小鼠晶体蛋白质组的双向电泳和质谱鉴定研究

目的应用双向电泳和质谱技术研究5周龄小鼠晶体蛋白质组。方法提取小鼠晶体总蛋白,进行固相pH梯度（IPG）等电聚焦双向电泳,胶体考马斯亮蓝R-250染色,使用PDQuest7．30图像分析软件分析电泳图像。选择主要蛋白点胶上酶解,应用基质辅助激光解析电离飞行时间／飞行时间（MALDI—TOF／TOF）仪器进行串联质谱（MS／MS）鉴定。结果上样量为882μg和190μg时,分别检测370±41蛋白点（n=3）和57±5个蛋白点（n=3）。高上样量能够较好地分离晶体低丰度蛋白,如念珠状纤维结构蛋白BFSP;低上样量可很好地分离高丰度蛋白-晶体蛋白（包括αA、αB;βA1～βA4;βB1～βB3;γA～γF和γS等）。质谱鉴定得到1种细胞骨架蛋白和16种高丰度晶体蛋白。结论双向电泳和质谱技术有效考察了晶体总蛋白质,为分析白内障形成过程中蛋白质的表达改变提供了新的方法和途径。     

电针对大鼠胃黏膜损伤修复的血清蛋白质差异表达研究

目的：观察电针胃经穴对大鼠胃黏膜损伤修复的血清蛋白质差异表达,为进一步阐明针刺效应的体液机理提供理论依据。方法：用表面增强激光解吸离子化飞行时间质谱（SELDI—TOF—MS）技术和WCX2（弱阳离子交换芯片）对正常大鼠血清和电针大鼠血清进行蛋白质指纹图谱检测分析,通过Biomarker Wizard和Biomarker Patterns System软件判别分析处理数据并结合生物信息学方法筛选差异表达蛋白质。结果：与正常大鼠血清比较,电针大鼠血清蛋白质在质荷比为2000-50000有25个蛋白质峰差异有显著意义,其中有19个标志蛋白在电针胃经大鼠血清中呈现高表达,6个标志蛋白在电针胃经大鼠血清中呈现低表达。结论：电针可促进胃黏膜损伤大鼠血清蛋白质差异表达,这种差异蛋白质可能与电针促进胃黏膜损伤修复效应密切相关。     

基于LC-MS/MS和GC-MS/MS技术分析“川朴”与“温朴”的差异化学成分

为了探讨厚朴不同商品规格药材化学成分的整体差异,本文采用液相色谱-串联四极杆飞行时间高分辨质谱(LC-Triple TOF MS/MS)和气相色谱-串联质谱(GC-MS/MS)结合多元统计分析技术对"川朴"与"温朴"的化学成分进行比较分析。通过串联质谱分析,对其质谱数据进行峰匹配、峰对齐、滤噪处理等进行特征峰提取;用主成分分析(PCA)和偏最小二乘法-判别分析(PLS-DA)进行数据处理。非挥发性成分的LC-Triple TOF MS/MS分析,根据一级质谱精确质荷比和二级质谱碎片信息,结合软件数据库搜索、标准品比对及相关文献进行成分鉴定;挥发性成分的GC-MS/MS分析,质谱图与NIST05质谱数据库匹配及参照相关文献进行成分鉴定。结果显示,"川朴"与"温朴"样品间的化学组成得到明显区分;初步筛选并鉴定出21种非挥发性差异成分和9种挥发性差异成分。该结果从化学角度为建立"川朴"与"温朴"药材辨识的新方法以及厚朴商品药材质量的综合评价提供基础资料。     

蓝莓提取物中花青素和黄酮类活性成分的UPLC-TOF MS联用分析

使用超高效液相色谱/飞行时间质谱,分别在TOF/MS全扫描和Q-TOF/MS碎片扫描两种模式下分析不同厂家生产的蓝莓提取物中的的花青素和黄酮类活性成分。首先依据高分辨精确质量在"待筛查化合物数据表"中查出可能的化合物,再结合二级质谱的子离子碎裂特征对化合物进行定性分析,结合参考文献,从蓝莓提取物中共鉴定出19个花青素类化合物、8个黄酮类化合物。同时,本文还对蓝莓提取物中的花青素苷和黄酮苷的质谱裂解规律进行了探讨。这一分析方法方便快捷、灵敏度高、准确性好,可将其推广至其它天然活性成分的无对照品筛查研究之中。     

MALDI TOF MS在细菌检测和鉴定中的应用

近年来质谱技术有了快速的发展,新的软电离技术,基质辅助激光解析电离和电喷雾电离使得质谱能够对核酸或蛋白质,多肽等生物大分子进行微量分析,且具有高灵敏度和高质量检测范围,通过串联质谱的分析还可以得到结构信息。MALDI TOF MS能给出微生物多方面的信息,包括分子量和结构信息等,用于微生物的各种研究中,如根据细菌的组成成分获得指纹图谱检测和鉴定细菌,细菌体内含有大量的生物标志分子能用于细菌的化学分类和鉴定。     

表面增强激光解吸电离质谱芯片在蛋白质组学研究中的应用

蛋白质组学是当今生命科学研究中最活跃的前沿领域。其主要技术手段是双向凝胶电泳,质谱技术和生物信息学,但各有其局限性。芯片技术和质谱技术相结合产生的表面增强激光解析离子化－飞行时间－质谱9SELDI－TOF－MS）技术,将蛋白质样品的制备,生化反应到检测分析的整个过程集成在芯片上进行,实现了新型,高效,快速,高通量的检测,不仅促进了蛋白质组学研究的迅速发展,而且为阐明生命活动的规律和疾病的发病机理以及寻找合适的医药提供提供了有力的工具。     

化学合成ω-芋螺毒素MⅦA的复性与质谱分析

为了探讨质谱分析在合成多肽氧化复性和分离纯化研究中的应用,用固相多肽合成方法合成ω－芋螺毒素MⅦA,在含谷胱甘肽的缓冲体系中进行氧化复性后,经离子交换和RP－HPLC分离纯化。利用基质辅助激光解吸电离飞行时间质谱（MALDI－TOF－MS）和电喷雾串联质谱（ESI－MS／MS）分析ω－芋螺毒素MⅦA氧化复性和分离纯化的效果,最后用电生理学实验测定复性ω－芋螺毒素MⅦA的生理活性。其结果表明,获得的ω－芋螺毒纱MⅦA纯化复性样品具有与天然ω－芋螺毒素MⅦ完全相同的空间构象和生理活性。     

固化金属离子亲和层析富集磷酸化多肽方法的选择及优化

在磷酸化蛋白质组学研究中,根据是否需要对待富集样品进行甲酯化处理,可将固化金属离子亲和层析（IMAC）方法分为两类,即需要甲酯化处理的IMAC方法（ME—IMAC）和不需要甲酯化处理的IMAC方法（Non—ME—IMAC）。要实现对磷酸化多肽的有效富集和鉴定,就必须对富集方法进行选择和优化。利用基质辅助激光解析离子化串联飞行时间质谱（MALDI—TOF—MS）对两种方法富集的磷酸化多肽进行了比较研究。结果表明,ME—IMAC方法容易发生样品丢失,质谱结果的分析也比较复杂,而Non—ME—IMAC方法则不仅操作简单而且富集效果理想。另外,优化了Non—ME—IMAC方法的实验条件,指出最佳的结合溶液是8％ACN／0．3％TFA,最佳的洗脱溶液是0．1mol／LEDTA（pH值8．0）,从而建立了一套完整而简单有效的磷酸化多肽富集方法。     

柞蚕抗菌肽CA1的分离

应用FPLC、HPLC系统配合MALDI TOF MS等技术 ,分离得到一个以灭活的Escherichiacoli诱导产生的具有明显杀菌活性的柞蚕抗菌肽CA₁。自动蛋白质序列分析仪测定其一级结构为WNPFKELERAGSRVRDAIISAGVAVATVAQATAILK ,含有 36个氨基酸残基 ,经联机检索 ,与cecropinD有 88%的同源性 ,仅有 4个氨基酸残基的差异 ,其中铰链区第 2 1～ 2 3位氨基酸为AGV ,与已知柞蚕抗菌肽A、D铰链区AGP有所不同 ,提示抗菌肽存在多态性。     

胃癌细胞高尔基体的蛋白质组学技术平台的建立

采用蔗糖密度梯度超速离心法分离纯化高尔基体,双向凝胶电泳（2-DE）分离高尔基体蛋白质,用ImageMaster 2D软件分析所得图谱,基质辅助激光解吸离子化飞行时间质谱(MALDI—TOF MS)鉴定蛋白质点等一系列亚细胞器蛋白质组学方法建立胃癌细胞内高尔基体的蛋白图谱。结果显示分离出的纯度较高的高尔基体建立了分辨率和重复性均较好的双向电泳图谱,运用质谱技术鉴定出12个蛋白质,包括蛋白合成相关蛋白、膜融合蛋白、调节蛋白、凋亡相关蛋白、运输蛋白、细胞增殖分化相关蛋白。通过亚细胞器分离纯化,双向电泳的蛋白分离及MALDI-TOF MS蛋白鉴定分析,首次成功建立了胃癌细胞SGC7901中高尔基体的蛋白质组学技术路线,为胃癌细胞内高尔基体功能的深入研究奠定了基础。     

蛋白质芯片SELDI-TOFMS技术的研究进展及其在临床中的应用

蛋白质芯片为新一代的蛋白质组研究技术,由美国Ciphergen生物系统公司引进,表面增强激光解吸电离-飞行时间质谱(SELDI-TOFMS)提供一个高通量和高灵敏度的检测平台。投放至今虽短短10来年,但卓越的成果已广为医学科学界重视,尤其在恶性肿瘤的早期诊断、监控和预后研究上。蛋白质是细胞内执行生物功能的最终分子,蛋白质组学研究让人类更深入了解疾病和生命的本源,不断发现的特异性肿瘤标志物更为攻克癌症带来新希望。这里除对表面增强激光解吸电离_飞行时间质谱作较详尽的介绍外,更重点阐述其近年来蛋白质芯片近期的研究进展和在临床中的应用,并就其优劣和发展前景作出评估。     

SELDI-TOF MS Proteomics in Breast Cancer

Background

Proteomic profiling is a rapidly developing technology that may enable early disease screening and diagnosis. Surface-enhanced laser desorption ionization–time of flight mass spectrometry (SELDI-TOF MS) has demonstrated promising results in screening and early detection of many diseases. In particular, it has emerged as a high-throughput tool for detection and differentiation of several cancer types. This review aims to appraise published data on the impact of SELDI-TOF MS in breast cancer.

Methods

A systematic literature search between 1965 and 2009 was conducted using the PubMed, EMBASE, and Cochrane Library databases. Studies covering different aspects of breast cancer proteomic profiling using SELDI-TOF MS technology were critically reviewed by researchers and specialists in the field.

Results

Fourteen key studies involving breast cancer biomarker discovery using SELDI-TOF MS proteomic profiling were identified. The studies differed in their inclusion and exclusion criteria, biologic samples, preparation protocols, arrays used, and analytical settings. Taken together, the numerous studies suggest that SELDI-TOF MS methodology may be used as a fast and robust approach to study the breast cancer proteome and enable the analysis of the correlations between proteomic expression patterns and breast cancer.

Conclusion

SELDI-TOF MS is a promising high-throughput technology with potential applications in breast cancer screening, detection, and prognostication. Further studies are needed to resolve current limitations and facilitate clinical utility.     

The nucleotide-independent Fe(III)-binding site is located on beta subunit of the mitochondrial F(1)-ATPase

The need for methods to identify disease biomarkers is underscored by the survival-rate of patients diagnosed at early stages of cancer progression. Surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) is a novel approach to biomarker discovery that combines two powerful techniques: chromatography and mass spectrometry. One of the key features of SELDI-TOF MS is its ability to provide a rapid protein expression profile from a variety of biological and clinical samples. It has been used for biomarker identification as well as the study of protein-protein, and protein-DNA interaction. The versatility of SELDI-TOF MS has allowed its use in projects ranging from the identification of potential diagnostic markers for prostate, bladder, breast, and ovarian cancers and Alzheimer's disease, to the study of biomolecular interactions and the characterization of posttranslational modifications. In this minireview we discuss the application of SELDI-TOF MS to protein biomarker discovery and profiling.     

Limitations in quantitation of the biomarker CCL18 in Gaucher disease blood samples by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry

SELDI-TOF MS assisted the discovery of the chemokine CCL18/PARC as plasma biomarker for pathological storage cells in Gaucher disease patients. Prognostic elevation of CCL18 in blood of Gaucher patients has been confirmed by ELISA. Given its low molecular mass, positive charge, and relatively high abundance, CCL18 seems a particular attractive protein for SELDI-TOF based quantitation. Therefore, we determined CCL18 levels in plasma using SELDI-TOF MS and ELISA, in parallel. CCL18 levels in some blood samples were significantly underestimated when determined by SELDI-TOF MS. Spiking of recombinant CCL18 indicated that its detection by SELDI-TOF MS is strongly determined by the nature of the sample, even markedly varying between samples obtained from one donor at different time points. Independent of the total CCL18 concentration in blood only 1-10% of the chemokine bound to the ProteinChip Array. Even when comparable amounts of CCL18 from distinct samples were bound to the ProteinChip Array, diverse peak intensities could be observed. Thus, limited binding capacity and sample-dependent suppression of CCL18 ionization contribute significantly to the final peak intensity. In conclusion, SELDI-TOF MS offers no reliable procedure to quantitatively monitor CCL18 levels in blood and thus cannot be applied in evaluation of disease status of Gaucher patients.     

Proteomic analysis of fast and slow muscles from normal and kyphoscoliotic mice using protein arrays, 2-DE and MS

A proteomic strategy based upon the integrated use of SELDI-TOF/MS, 2-DE and MALDI-TOF/MS has been used to identify a panel of fast muscle protein markers: MLC1F, MLC3F, fast troponin C (STNC) and slow muscle markers: MLC1SB and MLC2v. MLC3F, MLC1F and STNC were virtually absent in the physiologically pure slow soleus muscle of kyphoscoliotic mutant mice compared to control BDmice, whereas MLC2v increased threefold. A SELDI-TOF/MS peak at 18,012 Da in spectra from strong anionic exchange protein array fractions of fast vastus muscle was confirmed as STNC by its specific depletion from crude extracts of vastus muscle using an anti-TNC mAb. SELDI-TOF/MS also identified MLC2F phosphorylation in crude muscle extracts after treatment with alkaline phosphatase. High probability protein identifications were achieved by SELDI-TOF/MS PMF based upon the resolution of large peptides formed by partial cleavage and high peptide coverage. When the pI from 2-D gels and molecular weight estimations from SELDI-TOF/MS were entered into the TagIdent algorithm, high probability protein identity predictions were obtained that were confirmed later by PMF. We confirm that SELDI-TOF/MS can be integrated with other proteomics techniques for the efficient analysis of protein expression changes and PTMs associated with physiological changes in skeletal muscle.     

In-source decay causes artifacts in SELDI-TOF MS spectra

SELDI-TOF MS is a mass spectrometric technique which has been extensively used for biomarker discovery. In this study, we show that in-source decay is an important source for the generation of additional spectral peaks with this technique, both for pure proteins and proteins in serum samples. Thus, SELDI-TOF MS could be used to gain sequence information from proteins, but the results also question the uncritical use of SELDI-TOF MS as a general method for the detection of biomarkers.     

From SELDI-TOF MS to protein identification by on-chip elution

SELDI-TOF MS has been demonstrated as a powerful tool for biomarker discovery. However, a major disadvantage of SELDI-TOF MS is the lack of direct identification of the discriminatory peaks discovered. We describe a novel experimental identification strategy where peptides/proteins captured to a weak cation exchange ProteinArray surface (CM10) are eluted, and thereafter identified by utilizing a sensitive LC-MS/MS (i.e. LTQ Orbitrap). A mixture of four known proteins was used to test the novel experimental approach described, and all four proteins were successfully identified. Additionally, a biomarker candidate previously discovered in plasma of Atlantic cod (Gadus morhua) by SELDI-TOF MS was identified. Thus, this study indicated that a combination of on-chip elution and a highly sensitive LC-MS/MS system can be an alternative approach to identify biomarker candidates discovered by use of SELDI-TOF MS.     

Identification of treatment efficacy-related host factors in chronic hepatitis C by ProteinChip serum analysis

Recent development of proteomic array technology, including protein profiling coupling ProteinChip array with surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF/MS), provides a potentially powerful tool for discovery of new biomarkers by comparison of its profiles according to patient phenotypes. We used this approach to identify the host factors associated with treatment response in patients with chronic hepatitis C (CHC) receiving a 48-wk course of pegylated interferon (PEG-IFN) alpha 2b plus ribavirin (RBV). Protein profiles of pretreatment serum samples from 32 patients with genotype 1b and high viral load were conducted by SELDI-TOF/MS by using the three different ProteinChip arrays (CM10, Q10, IMAC30). Proteins showed significantly different peak intensities between sustained virological responders (SVRs), and non-SVRs were identified by chromatography, SDS-PAGE, TOF/MS and tandem mass spectrometry (MS/MS) assay. Eleven peak intensities were significantly different between SVRs and non-SVRs. The three SVR-increased peaks could be identified as two apolipoprotein (Apo) fragments and albumin and, among the eight non-SVR-increased proteins, four peaks identified as two iron-related and two fibrogenesis-related protein fragments, respectively. Multivariate analysis showed that the serum ferritin and three peak intensity values (Apo A1, hemopexin and transferrin) were independent variables associated with SVRs, and the area under the receiver operating characteristic (ROC) curves for SVR prediction by using the Apo A1/hemopexin and hemopexin/transferrin were 0.964 and 0.936. In conclusion, pretreatment serum protein profiling by SELDI-TOF/MS is variable for identification of response-related host factors, which are useful for treatment efficacy prediction in CHC receiving PEG-IFN plus RBV. Our data also may help us understand the mechanism for treatment resistance and development of more effective antiviral therapy targeted toward the modulation of lipogenesis or iron homeostasis in CHC patients.     

Methods for on-chip protein analysis

The unambiguous identification of peptides/proteins is crucial for the definition of the proteome. Using ProteinChip Array technology also known as surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS), we developed experimental protocols and probed test conditions required for the protein identification on ProteinChip surfaces. We were able to directly digest peptides/proteins on-chip surfaces by specific proteases, such as trypsin, and to obtain the peptide mass fingerprint of the sample under investigation by its direct analysis on a simple laser desorption/ionization mass spectrometer. Furthermore, tandem mass spectrometry was performed on several of the resulting tryptic peptides by using collision quadrupole time of flight (Qq-TOF) MS/MS via the ProteinChip interface, thus allowing the unambiguous identification of the protein(s) within the sample. In addition, we were able to identify the C-terminal sequence of peptides by their digestion with carboxypeptidase Y directly on ProteinChip surfaces coupled with SELDI-TOF MS analysis of the resulting peptide mass ladders employing the instrument's protein ladder sequence software. Moreover, the removal of up to nine amino acid residues from the C-terminal end of a peptide extends the functional range of Qq-TOF MS/MS sequence determination to over 3000 m/z. The utility of these procedures for the proteome exploration are discussed.     

Quantitative quality-assessment techniques to compare fractionation and depletion methods in SELDI-TOF mass spectrometry experiments

Motivation: Mass spectrometry (MS), such as the surface-enhancedlaser desorption and ionization time-of-flight (SELDI-TOF) MS,provides a potentially promising proteomic technology for biomarkerdiscovery. An important matter for such a technology to be usedroutinely is its reproducibility. It is of significant interestto develop quantitative measures to evaluate the quality andreliability of different experimental methods. Results: We compare the quality of SELDI-TOF MS data using unfractionated,fractionated plasma samples and abundant protein depletion methodsin terms of the numbers of detected peaks and reliability. Severalstatistical quality-control and quality-assessment techniquesare proposed, including the Graeco–Latin square designfor the sample allocation on a Protein chip, the use of thepairwise Pearson correlation coefficient as the similarity measurebetween the spectra in conjunction with multi-dimensional scaling(MDS) for graphically evaluating similarity of replicates andassessing outlier samples; and the use of the reliability ratiofor evaluating reproducibility. Our results show that the numberof peaks detected is similar among the three sample preparationtechnologies, and the use of the Sigma multi-removal kit doesnot improve peak detection. Fractionation of plasma samplesintroduces more experimental variability. The peaks detectedusing the unfractionated plasma samples have the highest reproducibilityas determined by the reliability ratio. Availability: Our algorithm for assessment of SELDI-TOF experimentquality is available at http://www.biostat.harvard.edu/~xlin Contact: harezlak{at}post.harvard.edu Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Thomas Lengauer