Mass Spectrometric Identification of Proteotypic Peptides from Clinically Used Tumor Markers

Introduction

With the rapid development of mass spectrometry-based technologies such as multiple reaction monitoring and heavy-isotope-labeled-peptide standards, quantitative analysis of biomarker proteins using mass spectrometry is rapidly progressing toward detection of target proteins/peptides from clinical samples. Proteotypic peptides are a few peptides that are repeatedly and consistently identified from a protein in a mixture and are used for quantitative analysis of the protein in a complex biological sample by mass spectrometry.

Materials and Methods

Using mass spectrometry, we identified peptide sequences and provided a list of tryptic peptides and glycopeptides as proteotypic peptides from five clinically used tumor markers, including prostate-specific antigen, carcinoembryonic antigen, Her-2, human chorionic gonadotropin, and CA125.

Conclusion

These proteotypic peptides have potential for targeted detection as well as heavy-isotope-peptide standards for quantitative analysis of marker proteins in clinical specimens using a highly specific, sensitive, and high-throughout mass spectrometry-based analysis method.     

Direct class I HLA antigen discovery to distinguish virus-infected and cancerous cells

Class I human leukocyte antigen molecules are nature’s proteome-scanning chips, presenting thousands of endogenously loaded peptides on the surface of virtually every cell in the body. Cytotoxic T cells survey the class I human leukocyte antigen peptide cargo presented, recognize peptides unique to unhealthy cells and destroy diseased cells. A precise understanding of how class I molecules distinguish diseased cells is positioned to drive immune-based diagnostics, therapies and vaccines. When identifying epitopes unique to unhealthy cells, the most experimentally direct approach is to examine the class I-presented peptides of infected/cancerous cells. Here we discuss the strategies adapted for protein production, protein/peptide purification, peptide separation and for maintaining experimental reproducibility during the direct characterization of class I human leukocyte antigen peptides.     

Direct class I HLA antigen discovery to distinguish virus-infected and cancerous cells

Class I human leukocyte antigen molecules are nature's proteome-scanning chips, presenting thousands of endogenously loaded peptides on the surface of virtually every cell in the body. Cytotoxic T cells survey the class I human leukocyte antigen peptide cargo presented, recognize peptides unique to unhealthy cells and destroy diseased cells. A precise understanding of how class I molecules distinguish diseased cells is positioned to drive immune-based diagnostics, therapies and vaccines. When identifying epitopes unique to unhealthy cells, the most experimentally direct approach is to examine the class I-presented peptides of infected/cancerous cells. Here we discuss the strategies adapted for protein production, protein/peptide purification, peptide separation and for maintaining experimental reproducibility during the direct characterization of class I human leukocyte antigen peptides.     

Validation of immunity induced by inactivated CCPP vaccine with different adjuvants

The study was conducted in the premises National Veterinary Institute (NVI) to validate the immunity induced by inactivated F38 antigen adjuvated with saponin and Montanide ISA 50 and combined with and without anthrax vaccine.Post-inoculation reactions; pyrogenic effects, safety and inocuity of the vaccines were assessed. Increased body temperature and local edematous reactions were seen in animals inoculated with saponin adjuvated CCPP vaccine (100%) while 20% of the goats in ISA 50 adjuvated group showed local reaction. Sera collected from day 0 to 10th week were tested to assess the sero-conversion using monoclonal antibody based B-ELISA technique. Saponin adjuvated groups, in both monovalent CCPP and in the combined CCPP with anthrax vaccine showed a higher mean percentage of inhibition value as compared with ISA 50 adjuvated vaccine.After 8 months of post vaccination, contact challenge trial was conducted in 66 experimentally vaccinated and 20 negative control goats combined with 15 actively CCPP sick goats. Various clinical signs were recorded daily, autopsy was done on died goats and the live goats were sacrificed after 2 months of contact. The side by side samples from thoracic exudates, lung and mediastinal and bronchial lymph nodes were collected from goats shown to have developed indicative CCPP lesion for isolation and F38 antigen detection.The present experimental study indicated that application of inactivated and adjuvated CCPP vaccine significantly reduced the morbidity and development of lesions (P < 0.001). Among vaccinated groups CCPP + anthrax + saponin showed better protection, with low rate of nasal discharge and cough at 33% and 28.6%, respectively, and protection level of 94.1% from death and 65% from lung lesion development. However, the variation in protection among the vaccinated groups was not significant (P > 0.05).These findings disclosed that inactivated CCPP vaccine adjuvated with saponin and ISA 50 significantly reduce morbidity and mortality of goats due to CCPP and also indicated the importance of utilization of ISA 50 as alternative adjuvant to minimize post-vaccinal reactions encountered in use of saponin as adjuvant.     

Type 1 fimbriae of Escherichia coli as carriers of heterologous antigenic sequences

A strategy has been designed for the construction of recombinant bacterial strains which eventually may become useful as live vaccines and which may also be relevant for the preparation of conventional vaccines. The approach used is the fusion of small antigenic peptide sequences into specific segments of a protein whose location on the bacterial surface ensures that the recombinant organism is able to present the inserted antigen to the host (animal or human) infected by the bacterium. The chosen surface protein is a naturally occurring polymer of Escherichia coli, viz., type 1 fimbriae. The results obtained show that fusion of such foreign sequences into selected points of the structural protein of the fimbriae results in the production of functionally normal type 1 fimbriae. Furthermore, hybrid fimbriae carrying such small epitope sequences can be recognized by antibodies directed against the foreign parent protein. This observation is an important prerequisite for the eventual design of useful vaccines. The analysis of the fimbrial protein and its potential as a carrier of foreign peptides from hepatitis B surface antigen, foot-and-mouth disease virus and poliovirus indicated that there may be several positions in the protein which may turn out to be relevant for this purpose and be important fusion sites.     

The implications of proteolytic background for shotgun proteomics

The analysis by liquid chromatography coupled to tandem mass spectrometry of complex peptide mixtures, generated by proteolysis of protein samples, is the main proteomics method used today. The approach is based on the assumption that each protein present in a sample reproducibly and predictably generates a relatively small number of peptides that can be identified by mass spectrometry. In this study this assumption was examined by a targeted peptide sequencing strategy using inclusion lists to trigger peptide fragmentation attempts. It was found that the number of peptides observed from a single protein is at least one order of magnitude greater than previously assumed. This unexpected complexity of proteomics samples implies substantial technical challenges, explains some perplexing results in the proteomics literature, and prompts the need for developing alternative experimental strategies for the rapid and comprehensive analysis of proteomes.     

直接培养法检测支原体方法的建立

采用牛心消化液,加入支原体营养成份及琼脂,制备成固体培养基。以此培养基检测支原体,并根据其灵敏度及适用性确定培养基的配方。结果表明,用此法可以检测牛血清、胰酶、细胞及疫苗中的支原体生长,并且检测时间短,重复性好,灵敏度高,可以用于生物制品的质量控制。     

High Immunogenicity of the Human Leukocyte Antigen Peptidomes of Melanoma Tumor Cells

Human leukocyte antigens (HLA) bind peptides generated by limited proteolysis in cells and present them at the cell surfaces for recognition by T cells. Through this antigen presentation function they control the specificity of T cell responses and thereby adaptive immune responses. Knowledge of HLA-bound peptides is thus key to understanding adaptive immunity and to the development of vaccines and other specific immune intervention strategies. To gain insight into the antigenicity of melanomas, peptides were extracted from HLA isolated from the tumor cells, separated by two-dimensional HPLC, and sequenced by mass spectrometry. The spectra were analyzed by database-dependent MASCOT searches and database-independent de novo sequencing and, where required, confirmed with synthetic peptides, which were also used to determine their immunogenicity. Comparing four different melanoma cell lines, little overlap of the HLA-bound peptides was found, suggesting a high degree of individualization of the HLA peptidomes. This notwithstanding, the peptidomes were highly immunogenic in the patients from whom the tumor cells had been established and in unrelated patients. This broad cross-patient immunogenicity was only exceptionally related to individual peptides. The majority of the identified epitopes were derived from low to medium abundance proteins, mostly involved in sensitive cellular processes such as cell cycle control, DNA replication, control of gene expression, tumor suppressor function, and protein metabolism. The peptidomes thus provide insights into processes potentially related to tumorigenesis. Furthermore, analyses of the peptide sequences yield information on the specificity of peptide selection by HLA applicable to the developing prediction algorithms for T cell epitopes.     

Determination of proteins in infant formula by high-performance liquid chromatography-electrospray tandem mass spectrometry

To determine the protein content of formula, gel electrophoresis was performed on the infant formula samples and the entire protein patterns were analyzed by nano-high performance liquid chromatography-electrospray tandem mass spectrometry (nano-HPLC/ESI/MS/MS). From the commercial infant formula profiled in this study, a total of 154 peptides, corresponding to 31 unique proteins were identified by nano-HPLC/ESI/MS/MS. Each of the identified peptides was reconfirmed by a strict integrated approach using tandem mass spectra. This protein profiling method using gel electrophoresis coupled with nano-HPLC/ESI/MS/MS and manual evaluation is a sensitive and accurate method for protein identification as well as a powerful tool for monitoring various types of food products.     

Properties of the co-chaperone protein p23 erroneously attributed to ALG-2 (apoptosis-linked gene 2)

A commercial antibody (clone 22) directed against the apoptosis-linked gene 2 (alg2, pdcd6) encoded protein has been used by several groups. Up-regulated expression of the antigen was observed in primary tumours and in metastatic tissue and also during rat brain ischemia. Furthermore, antigen down-regulation was found in human atherosclerotic plaques. Recently, we found that the clone 22 antibody does not recognise ALG-2. In the present study the antigen of the clone 22 antibody was identified as the heat shock protein 90 (HSP90) co-chaperone protein p23, identical to the cytosolic prostaglandin E2 synthase, by immunoprecipitation followed by tryptic in-gel digests and mass spectrometry of the purified peptides. Moreover, the heterogeneous ribonuclear protein A2/B1 was found to be a part of the p23 co-immunoprecipitated protein complex.     

A neuroproteomic approach to targeting neuropeptides in the brain

A novel universal neuropeptide display approach in the mass range of 300-5000 Da was developed to complement two-dimensional gel electrophoresis in the analysis of peptides and small proteins from brain tissue samples. For the analysis of neuropeptides we utilized on-line nanoscale capillary reversed phase liquid chromatography and electrospray ionization quadrupole-time of flight mass spectrometry. The method was employed for the analysis of a large number of peptides from three specific rat brain regions. Approximately 1500 peptides from each brain region were detected in the same analysis. Several of these peptides were sequenced using collision-induced dissociation and identified by database search tools. In addition, a method for comparing peptide elution profiles between samples was developed, to provide two- and three-dimensional computer graphics of the profiles and to pinpoint differences for statistical measurements. Among the characterized peptides were fragments from proteins such as hemoglobin, alpha-synuclein, stathmin, cyclophilin, actin, NADH dehydrogenase, cytochrome c oxidase and prosomatostatin, as well as the bioactive neuropeptides W-hemorphin-4, and LW-hemorphin-7. The present study showed that the combination of nanoscale reversed phase liquid chromatography and high-resolution tandem mass spectrometry provides a novel and powerful approach to investigate a large number of peptides and protein fragments in the brain.     

Multiple display of foreign peptides on a filamentous bacteriophage. Peptides from Plasmodium falciparum circumsporozoite protein as antigens

We describe here two systems for encoding foreign amino acid sequences in the exposed N-terminal segment of the major coat protein of bacteriophage fd. Small peptides can be encoded directly; larger peptides are encoded in hybrid bacteriophage particles, in which the capsid is formed from a mixture of wild-type and modified coat proteins. In both cases, the peptides are present in multiple copies per phage particle. Peptides that represent the circumsporozoite protein, the major surface antigen of the sporozoites of the malaria parasite, Plasmodium falciparum, were inserted in this way and found to be highly immunogenic. These systems should prove to be valuable in displaying specific or random peptides as antigens, and could lead to cheap and effective vaccines. They will also allow rapid screening of peptides as potential agents of other biological effects, with important applications in biomolecular design.     

Proteomics in cancer vaccine development

Proteomics is a new scientific field aimed at the large-scale characterization of the protein constituents of biologic systems. It facilitates comparisons between different protein preparations by searching for minute differences in their protein expression repertoires and the patterns of their post-translational modifications. These attributes make proteomics perfectly suited for searching for proteins and peptides expressed exclusively or preferentially in cancer cells as candidates for cancer vaccines. The main proteomics technologies include 2D polyacrylamide gel electrophoresis, multidimensional high-performance liquid chromatography, mass spectrometry and protein arrays. Proteomics technologies used to analyze cancer culture cells, fresh tumor specimens, human leukocyte antigen peptides, serum and serum antibodies (serologic proteomics) have successfully identified tumor markers. Turning the potential vaccine candidates identified by proteomics technologies into clinical treatments awaits demonstration.     

液质联用多反应监测法定量目标多肽或蛋白质

为建立优化的血浆内源性多肽提取方法,并且构建目标多肽和蛋白质的质谱定量方 法,本研究考察了超滤法、有机溶剂沉淀法和固相萃取法对血浆内源性多肽的提取效果 ,并通过Tricine-SDS-PAGE对提取效果进行比较.通过液相色谱串联质谱多反应监测 （MRM）分析,建立了多肽标准品ESAT-6定量方法,并将ESAT-6定量建立的液相色谱和质谱条件应用于蛋白质的定量,对多肽和蛋白质MRM定量的标准曲线进行了考 察.Tricine-SDS-PAGE结果表明,乙腈沉淀法是最佳的血浆内源性多肽提取方法,低分子量的多肽可以得到很好的富集,且能有效地去除高分子蛋白质的污染.液相色谱串联 质谱MRM法检测血浆内提取的多肽,标准曲线的线性较好,相关系数为0.999.另外,采 用MRM法对胶内分离的蛋白质进行定量,标准曲线的线性相关系数为0.995.综上所述, 本研究构建了一种简单有效的血浆多肽提取方法,通过液质联用MRM法成功地实现了目标多肽和蛋白质定量测定.该定量方法可以推广应用于复杂样品中的多肽和蛋白质的定 量分析.     

MHC class II presentation of endogenous tumor antigen by cellular vaccines depends on the endocytic pathway but not H2-M

We have developed cell-based cancer vaccines that activate anti-tumor immunity by directly presenting endogenously synthesized tumor antigens to CD4⁺ T helper lymphocytes via MHC class II molecules. The vaccines are non-conventional antigen-presenting cells because they express MHC class II, do not express invariant chain or H-2M, and preferentially present endogenous antigen. To further improve therapeutic efficacy we have studied the intracellular trafficking pathway of MHC class II molecules in the vaccines using endoplasmic reticulum-localized lysozyme as a model antigen. Experiments using endocytic and cytosolic pathway inhibitors (chloroquine, primaquine, and brefeldin A) and protease inhibitors (lactacystin, LLnL, E64, and leupeptin) indicate antigen presentation depends on the endocytic pathway, although antigen degradation is not mediated by endosomal or proteasomal proteases. Because H2-M facilitates presentation of exogenous antigen via the endocytic pathway, we investigated whether transfection of vaccine cells with H-2M could potentiate endogenous antigen presentation. In contrast to its role in conventional antigen presentation, H-2M had no effect on endogenous antigen presentation by vaccine cells or on vaccine efficacy. These results suggest that antigen/MHC class II complexes in the vaccines may follow a novel route for processing and presentation and may produce a repertoire of class II-restricted peptides different from those presented by professional APC. The therapeutic efficacy of the vaccines, therefore, may reside in their ability to present novel tumor peptides, consequently activating tumor-specific CD4⁺ T cells that would not otherwise be activated.     

In silico tools for predicting peptides binding to HLA-class II molecules: more confusion than conclusion

Identification of promiscuous peptides, which bind to human leukocyte antigen, is indispensable for global vaccination. However, the development of such vaccines is impaired due to the exhaustive polymorphism in human leukocyte antigens. The use of in silico tools for mining such peptides circumvents the expensive and laborious experimental screening methods. Nevertheless, the intrepid use of such tools warrants a rational assessment with respect to experimental findings. Here, we have adopted a 'bottom up' approach, where we have used experimental data to assess the reliability of existing in silico methods. We have used a data set of 179 peptides from diverse antigens and have validated six commonly used in silico methods; ProPred, MHC2PRED, RANKPEP, SVMHC, MHCPred, and MHC-BPS. We observe that the prediction efficiency of the programs is not balanced for all the HLA-DR alleles and there is extremely high level of discrepancy in the prediction efficiency apropos of the nature of the antigen. It has not escaped our notice that the in silico methods studied here are not very proficient in identifying promiscuous peptides. This puts a much constraint on the intrepid use of such programs for human leukocyte antigen class II binding peptides. We conclude from this study that the in silico methods cannot be wholly relied for selecting crucial peptides for development of vaccines.     

SIR: Deterministic protein inference from peptides assigned to MS data

Currently the bottom up approach is the most popular for characterizing protein samples by mass spectrometry. This is mainly attributed to the fact that the bottom up approach has been successfully optimized for high throughput studies. However, the bottom up approach is associated with a number of challenges such as loss of linkage information between peptides. Previous publications have addressed some of these problems which are commonly referred to as protein inference. Nevertheless, all previous publications on the subject are oversimplified and do not represent the full complexity of the proteins identified. To this end we present here SIR (spectra based isoform resolver) that uses a novel transparent and systematic approach for organizing and presenting identified proteins based on peptide spectra assignments. The algorithm groups peptides and proteins into five evidence groups and calculates sixteen parameters for each identified protein that are useful for cases where deterministic protein inference is the goal. The novel approach has been incorporated into SIR which is a user-friendly tool only concerned with protein inference based on imports of Mascot search results. SIR has in addition two visualization tools that facilitate further exploration of the protein inference problem.     

Efficient method for the proteomic analysis of fixed and embedded tissues

Formalin-fixed and paraffin-embedded (FFPE) tissues present a particular challenge for proteomic analysis. Yet, most of the archived tissues in hospitals and tissue banks worldwide are only available in this form. We have developed conditions for removal of the embedding medium and protein digestion, such that informative tryptic peptides are released from fixed proteins which are suitable for analysis by liquid chromatography-mass spectrometry (LC-MS). We demonstrate that the peptide identifications made by this approach compare favorably to those made from matched fresh frozen tissue. Moreover, we demonstrate that a high level of sequence coverage can be observed for proteins of interest.     

基于可见光测定的山羊支原体山羊肺炎亚种抗原定量

山羊支原体山羊肺炎亚种(Mycoplasma capricolum subsp. capripneumoniae, Mccp)是山羊传染性胸膜肺炎(contagious caprine pleuropneumonia, CCPP)的病原,可用灭活疫苗和荚膜多糖(capsular polysaccharide, CPS)间接血凝试剂进行预防和血清学检测,但高昂的培养成本和复杂的抗原定量一直困扰着生产人员。为解决生产实际中出现的这些问题,本研究基于Mccp代谢组学的前期理论基础,通过改变初始pH值的方法,初步筛选出初始pH值为7.8的可以同时提高2种抗原产量的糖发酵培养基。利用紫外可吸收光谱可识别酚红,以及十六烷基三甲基溴化铵(cetyltrimethylammonium bromide, CTAB)可与阴离子荚膜多糖结合的理论依据,建立了利用紫外光谱分析Mccp达到的培养阶段,以及利用CTAB沉淀法相对定量发酵液荚膜多糖抗原产量的方法。通过紫外图谱观察的方法可对应Mccp生长曲线进行指导生产,大大节省传统颜色变化单位(color change unit, CCU)法的监测时间,提高了原肉眼观察方法的精确度。建立的CTAB沉淀法可在5 h内完成对CPS含量的监测,与传统的差值法相比大大缩短了时间,并且其准确度得到苯酚-硫酸法的验证。本研究优化的一种培养基和建立的两种相关性比较方法,可有效降低Mccp生产成本,提高生产效率,这些方法已在本实验室的研究阶段得到应用,为进一步改进CCPP灭活疫苗和荚膜多糖的生产工艺以及快速定量提供了实验数据。     

Quantitative proteome analysis using differential stable isotopic labeling and microbore LC-MALDI MS and MS/MS

We demonstrate an approach for global quantitative analysis of protein mixtures using differential stable isotopic labeling of the enzyme-digested peptides combined with microbore liquid chromatography (LC) matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS). Microbore LC provides higher sample loading, compared to capillary LC, which facilitates the quantification of low abundance proteins in protein mixtures. In this work, microbore LC is combined with MALDI MS via a heated droplet interface. The compatibilities of two global peptide labeling methods (i.e., esterification to carboxylic groups and dimethylation to amine groups of peptides) with this LC-MALDI technique are evaluated. Using a quadrupole-time-of-flight mass spectrometer, MALDI spectra of the peptides in individual sample spots are obtained to determine the abundance ratio among pairs of differential isotopically labeled peptides. MS/MS spectra are subsequently obtained from the peptide pairs showing significant abundance differences to determine the sequences of selected peptides for protein identification. The peptide sequences determined from MS/MS database search are confirmed by using the overlaid fragment ion spectra generated from a pair of differentially labeled peptides. The effectiveness of this microbore LC-MALDI approach is demonstrated in the quantification and identification of peptides from a mixture of standard proteins as well as E. coli whole cell extract of known relative concentrations. It is shown that this approach provides a facile and economical means of comparing relative protein abundances from two proteome samples.