Analysis of the human testis proteome by mass spectrometry and bioinformatics

The testis is a unique organ responsible for sperm production and androgen secretion in men. To analyze the human testis proteome on a large scale, 1-D SDS-PAGE and RP-LC-MS/MS were applied and 1430 proteins in the human testis were identified. Both the false-positive rate of peptides and protein identification confidence scores were calculated in the present study. Subsequent bioinformatics analysis of the human testis proteome revealed 39 testis-specific proteins which may be important for testis functions. And a large family of proteins were identified possibly involved in alternative splicing, which may also be involved in testis-specific splicing events and explain why splicing is so prevalent in the testis. Compared with the studies on brain proteome, researches on the testis proteome is still very limited. Studies of these proteins will give a better understanding on the function of the testis. Moreover, this large-scale identification of testis proteins in humans could serve as a reference for future studies on the mechanisms underlying male infertility, searching for potential contraceptive targets, and developing new treatments for testis cancer.     

Analysis of the differential proteome of human erythroblasts during in vitro erythropoiesis by 2-D DIGE

In the present study we have used an in vitro culture system that induces differentiation of human CD34(+) cells down the erythroid lineage along with 2-D DIGE to determine the differential proteome of erythroblasts at specific developmental stages during erythropoiesis. We initially distinguished 154 proteins differentially expressed between pro-normoblasts and polychromatic/orthochromatic erythroblasts, of which 24 protein spots, representing 21 different proteins, were identified following MS/MS and verification in replicate experiments with cells from different individuals. These data were confirmed by analysis of the differential proteome of erythroblasts at more discrete stages of erythropoiesis using 2-D DIGE and by mapping the expression of three identified proteins (Annexin I, Annexin II, Carbonic Anhydrase I) throughout erythropoiesis by Western blot with specific antisera. In addition, the differential expression of proteins due to biological variation, such as polymorphism, was determined by comparing erythroblasts at the same developmental stage from different individuals; none of the proteins thus identified were represented in the above data set. Finally, we discuss the problems associated with 2-D DIGE gel-based proteomic approaches such as ours and suggest a modified approach for decreased inter-gel variation, improved protein resolution and increased protein concentration, which should significantly facilitate protein identification.     

Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: an NCI-CPTC initiative perspective

Proteomics holds great promise in personalized medicine for cancer in the post-genomic era. In the past decade, clinical proteomics has significantly evolved in terms of technology development, optimization and standardization, as well as in advanced bioinformatics data integration and analysis. Great strides have been made for characterizing a large number of proteins qualitatively and quantitatively in a proteome, including the use of sample fractionation, protein microarrays and MS. It is believed that differential proteomic analysis of high-quality clinical biospecimen (tissue and biofluids) can potentially reveal protein/peptide biomarkers responsible for cancer by means of their altered levels of expression and/or PTMs. Multiple reaction monitoring, a multiplexed platform using stable isotope dilution-MS with sensitivity and reproducibility approaching that of traditional ELISAs commonly used in the clinical setting, has emerged as a potentially promising technique for next-generation high-throughput protein biomarker measurements for diagnostics and therapeutics.     

The human synovial fluid proteome: A key factor in the pathology of joint disease

This review aims to summarise our knowledge to date on the protein complement of the synovial fluid (SF). The tissues, structure and pathophysiology of the synovial joint are briefly described. The salient features of the SF proteome, how it is composed and the influence of arthritic disease are highlighted and discussed. The concentrations of proteins that have been detected and quantified in SF are drawn together from the literature on osteoarthritis, rheumatoid arthritis and juvenile idiopathic arthritis. The measurements are plotted to give a perspective on the dynamic range of protein levels within the SF. Approaches to proteomic analysis of SF to date are discussed along with their findings. From the recent literature reviewed within, it is becoming increasingly clear that analysis of the SF proteome as a whole, could deliver the most valuable differential diagnostic fingerprints of a number of arthritic disorders. Further development of proteomic platforms could characterise prognostic profiles to improve the clinician's ability to resolve unremitting disease by existing and novel therapeutics.     

On-chip cell migration assay for quantifying the effect of ethanol on MCF-7 human breast cancer cells

Ethanol consumption is associated with the risk of breast cancer progression; however, the mechanism of relationship has not yet been fully explained. Research on breast cancer cell migration after ethanol stimulation may give hope for a better understanding of the disease and oncotherapy. Conventional cell migration assays such as Boyden chamber and wound-healing assays are easy to conduct for this purpose; however, these assays have inherent limitations. In this study, we quantified the effect of ethanol on MCF-7 hunam breast cancer cells using a microfluidics-based wound-healing assay. Wounds were prepared by partially digesting a confluent cell sheet using parallel laminar flows in the presence of protease trypsin. The cells at the leading edge of the wound remained intact. Cell image analysis indicates that all the cells cultured in the microdevice took on a good morphology and monolayer growth status. Cell viability assay demonstrates that cell viability decreased with the increase in ethanol concentration and treatment time. For 0, 22, 43, and 65 mmol/l of ethanol, cell viability after being cultured for 24 h was 100%, 99.6%, 99.4%, and 98.4%, respectively. Studying MCF-7 human breast cancer cell migration when treated with different ethanol concentrations revealed that the cell migration distance is directly proportional with ethanol concentration. After being cultured for 24 h at 37°C and 5% CO₂, the maximal cell migration distance was 231, 283, and 332 μm for 22, 43, and 65 mmol/l ethanol, respectively; all results were higher than the blank test (i.e., ethanol-free test, 218 μm). These findings will be beneficial in developing microfluidic device applications for future research on breast tumor therapy in a biomimetic microenvironment and for developing new methods for breast cancer therapy.     

Old proteins and the Achilles heel of mass spectrometry. The role of proteomics in the etiology of human cataract

Proteomics may have enabled the root cause of a major human-blinding condition, age-related cataract, to be established. Cataract appears to result from the spontaneous decomposition of long-lived macromolecules in the human lens, and recent proteomic analysis has enabled both the particular crystallins, and the specific sites of amino acid modification within each polypeptide, to be identified. Analysis of proteins from cataract lenses has demonstrated that there are key sites on some structural proteins that show a consistently greater degree of deterioration than age-matched normal lenses. Proteomic analysis, using MS, revealed that the most abundant posttranslational modification of aged lens proteins is racemization. This is somewhat ironic, since structural isomers can be viewed as the “Achilles heel” of MS and there are typically few, if any, differences in the MS/MS spectra of tryptic peptides containing one d -amino acid. It is proposed that once a certain level of spontaneous PTM at key sites occurs, that protein–protein interactions are disrupted, and binding of complexes to cell membranes takes place that impairs cell-to-cell communication. These findings may apply more widely to age-related human diseases, in particular where the deterioration of long-lived proteins is a crucial component in the etiology.     

Clinical applications of capillary electrophoresis coupled to mass spectrometry in biomarker discovery: Focus on bladder cancer

A major requirement in the application of proteins as clinical biomarkers is that they provide a highly sensitive and specific result in disease assessment. Since single biomarkers are generally of limited accuracy, a group or panel of well-characterized biomarkers appears appropriate, providing a more robust and sensitive MS-based analytical platform. CE coupled to MS has been successfully used in biomarker discovery and application, as it enables the selective detection of peptides and small proteins, combining the high separation capacity of CE with the advanced sensitivity of MS. CE-MS allows the characterization of highly complex samples (such as urine, plasma, and other biofluids) in a consistent and reproducible way. It has a range of applications, many focusing especially in studies on urinary peptide biomarkers in kidney and cardiovascular diseases. Another major field of interest has been malignancy of the genitourinary system. In the first part of this review, we cover technical aspects and performance characteristics of CE-MS, with special focus on the requirements for biomarker discovery and clinical application. In the second part, we review the potential and development of CE-MS in the management of genitourinary cancers, especially bladder cancer. CE-MS has been employed in several studies aimed at discovering biomarkers for bladder cancer that may be useful in diagnosis, monitoring for recurrence, and prediction of the risk for the muscle-invasive stage. In the last part of the review, we discuss current challenges and provide an outlook for ongoing and possible future developments.     

High-throughput measurement of Ca by accelerator mass spectrometry to quantitate small changes in individual human bone turnover rates

Biochemical markers of bone turnover suffer from large analytical and natural fluctuations (20–30%), making small differences in bone resorption impossible to resolve. This limits the clinical utility of such markers for individuals with the skeletal complications associated with many disease states (e.g., metastatic cancer, renal failure, osteoporosis). We are developing the capability to measure small changes (5–10%) in bone turnover rate in vivo by tagging the living skeleton with ⁴¹Ca. Among the stable and radioactive calcium isotopes, only ⁴¹Ca is useful for direct quantitation of bone turnover because it is extremely rare in nature and radiologically benign (10⁵ years half-life, pure electron capture decay). The ratio of this tracer to total calcium remains quantifiable in body fluids and excreta via accelerator mass spectrometry (AMS) for many years following a single physiological-sized oral or intravenous dose. The highly automated AMS instrumentation and streamlined sample preparation allows a single operator to prepare or run more than 100 samples per day—significantly more than other ⁴¹Ca programs worldwide. We intend to exploit these measurements for earlier diagnosis of pathological processes and interactive intervention with therapeutic agents, allowing modulation of these agents to obtain the best individual result for a patient.     

Expression of tropomyosin alpha 4 chain is increased in esophageal squamous cell carcinoma as evidenced by proteomic profiling by two-dimensional electrophoresis and liquid chromatography-mass spectrometry/mass spectrometry

To identify proteins associated with esophageal carcinogenesis, we performed protein profiling of 16 esophageal squamous cell carcinomas (ESCCs) and paired noncancerous tissues by 2-DE and MS/MS. In cancerous tissues, three spots showed significant up-regulation in the amount of protein, while eight spots were significantly down-regulated. The identities of the spots were determined by PMF with LC-MS/MS and were confirmed by immunoblotting. The up-regulated proteins were tropomyosin alpha 4 chain, transgelin, and pyruvate kinase. The down-regulated proteins were serum albumin precursor, isoforms of annexin A1, tropomyosin beta chain, 14-3-3 protein sigma, and isoforms of serotransferrin precursor. In all 16 cases, up-regulation of the tropomyosin alpha 4 chain was confirmed by immunoblotting. Localization of the tropomyosin alpha 4 chain in ESCC cells and adjacent fibroblasts was confirmed by immunohistochemistry.     

Computer-aided thermodynamics of fcc solid ternary Fe–Co–Cr alloys by Knudsen cell mass spectrometry

The fcc solid ternary Fe–Co–Cr alloys have been investigated thermodynamically by means of computer-aided Knudsen cell mass spectrometry. The “Digital Intensity Ratio” (DIR) method has been applied for the determination of the thermodynamic excess properties. The ternary thermodynamically adapted power (TAP) series concept is used for the algebraic representation of the molar excess properties. The corresponding TAP parameters as well as the values of the molar excess Gibbs energies G^E, of the molar heats of mixing H^E, of the molar excess entropies S^E, and of the thermodynamic activities at 1673 K are presented.     

Comparative proteome profiling of MCF10A and 184A1 human breast epithelial cells emphasized involvement of CDK4 and cyclin D3 in cell proliferation

Acquiring high proliferation rate is crucial for carcinogenic transformation of cells. We report here proteome profiling of human breast epithelial cells with low (184A1) and high (MCF10A) proliferation rates. We identified 183 proteins in 184A1 and 318 proteins in MCF10A cells. These datasets provide the most comprehensive proteome annotations of 184A1 and MCF10A cells. Proteins were taken for identification from 2-D gels in a systematic and unbiased way. Functional clustering of the identified proteins showed similarities in distribution of proteins to the same functional domains, indicating similarities in proteomes of 184A1 and MCF10A cells. Among observed differences in protein expression, we validated correlation of expression of endogenous cyclin-dependent kinase 4 (CDK4), cyclin D3, cdc25B, and p38γ with cell proliferation. Furthermore, down-regulation of CDK4 and cyclin D3 with specific siRNA inhibited cell proliferation, which emphasized the role of CDK4 and cyclin D3 in enhancement of cell proliferation rate of human breast epithelial cells.     

相似度算法在手写签名质谱成像鉴定中的应用研究

质谱成像技术无需任何样品预处理,即可获取待测样品的分子信息和分布情况。本文采用表面解吸常压化学电离质谱(SDAPCI-MS)技术对手写签名样品进行检测,通过对所得的质谱特征峰信号进行成像处理,获取书写油墨分布的强度信息。实验结果表明真实签名和伪造签名因为笔压轻重不同而油墨分布位置不同,据此能够区分签名的真伪。应用相似度算法对手写签名的特征成像数据进行分析,在样品量较少的情况下,能够客观的比较真迹之间以及真迹和伪迹之间的相似程度,进而实现对真伪签名的准确鉴定。本方法操作简便,耗时较短,对手写笔迹的鉴定具有重要的借鉴意义。     

激光质谱系统中激光波长高实时集中控制研究与应用

随着激光共振电离质谱系统的迅速发展,更准确地研究激光波长与电离质谱信号的关系,实现激光波长与电离质谱信号的自动对比,开展了激光波长高实时集中控制的研究。采用数据库技术、多线程技术和RS485通讯技术等完成了激光波长的高实时控制的研制工作。该系统实现了对激光波长的闭环和各种方式的扫描控制及运行状态的实时监测功能,能够以外触发方式与质谱系统进行同步,满足了激光质谱系统对波长的大范围、小范围及精细扫描的需求,实现了波长单步扫描数据响应时间小于250ms。     

A qualitative proteome investigation of the sediment portion of human urine: Implications in the biomarker discovery process

Inherent to the biomarker discovery process is a comparative analysis of physiological states. It is therefore critical that the proteome detection protocol does not bias the analysis. With urine, the sediment portion, obtained upon thawing frozen urine, is routinely discarded prior to proteome analysis. However, our results demonstrate that such a practice inadvertently induces bias, having significant implications in the biomarker discovery process. We present the first proteome investigation of human urinary sediments, identifying 60 proteins in this phase by MS. Many sediment proteins were also detected in the urinary supernatant, indicating that several proteins partition between the two phases. This partitioning is dependant on the pH of the sample, as well as the degree of sample agitation. As a consequence of discarding the sediment portion of urine, the concentration of potential candidate biomarkers in the supernatant phase will be altered or, in other instances, may be completely removed from the sample. To minimize this, the pH of all samples should first be normalized, and the samples vigorously vortexed prior to discarding the sediments. For more comprehensive biomarker investigations, we suggest that urinary sediments be analyzed along with the supernatant proteins.     

Analysis of mass spectrometry data of cerebral stroke samples: an evolutionary computation approach to resolve and quantify peptide peaks

A preliminary investigation of cerebral stroke samples injected into a mass spectrometer is performed from an evolutionary computation perspective. The detection and resolution of peptide peaks is pursued for the purpose of automatically and accurately determining unlabeled peptide quantities. A theoretical peptide peak model is proposed and a series of experiments are then pursued (most within a distributed computing environment) along with a data preprocessing strategy that includes (i) a deisotoping step followed by (ii) a peak picking procedure, followed by (iii) a series of evolutionary computation experiments oriented towards the investigation of their capability for achieving the aforementioned goal. Results from four different genetic algorithms (GA) and one differential evolution (DE) algorithm are reported with respect to their ability to find solutions that fit within the framework of the presented theoretical peptide peak model. Both unconstrained and constrained (as determined by a course grained preprocessing stage) solution space experiments are performed for both types of evolutionary algorithms. Good preliminary results are obtained.     

Analysis of the human immune response to vaccinia by use of a novel protein microarray suggests that antibodies recognize less than 10% of the total viral proteome

Control of smallpox by mass vaccination was one of the most effective public health measures ever employed for eradicating a devastating infectious disease. However, new methods are needed for monitoring smallpox immunity within current vulnerable populations, and for the development of replacement vaccines for use by immunocompromized or low-responding individuals. As a measure for achieving this goal, we developed a protein microarray of the vaccinia virus proteome by using high-throughput baculovirus expression and purification of individual elements. The array was validated with therapeutic-grade, human hyperimmune sera, and these data were compared to results obtained from individuals vaccinated against smallpox using Dryvax. A high level of reproducibility with a very low background were apparent in repetitive assays that confirmed previously reported antigens and identified new proteins that may be important for neutralizing viral infection. Our results suggest that proteins recognized by antibodies from all vaccinees constituted <10% of the total vaccinia proteome.