., Pergande, M., Schimke, E., Ratzmann, K. P., and Ilius, A. (1988) Urinary enzymes and low-molecular-mass proteins as indicators of diabetic nephropathy. Clin Chem 34, 544-547.
45. Utsunomiya, T., Ogawa, K., Yoshinaga, K., Ohta, M., Yamashita, K., Mimori, K., Inoue, H., Ezaki, T., Yoshikawa, Y, and Mori, M. (2005) Clinicopathologic and prognostic values of apolipoprotein D alterations in hepatocellular carcinoma. Int J Cancer 116, 105-109.
46. Rodriguez, J. C., Diaz, M., Gonzalez, L. O., Sanchez, J., Sanchez, M. T., Merino, A. M., and Vizoso, F. (2000) Apolipoprotein D expression in benign and malignant prostate tissues. Int J Surg Investig 2, 319-326.
47. Zolg, W. (2006) The proteomic search for diagnostic biomarkers: lost in translation? Mol Cell Proteomics 5,1720-1726.
1. Wilkins MR, Sanchez JC, Gooley AA. et al. Progress with proteome projects: why all proteins expressed by a gonome should be identified and how to do it. Biotech &Genetic Engineering Rev, 1995, 13, 19-50.
2. Erica Golemis, Protein-protein interactions—a molecular cloning manual Gold Spring Harbor Laborary Press, 2001.
3. DOUBLE-AGENTS? Cross-Linking Reagents—Selection Guide Pierce
4. Alexander Leitner, Wolfgang Lindner; Current chemical tagging strategies for proteome analysis by mass spectrometry. Journal of Chromatography B, 813 (2004) 1-26
5.Ronald Kluger, Amer Alagic; Chemical cross-linking and protein-protein interactions—a review with illustrative protocols. Bioorganic Chemistry 32 (2004)451-472
6. Back JW, de Jong L, Muijsers AO, de Koster CG, etc; Chemical Cross-linking and Mass Spectrometry for Protein Structural Modeling. J Mol Biol. 2003 Aug8;331(2):303-13
7.Pearson KM, Pannell LK, Fales HM; Intramolecular cross-linking experiments on cytochrome c and ribonuclease A using an isotope multiplet method. Rapid Commun Mass Spectrom. 2002;16(3): 149-59.
8. Dihazi GH, Sinz A. Mapping low-resolution three-dimensional protein structures using chemical cross-linking and Fourier transform ion-cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom. 2003;17(17):2005-14.
9. Kaltashov IA, Eyles SJ. Studies of biomolecular conformations and conformational dynamics by mass spectrometry. Mass Spectrom Rev. 2002 Jan-Feb;21(1):37-71.
10. Monzon LG, Manelyte L, Ahrends R, etc. Mapping Protein-Protein Interactions between MutL and MutH by Cross-linking. J. Biol. Chem., 2004, 279, (47): 49338-49345
11.Chen LL, Rosa JJ, Turner S, Pepinsky RB. Production of multimeric forms of CD4 through a sugar-based cross-linking strategy. J Biol Chem. 1991,266(27): 18237-43.
12. Carlsohn E, Jonas Angstrom, Mark R. E, etc; Chemical cross-linking of the urease complex from Helicobacter pylori and analysis by Fourier transform ion cyclotron resonance mass spectrometry and molecular modeling. International Journal of Mass Spectrometry, 234 (2004) pp. 137-144
13. Sorgen PL, Hu Y, Guan L, etc; An approach to membrane protein structure without crystals. PNAS. 2002 Oct 29;99(22): 14037-40. Epub 2002 Oct 21.
14. Regina B. Troyanovsky, Eugene Sokolov; Adhesive and Lateral E-Cadherin Dimers Are Mediated by the Same Interface. Molecular and Cellular Biology, 2003,23(22): 7965-7972
15. Bennett KL, Kussmann M, Bjork P, etc Chemical cross-linking with thiol-cleavable reagents combined with differential mass spectrometric peptide mapping—a novel approach to assess intermolecular protein contacts. Protein Sci. 2000 Aug;9(8): 1503-18.
16. Cai K, Itoh Y, Khorana GH, Mapping of contact sites in complex formation between transducin and light-activated rhodopsin by covalent crosslinking: Use of a photoactivatable reagent. PNAS, 2001, 98(9): 4877-4882
17. Wine RN, Dial JM, Tomer KB, Borchers CH. Identification of components of protein complexes using a fluorescent photo-cross-linker and mass spectrometry. Anal Chem. 2002,74(9): 1939-45.
18. Gygi SP, Rist B, Gerber SA, etc; Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 1999 Oct; 17(10): 994-9.
19. Muller DR, Schindler P, Towbin H, etc; Isotope-tagged cross-linking reagents. A new tool in mass spectrometric protein interaction analysis. Anal Chem. 2001 May 1;73(9): 1927-34.
20. Back JW, Notenboom V, de Koning LJ, etc; Identification of cross-linked peptides for protein interaction studies using mass spectrometry and ~(18)O labeling. Anal. Chem. 2002; 74: 4417-22.
21. Gregory B. Hurst, Mass Spectrometric Detection of Affinity Purified Crosslinked Peptides. J Am Soc Mass Spectrom, 2004, 15. 832-839
22. Ishmael FT, AlleyAC, Benkovic SJ; Identification and Mapping of Protein-Protein Interactions between gp32 and gp59 by Cross-linking. J. Biol. Chem., 2001,276, (27),:25236-25242.
23. Trester-Zedlitz M, Kamada K, Burley SK, etc; A modular cross-linking approach for exploring protein interactions. J Am Chem Soc. 2003, 125(9):2416-25.
24. Suchanek M, Radzikowska A, Thiele C. Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells. Nat Methods. 2005 Apr;2(4):261-7. Epub 2005 Mar 23
25. Xiaoting Tang, Gerhard R. Munske, etc, Mass Spectrometry Identifiable Cross-Linking Strategy for Studying Protein-Protein Interactions. Anal. Chem.2005, 77,311-318
26. Monzon GL, Manelyte L, Ahrends R, etc. Mapping Protein-Protein Interactions between MutL and MutH by Cross-linking. J. Biol. Chem. 2004,279,(47):49338-49345
27. Ishmael FT, Alley SC,Benkovic SJ; Identification and Mapping of Protein-Protein Interactions between gp32 and gp59 by Cross-linking. J. Biol. Chem., 2001,276, (27):25236-25242
28. Grabner R, Till U, Heller R. Flow cytometric determination of E-selectin, vascular cell adhesion molecule-1, and intercellular cell adhesion molecule-1 in formaldehyde-fixed endothelial cell monolayers. Cytometry. 2000 Jul l;40(3):238-44
29.Konikova E, Babusikova O, Kusenda J, etc, Detection of cytoplasmic and surface membrane markers in cells of some human hematopoietic cell lines. Neoplasma. 1992;39(6):337-42.
30.Metz B, Kersten GF, Hoogerhout P, etc, Identification of formaldehyde-induced modifications in proteins:reactions with model peptides.J Biol Chem.2004,279(8):6235-43.
31.Schmitt-Ulms G,Hansen K,Liu J,etc,Time-controlled transcardiac perfusion cross-linking for the study of protein interactions in complex tissues.Nature Biotechnology 2004,22,724-731
32.Vasilescu J,Guo XC,Kast J,etc,Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry.PROTEOMICS 2004,4,3845-3854
2. Florens, L., Liu, X., Wang. Y. et al. (2004) Proteomics approach reveals novel proteins on the surface of malaria-infected erythrocytes, Mol Biochem Parasitol 135, 1-11.
3. Knudsen, G. M., Medzihradszky, K. F., Lim, K. C. Hansell, E. & McKerrow, J. H. (2005) Proteomic analysis of Schistosoma mansoni cercarial secretions, Mol Cell Proteomics, 4, 1862-75.
4. Trost, M., Wehmhoner, D., Karst, U. et al. (2005) Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species, Proteomics, 5, 1544-57.
5. Volmer, M. W., Stuhler, K., Zapatka, M. et al. (2005) Differential proteome analysis of conditioned media to detect Smad4 regulated secreted biomarkers in colon cancer, Proteomics, 5, 2587-601.
6. Xiao, T., Ying, W, Li, L. et al. (2005) An approach to studying lung cancer-related proteins in human blood, Mol Cell Proteomics, 4, 1480-6.
7. Kobayashi, Y, Yamamoto, K., Saido, T. et al. (1990) Identification of calcium-activated neutral protease as a processing enzyme of human interleukin 1 alpha, Proc Natl Acad Sci U S A, 87, 5548-52.
8. Chen, X., Cushman, S. W., Pannell, L. K. & Hess, S. (2005) Quantitative proteomic analysis of the secretory proteins from rat adipose cells using a 2D liquid chromatography-MS/MS approach, J Proteome Res, 4, 570-7.
9. Mbeunkui, F., Fodstad, O. & Pannell, L. K. (2006) Secretory protein enrichment and analysis: an optimized approach applied on cancer cell lines using 2D LC-MS/MS, J Proteome Res, 5, 899-906.
10. Pellitteri-Hahn, M. C, Warren, M. C, Didier, D. N. et al. (2006) Improved mass spectrometric proteomic profiling of the secretome of rat vascular endothelial cells, J Proteome Res, 5, 2861-4.
11. Tjalsma, H., Stover, A. G, Driks, A. et al. (2000) Conserved serine and histidine residues are critical for activity of the ER-type signal peptidase SipW of Bacillus subtilis, J Biol Chem, 275, 25102-8.
12. Glaser, P., Frangeul, L., Buchrieser, C. et al. (2001) Comparative genomics of Listeria species, Science, 294, 849-52.
13. Nielsen, H., Brunak, S. & von Heijne, G. (1999) Machine learning approaches for the prediction of signal peptides and other protein sorting signals, Protein Eng, 12, 3-9.
14. Lamonica, J. M., Wagner, M., Eschenbrenner, M. et al. (2005) Comparative secretome analyses of three Bacillus anthracis strains with variant plasmid contents, Infect Immun, 73, 3646-58.
15. Menne, K. M., Hermjakob, H. & Apweiler, R. (2000) A comparison of signal sequence prediction methods using a test set of signal peptides, Bioinformatics. 16, 741-2.
16. Zhou, S., Liu, Y., Weng, J. et al. (2005) Expression profiles of mouse dendritic cell sarcoma are similar to those of hematopoietic stem cells or progenitors by clustering and principal component analyses, Biochem Biophys Res Commun, 331, 194-202.
17. Monda, L., Warnke, R. & Rosai, J. (1986) A primary lymph node malignancy with features suggestive of dendritic reticulum cell differentiation. A report of 4 cases, Am J Pathol, 122, 562-72.
18. Shia, J., Chen, W., Tang, L. H. et al. (2006) Extranodal follicular dendritic cell sarcoma: clinical, pathologic, and histogenetic characteristics of an underrecognized disease entity, Virchows Arch, 449, 148-58.
19. Delahunty, C. & Yates, J. R., 3rd (2005) Protein identification using 2D-LC-MS/MS, Methods, 35, 248-55.
20. Washburn, M. P., Wolters, D. & Yates, J. R., 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology, Nat Biotechnol, 19, 242-7.
21. Sun, W., Li, F., Wang, J., Zheng, D. & Gao, Y. (2004) AMASS: software for automatically validating the quality of MS/MS spectrum from SEQUEST results, Mol Cell Proteomics, 3, 1194-9.
22. Bendtsen, J. D., Nielsen, H., von Heijne, G. & Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0, J Mol Biol, 340, 783-95.
23. Chang, H. C, Samaniego, F., Nair, B. C, Buonaguro, L. & Ensoli, B. (1997) HIV-1 Tat protein exits from cells via a leaderless secretory pathway and binds to extracellular matrix-associated heparan sulfate proteoglycans through its basic region, Aids, 11, 1421-31.
24. Watanabe, N. & Kobayashi, Y. (1994) Selective release of a processed form of interleukin 1 alpha, Cytokine, 6, 597-601.
25. Hamon, Y, Luciani, M. F., Becq, F. et al. (1997) Interleukin-1 beta secretion is impaired by inhibitors of the Atp binding cassette transporter, ABC1, Blood, 90,2911-5.
26. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, J Mol Biol, 305, 567-80.
27. Wang, P., Mariman, E., Keijer, J. et al. (2004) Profiling of the secreted proteins during 3T3-L1 adipocyte differentiation leads to the identification of novel adipokines, Cell Mol Life Sci, 61, 2405-17.
28. Bendtsen, J. D., Jensen, L. J., Blom, N., Von Heijne, G. & Brunak, S. (2004) Feature-based prediction of non-classical and leaderless protein secretion, Protein Eng Des Sel, 17, 349-56.
29. Duckert, P., Brunak, S. & Blom, N. (2004) Prediction of proprotein convertase cleavage sites, Protein Eng Des Sel, 17, 107-12.
30. Lancaster, G. I. & Febbraio, M. A. (2005) Exosome-dependent trafficking of HSP70: a novel secretory pathway for cellular stress proteins, J Biol Chem, 280, 23349-55.
31. Clayton, A., Turkes. A.. Dewitt, S. et al. (2004) Adhesion and signaling by B cell-derived exosomes: the role of integrins, Faseb J, 18, 977-9.
32. Liegeois, S., Benedetto, A., Garnier, J. M., Schwab, Y. & Labouesse. M. (2006) The VO-ATPase mediates apical secretion of exosomes containing Hedgehog-related proteins in Caenorhabditis elegans, J Cell Biol, 173, 949-61.
33. Hardy, K. M., Hoffman, E. A., Gonzalez, P., McKay, B. S. & Stamer. W. D. (2005) Extracellular trafficking of myocilin in human trabecular meshwork cells, J Biol Chem, 280, 28917-26.
34. Foster, L. J., De Hoog, C. L. & Mann, M. (2003) Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors, Proc Natl Acad Sci U S A, 100, 5813-8.
35. Fevrier, B., Vilette, D., Laude, H. & Raposo, G (2005) Exosomes: a bubble ride for prions?, Traffic, 6, 10-7.
36. Bard, M. P., Hegmans, J. P., Hemmes, A. et al. (2004) Proteomic analysis of exosomes isolated from human malignant pleural effusions, Am J Respir Cell Mol Biol, 31,114-21.
37. van Niel, G, Raposo, G, Candalh, C. et al. (2001) Intestinal epithelial cells secrete exosome-like vesicles, Gastroenterology, 121, 337-49.
38. Morciano, M., Burre, J., Corvey, C. et al. (2005) Immunoisolation of two synaptic vesicle pools from synaptosomes: a proteomics analysis, J Neurochem, 95, 1732-45.
39. Barile, M., Pisitkun, T., Yu, M. J. et al. (2005) Large scale protein identification in intracellular aquaporin-2 vesicles from renal inner medullary collecting duct, Mol Cell Proteomics, 4, 1095-106.
40. Brunner, Y, Coute, Y, Iezzi, M. et al. (2007) Proteomic analysis of insulin secretory granules, Mol Cell Proteomics.
41. Casey, T. M., Meade, J. L. & Hewitt, E. W. (2007) Organelle Proteomics: Identification of the Exocytic Machinery Associated with the Natural Killer Cell Secretory Lysosome, Mol Cell Proteomics, 6, 767-780.
42. Segura, E., Amigorena, S. & Thery, C. (2005) Mature dendritic cells secrete exosomes with strong ability to induce antigen-specific effector immune responses, Blood Cells Mol Dis, 35, 89-93.
43. Segura, E., Nicco, C, Lombard, B. et al. (2005) ICAM-1 on exosomes from mature dendritic cells is critical for efficient naive T-cell priming, Blood, 106, 216-23.
44. Vipond, C, Suker, J., Jones, C. et al. (2006) Proteomic analysis of a meningococcal outer membrane vesicle vaccine prepared from the group B strain NZ98/254, Proteomics, 6, 3400-13.
45. Silver, R. B. & Pappas, G. D. (2005) Secretion without membrane fusion: porocytosis, Anat Rec B New Anat, 282, 18-37.
46. Thery, C, Regnault, A., Garin, J. et al. (1999) Molecular characterization of dendritic cell-derived exosomes. Selective accumulation of the heat shock protein hsc73, J Cell Biol, 147, 599-610.
47. Sahaf, B. & Rosen, A. (2000) Secretion of 10-kDa and 12-kDa thioredoxin species from blood monocvtes and transformed leukocytes,Antioxid Redox Signal,2,717-26.
48.高进,刘玉琴,段德义,李存玺(1997)《小鼠树突状肉瘤细胞系的建立和鉴定及其与转移相关特性的研究》中国肿瘤生物治疗杂志4(4):310-312。
49.刘玉琴,顾蓓,高进,段德义,赵雪梅(2000)《转移性癌细胞体外水解酶表达及影响因素的作用》中国医学科学院学报22(2):149-153。
50.ABOUFARHA,K.M.,MENHEERE,P.P.,NIEMAN,F.H.,ARENDS,J.W.&JANKNEGT,R.A.(1992) Value of serum laminin P1 as a diagnostic and monitoring parameter in transitional cell carcinoma of the bladder,Urol Int,49,130-6.
51.GOLDBERG,I.,DAVIDSON,B.,LERNER-GEVA,L.et al.(1998) Expression of extracellular matrix proteins in cervical squamous cell carcinoma—a clinicopathological study,J Clin Pathol,51,781-5.
52.AUSTYN,J.M.(1993) The dendritic cell system and anti-tumour immunity,In Vivo,7,193-201.
53.CAVANAGH,L.L.,SAAL,R.J.,GRIMMETT,K.L.& THOMAS,R.(1998)Proliferation in monocyte-derived dendritic cell cultures is caused by progenitor cells capable of myeloid differentiation,Blood,92,1598-607.
54.OKI,M.,ANDO,K.,HAG[HARA,M.et al.(2001) Efficient lentiviral transduction of human cord blood CD34(+) ceils followed by their expansion and differentiation into dendritic cells,Exp Hematol,29,1210-7.
55.LIN,C.L.,SURI,R.M.,RAHDON,R.A.,AUSTYN,J.M.& ROAKE,J.A.(1998)Dendritic cell chemotaxis and transendothelial migration are induced by distinct chemokines and are regulated on maturation,Eur J Immunol,28,4114-22.
56.JOHNSTONE,R.M.,ADAM,M.,HAMMOND,J.R.,ORR,L.& TURBIDE,C.(1987)Vesicle formation during reticulocyte maturation.Association of plasma membrane activities with released vesicles(exosomes),J Biol Chem,262,9412-20.
57.THERY,C.,BOUSSAC,M.,VERON,P.et al.(2001) Proteomic analysis of dendritic cell-derived exosomes:a secreted subcellular compartment distinct from apoptotic vesicles,J Immunol,166,7309-18.
58.RITTLING,S.R.& CHAMBERS,A.F.(2004) Role of osteopontin in tumour progression,Br J Cancer,90,1877-81.
1. Washburn, M. P., Wolters, D., and Yates, J. R., 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19, 242-247.
2. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17, 994-999.
3. Zhou, H., Ranish, J. A., Watts, J. D., and Aebersold, R. (2002) Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat Biotechnol 20, 512-515.
4. Unlu, M., Morgan, M E., and Minden, J. S. (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18, 2071-2077.
5. States, D. J., Omenn, G. S., Blackwell, T. W., Fermin, D., Eng, J., Speicher, D. W., and Hanash, S. M. (2006) Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol 24, 333-338.
6. Thongboonkerd, V, McLeish, K. R., Arthur, J. M., and Klein, J. B. (2002) Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int 62, 1461-1469.
7. Pieper, R., Gatlin, C. L., McGrath, A. M., Makusky, A. J., Mondal, M., Seonarain, M., Field, E., Schatz, C. R., Estock, M. A., Ahmed, N., Anderson, N. G, and Steiner, S. (2004) Characterization of the human urinary proteome: a method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots. Proteomics 4, 1159-1174.
8.Oh, J., Pyo, J. H., Jo, E. H., Hwang, S. I., Kang, S. C, Jung, J. H., Park, E. K., Kim, S. Y, Choi, J. Y, and Lim, J. (2004) Establishment of a near-standard two-dimensional human urine proteomic map. Proteomics 4, 3485-3497.
9. Khan, A., and Packer, N. H. (2006) Simple urinary sample preparation for proteomic analysis. J Proteome Res 5, 2824-2838.
10. Spahr, C. S., Davis, M. T., McGinley, M. D, Robinson, J. H., Bures, E. J., Beierle, J., Mort, J., Courchesne, P. L., Chen, K., Wahl, R. C, Yu, W., Luethy, R., and Patterson, S. D. (2001) Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest. Proteomics 1, 93-107.
11. Davis, M. T., Spahr, C. S., McGinley, M. D., Robinson, J. H., Bures, E. J., Beierle, J., Mort, J., Yu, W., Luethy, R., and Patterson, S. D. (2001) Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. II. Limitations of complex mixture analyses. Proteomics 1, 108-117.
12. Sun, W., Li, R, Wu, S., Wang, X., Zheng, D., Wang, J., and Gao, Y. (2005) Human urine proteome analysis by three separation approaches. Proteomics 5, 4994-5001.
13. Castagna, A., Cecconi, D., Sennels, L., Rappsilber, J., Guerrier, L., Fortis, R, Boschetti, E., Lomas, L., and Righetti, P. G. (2005) Exploring the hidden human urinary proteome via ligand library beads. J Proteome Res 4, 1917-1930.
14. Adachi, J., Kumar, C, Zhang, Y, Olsen, J. V., and Mann, M. (2006) The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol 7, R80.
15. Wang, L., Li, R, Sun, W., Wu, S., Wang, X., Zhang, L., Zheng, D., Wang, J., and Gao, Y (2006) Concanavalin A-captured glycoproteins in healthy human urine. Mol Cell Proteomics 5, 560-562.
16. Vlahou. A., Schellhammer, P. F., Mendrinos, S., Patel, K., Kondylis, R I.. Gong. L. Nasim, S., and Wright Jr, G. L., Jr. (2001) Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. Am J Pathol 158, 1491-1502.
17. Rogers, M. A., Clarke, P., Noble, J., Munro, N. P., Paul, A., Selby, P. J.. and Banks, R. E. (2003) Proteomic profiling of urinary proteins in renal cancer by surface enhanced laser desorption ionization and neural-network analysis: identification of key issues affecting potential clinical utility. Cancer Res 63, 6971-6983.
18. Schaub, S., Rush, D., Wilkins, J., Gibson, I. W., Weiler, T., Sangster, K., Nicolle, L, Karpinski, M., Jeffery, J., and Nickerson, P. (2004) Proteomic-based detection of urine proteins associated with acute renal allograft rejection. J Am Soc Nephrol 15, 219-227.
19. Cutillas, P. R., Norden, A. G, Cramer, R., Burlingame, A. L., and Unwin, R. J. (2003) Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome. Clin Sci (Lond) 104, 483-490.
20. Pang, J. X., Ginanni, N., Dongre, A. R., Hefta, S. A., and Opitek, G. J. (2002) Biomarker discovery in urine by proteomics. J Proteome Res 1, 161-169.
21. Tantipaiboonwong, P., Sinchaikul, S., Sriyam, S., Phutrakul, S., and Chen, S. T. (2005) Different techniques for urinary protein analysis of normal and lung cancer patients. Proteomics 5, 1140-1149.
22. Nedelkov, D. (2005) Population proteomics: addressing protein diversity in humans. Expert Rev Proteomics 2, 315-324.
23. Nedelkov, D., Kiernan, U. A., Niederkofler, E. E., Tubbs, K. A., and Nelson, R. W. (2006) Population proteomics: the concept, attributes, and potential for cancer biomarker research. Mol Cell Proteomics 5, 1811-1818.
24. Hu, Y., Malone, J. P., Fagan, A. M, Townsend, R. R., and Holtzman, D. M. (2005) Comparative proteomic analysis of intra- and interindividual variation in human cerebrospinal fluid. Mol Cell Proteomics 4, 2000-2009.
25. Molloy, M. P., Brzezinski, E. E., Hang, J., McDowell, M. T., and VanBogelen, R. A. (2003) Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 3, 1912-1919.
26. Zhang, X., Guo, Y., Song, Y, Sun, W., Yu, C, Zhao, X., Wang, H., Jiang, H., Li, Y, Qian, X., Jiang, Y, and He, F. (2006) Proteomic analysis of individual variation in normal livers of human beings using difference gel electrophoresis. Proteomics 6, 5260-5268.
27. Thongboonkerd, V., Chutipongtanate, S., and Kanlaya, R. (2006) Systematic evaluation of sample preparation methods for gel-based human urinary proteomics: quantity, quality, and variability. J Proteome Res 5, 183-191.
28. Russo, L. M., Bakris, G. L., and Comper, W. D. (2002) Renal handling of albumin: a critical review of basic concepts and perspective. Am J Kidney Dis 39, 899-919.
29. Zhou, H., Yuen, P. S., Pisitkun, T., Gonzales, P. A., Yasuda, H., Dear, J. W., Gross, P., Knepper, M. A., and Star, R. A. (2006) Collection, storage, preservation, and normalization of human urinary exosomes for biomarker discovery. Kidney Int 69, 1471-1476.
30. Bradford, M. M (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72, 248-254.
31. Sun, W., Gao, S., Wang, L., Chen, Y, Wu, S., Wang, X., Zheng, D., and Gao, Y. (2006) Microwave-assisted protein preparation and enzymatic digestion in proteomics. Mol Cell Proteomics 5, 769-776.
32. Kersey, P. J., Duarte, J., Williams. A., Karavidopoulou, Y, Birney, E., and Apweiler, R. (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics 4, 1985-1988.
33. Wolters, D. A., Washburn, M. P., and Yates, J. R., 3rd (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 73, 5683-5690.
34. Peng, J, Elias, J. E., Thoreen, C. C, Licklider, L. J., and Gygi, S. P. (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res 2, 43-50.
35. Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., and Yates, J. R., 3rd (1999) Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 17, 676-682.
36. Sun, W., Wu, S., Wang, X., Zheng, D., and Gao, Y. (2004) A systematical analysis of tryptic peptide identification with reverse phase liquid chromatography and electrospray ion trap mass spectrometry. Genomics Proteomics Bioinformatics 2, 174-183.
37. Sun, W., Wu, S., Wang, X., Zheng, D., and Gao, Y. (2005) An analysis of protein abundance suppression in data dependent liquid chromatography and tandem mass spectrometry with tryptic peptide mixtures of five known proteins. Eur J Mass Spectrom (Chichester, Eng) 11, 575-580.
38. Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G., Mendoza, A., Sevinsky, J. R., Resing, K. A., and Ahn, N. G. (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4, 1487-1502.
39. Clarke, W., Silverman, B. C., Zhang, Z., Chan, D. W., Klein, A. S., and Molmenti, E. P. (2003) Characterization of renal allograft rejection by urinary proteomic analysis. Ann Surg 237, 660-664; discussion 664-665.
40. Voshol, H., Brendlen, N., Muller, D., Inverardi, B., Augustin, A., Pally, C., Wieczorek, G., Morris, R. E., Raulf, F., and van Oostrum, J. (2005) Evaluation of biomarker discovery approaches to detect protein biomarkers of acute renal aliograft rejection. J Proteome Res 4, 1192-1199.
41. Hirawa, N., Uehara, Y., Ikeda, T., Gomi, T., Hamano, K., Totsuka, Y., Yamakado, M., Takagi, M., Eguchi, N., Oda, H., Seiki, K., Nakajima, H., and Urade, Y. (2001) Urinary prostaglandin D synthase (beta-trace) excretion increases in the early stage of diabetes mellitus. Nephron 87, 321-327.
42. Hirawa, N., Uehara, Y., Yamakado, M., Toya, Y., Gomi, T., Ikeda, T., Eguchi, Y., Takagi, M., Oda, H., Seiki, K., Urade, Y, and Umemura, S. (2002) Lipocalin-type prostaglandin d synthase in essential hypertension. Hypertension 39, 449-454.
43. Jain, S., Rajput, A., Kumar, Y, Uppuluri, N., Arvind, A. S., and Tatu, U. (2005) Proteomic analysis of urinary protein markers for accurate prediction of diabetic kidney disorder. J Assoc Physicians India 53, 513-520.
44. Jung, K., Pergande, M., Schimke, E., Ratzmann, K. P., and Ilius, A. (1988) Urinary enzymes and low-molecular-mass proteins as indicators of diabetic nephropathy. Clin Chem 34, 544-547.
45. Utsunomiya, T., Ogawa, K., Yoshinaga, K., Ohta, M., Yamashita, K., Mimori, K., Inoue, H., Ezaki, T., Yoshikawa, Y, and Mori, M. (2005) Clinicopathologic and prognostic values of apolipoprotein D alterations in hepatocellular carcinoma. Int J Cancer 116, 105-109.
46. Rodriguez, J. C., Diaz, M., Gonzalez, L. O., Sanchez, J., Sanchez, M. T., Merino, A. M., and Vizoso, F. (2000) Apolipoprotein D expression in benign and malignant prostate tissues. Int J Surg Investig 2, 319-326.
47. Zolg, W. (2006) The proteomic search for diagnostic biomarkers: lost in translation? Mol Cell Proteomics 5,1720-1726.
1. Wilkins MR, Sanchez JC, Gooley AA. et al. Progress with proteome projects: why all proteins expressed by a gonome should be identified and how to do it. Biotech &Genetic Engineering Rev, 1995, 13, 19-50.
2. Erica Golemis, Protein-protein interactions—a molecular cloning manual Gold Spring Harbor Laborary Press, 2001.
3. DOUBLE-AGENTS? Cross-Linking Reagents—Selection Guide Pierce
4. Alexander Leitner, Wolfgang Lindner; Current chemical tagging strategies for proteome analysis by mass spectrometry. Journal of Chromatography B, 813 (2004) 1-26
5.Ronald Kluger, Amer Alagic; Chemical cross-linking and protein-protein interactions—a review with illustrative protocols. Bioorganic Chemistry 32 (2004)451-472
6. Back JW, de Jong L, Muijsers AO, de Koster CG, etc; Chemical Cross-linking and Mass Spectrometry for Protein Structural Modeling. J Mol Biol. 2003 Aug8;331(2):303-13
7.Pearson KM, Pannell LK, Fales HM; Intramolecular cross-linking experiments on cytochrome c and ribonuclease A using an isotope multiplet method. Rapid Commun Mass Spectrom. 2002;16(3): 149-59.
8. Dihazi GH, Sinz A. Mapping low-resolution three-dimensional protein structures using chemical cross-linking and Fourier transform ion-cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom. 2003;17(17):2005-14.
9. Kaltashov IA, Eyles SJ. Studies of biomolecular conformations and conformational dynamics by mass spectrometry. Mass Spectrom Rev. 2002 Jan-Feb;21(1):37-71.
10. Monzon LG, Manelyte L, Ahrends R, etc. Mapping Protein-Protein Interactions between MutL and MutH by Cross-linking. J. Biol. Chem., 2004, 279, (47): 49338-49345
11.Chen LL, Rosa JJ, Turner S, Pepinsky RB. Production of multimeric forms of CD4 through a sugar-based cross-linking strategy. J Biol Chem. 1991,266(27): 18237-43.
12. Carlsohn E, Jonas Angstrom, Mark R. E, etc; Chemical cross-linking of the urease complex from Helicobacter pylori and analysis by Fourier transform ion cyclotron resonance mass spectrometry and molecular modeling. International Journal of Mass Spectrometry, 234 (2004) pp. 137-144
13. Sorgen PL, Hu Y, Guan L, etc; An approach to membrane protein structure without crystals. PNAS. 2002 Oct 29;99(22): 14037-40. Epub 2002 Oct 21.
14. Regina B. Troyanovsky, Eugene Sokolov; Adhesive and Lateral E-Cadherin Dimers Are Mediated by the Same Interface. Molecular and Cellular Biology, 2003,23(22): 7965-7972
15. Bennett KL, Kussmann M, Bjork P, etc Chemical cross-linking with thiol-cleavable reagents combined with differential mass spectrometric peptide mapping—a novel approach to assess intermolecular protein contacts. Protein Sci. 2000 Aug;9(8): 1503-18.
16. Cai K, Itoh Y, Khorana GH, Mapping of contact sites in complex formation between transducin and light-activated rhodopsin by covalent crosslinking: Use of a photoactivatable reagent. PNAS, 2001, 98(9): 4877-4882
17. Wine RN, Dial JM, Tomer KB, Borchers CH. Identification of components of protein complexes using a fluorescent photo-cross-linker and mass spectrometry. Anal Chem. 2002,74(9): 1939-45.
18. Gygi SP, Rist B, Gerber SA, etc; Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 1999 Oct; 17(10): 994-9.
19. Muller DR, Schindler P, Towbin H, etc; Isotope-tagged cross-linking reagents. A new tool in mass spectrometric protein interaction analysis. Anal Chem. 2001 May 1;73(9): 1927-34.
20. Back JW, Notenboom V, de Koning LJ, etc; Identification of cross-linked peptides for protein interaction studies using mass spectrometry and ~(18)O labeling. Anal. Chem. 2002; 74: 4417-22.
21. Gregory B. Hurst, Mass Spectrometric Detection of Affinity Purified Crosslinked Peptides. J Am Soc Mass Spectrom, 2004, 15. 832-839
22. Ishmael FT, AlleyAC, Benkovic SJ; Identification and Mapping of Protein-Protein Interactions between gp32 and gp59 by Cross-linking. J. Biol. Chem., 2001,276, (27),:25236-25242.
23. Trester-Zedlitz M, Kamada K, Burley SK, etc; A modular cross-linking approach for exploring protein interactions. J Am Chem Soc. 2003, 125(9):2416-25.
24. Suchanek M, Radzikowska A, Thiele C. Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells. Nat Methods. 2005 Apr;2(4):261-7. Epub 2005 Mar 23
25. Xiaoting Tang, Gerhard R. Munske, etc, Mass Spectrometry Identifiable Cross-Linking Strategy for Studying Protein-Protein Interactions. Anal. Chem.2005, 77,311-318
26. Monzon GL, Manelyte L, Ahrends R, etc. Mapping Protein-Protein Interactions between MutL and MutH by Cross-linking. J. Biol. Chem. 2004,279,(47):49338-49345
27. Ishmael FT, Alley SC,Benkovic SJ; Identification and Mapping of Protein-Protein Interactions between gp32 and gp59 by Cross-linking. J. Biol. Chem., 2001,276, (27):25236-25242
28. Grabner R, Till U, Heller R. Flow cytometric determination of E-selectin, vascular cell adhesion molecule-1, and intercellular cell adhesion molecule-1 in formaldehyde-fixed endothelial cell monolayers. Cytometry. 2000 Jul l;40(3):238-44
29.Konikova E, Babusikova O, Kusenda J, etc, Detection of cytoplasmic and surface membrane markers in cells of some human hematopoietic cell lines. Neoplasma. 1992;39(6):337-42.
30.Metz B, Kersten GF, Hoogerhout P, etc, Identification of formaldehyde-induced modifications in proteins:reactions with model peptides.J Biol Chem.2004,279(8):6235-43.
31.Schmitt-Ulms G,Hansen K,Liu J,etc,Time-controlled transcardiac perfusion cross-linking for the study of protein interactions in complex tissues.Nature Biotechnology 2004,22,724-731
32.Vasilescu J,Guo XC,Kast J,etc,Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry.PROTEOMICS 2004,4,3845-3854