血清和血清外泌体的蛋白质组分析及其在肝内胆管癌中的应用

外泌体是由各种类型细胞在正常或非正常生理情况下分泌释放至细胞外且携带多种生物活性分子的细胞外囊泡,在细胞间通讯和免疫应答等生物过程中发挥着重要作用。肝内胆管癌是一种胆道上皮恶性肿瘤,早期无明显临床症状且生存率较低,目前常用的诊断手段包括依赖于影像设备的诊断方式和灵敏度及特异性较低的诊断标志物等,这些手段的不足对发展新的特异性标志物提出了需求。该文对血清中的外泌体进行了分离和表征,并采用液相色谱-质谱技术针对健康组与肝内胆管癌患者组的血清样本和血清外泌体样本进行了无标记定量蛋白质组学分析,分别从两种类型样本中鉴定并筛选到271和430种可信蛋白质。基于血清样本和血清外泌体样本的可信蛋白质定量表达值进行多维统计分析都能将健康组与肝内胆管癌患者组良好地区分开。对血清样本中鉴定到的蛋白质进行差异蛋白质筛选,肝内胆管癌患者组相对于健康组有15个上调和8个下调蛋白质;对血清外泌体样本中鉴定到的蛋白质进行差异蛋白质筛选,肝内胆管癌患者组相对于健康组有33个上调和18个下调蛋白质;基于两种样本筛选到的差异蛋白质中仅有4个是重复的,且基于血清外泌体样本的51个差异蛋白质中有35个蛋白质属于外泌体蛋白质数据库。针对差异蛋白质进行生物学信息分析,与差异蛋白质相关的分子功能、生物过程和信号通路主要涉及天然免疫反应、炎症反应和凝血等过程。该研究为发现肝内胆管癌的潜在生物标志物和探究肝内胆管癌的发生、发展和转移等过程提供了参考和借鉴价值。此外,通过比较研究发现血清外泌体样本能够获得较多的差异蛋白质和生物学信息,证明了外泌体作为组学分析样本的价值和应用潜力。     

A Pretreatment‐Free,Polymer‐Based Platform Prepared by Molecular Imprinting and Post‐Imprinting Modifications for Sensing Intact Exosomes

Exosomes are small (30–100 nm) membrane vesicles that serve as regulatory agents for intercellular communication in cancers. Currently, exosomes are detected by immuno‐based assays with appropriate pretreatments like ultracentrifugation and are time consuming (>12 h). We present a novel pretreatment‐free fluorescence‐based sensing platform for intact exosomes, wherein exchangeable antibodies and fluorescent reporter molecules were aligned inside exosome‐binding cavities. Such antibody‐containing fluorescent reporter‐grafted nanocavities were prepared on a substrate by well‐designed molecular imprinting and post‐imprinting modifications to introduce antibodies and fluorescent reporter molecules only inside the binding nanocavities, enabling sufficiently high sensitivity to detect intact exosomes without pretreatment. The effectiveness of the system was demonstrated by using it to discriminate between normal exosomes and those originating from prostate cancer and analyze exosomes in tear drops.     

A Pretreatment‐Free,Polymer‐Based Platform Prepared by Molecular Imprinting and Post‐Imprinting Modifications for Sensing Intact Exosomes

Exosomes are small (30–100 nm) membrane vesicles that serve as regulatory agents for intercellular communication in cancers. Currently, exosomes are detected by immuno‐based assays with appropriate pretreatments like ultracentrifugation and are time consuming (>12 h). We present a novel pretreatment‐free fluorescence‐based sensing platform for intact exosomes, wherein exchangeable antibodies and fluorescent reporter molecules were aligned inside exosome‐binding cavities. Such antibody‐containing fluorescent reporter‐grafted nanocavities were prepared on a substrate by well‐designed molecular imprinting and post‐imprinting modifications to introduce antibodies and fluorescent reporter molecules only inside the binding nanocavities, enabling sufficiently high sensitivity to detect intact exosomes without pretreatment. The effectiveness of the system was demonstrated by using it to discriminate between normal exosomes and those originating from prostate cancer and analyze exosomes in tear drops.     

Exosome isolation and purification via hydrophobic interaction chromatography using a polyester,capillary‐channeled polymer fiber phase

Extracellular vesicles, including microvesicles and exosomes, are lipidic membrane‐derived vesicles that are secreted by most cell types. Exosomes, one class of these vesicles that are 30–100 nm in diameter, hold a great deal of promise in disease diagnostics, as they display the same protein biomarkers as their originating cell. For exosomes to become useful in disease diagnostics, and as burgeoning drug delivery platforms, they must be isolated efficiently and effectively without compromising their structure. Most current exosome isolation methods have practical problems including being too time‐consuming and labor intensive, destructive to the exosomes, or too costly for use in clinical settings. To this end, this study examines the use of poly(ethylene terephthalate) (PET) capillary‐channeled polymer (C‐CP) fibers in a hydrophobic interaction chromatography (HIC) protocol to isolate exosomes from diverse matrices of practical concern. Initial results demonstrate the ability to isolate extracellular vesicles enriched in exosomes with comparable yields and size distributions on a much faster time scale when compared to traditional isolation methods. As a demonstration of the potential analytical utility of the approach, extracellular vesicle recoveries from cell culture milieu and a mock urine matrix are presented. The potential for scalable separations covering submilliliter spin‐down columns to the preparative scale is anticipated.     

Exosome enrichment of human serum using multiple cycles of centrifugation

In this work, we compared the use of repeated cycles of centrifugation at conventional speeds for enrichment of exosomes from human serum compared to the use of ultracentrifugation (UC). After removal of cells and cell debris, a speed of 110 000 × g or 40 000 × g was used for the UC or centrifugation enrichment process, respectively. The enriched exosomes were analyzed using the bicinchoninic acid assay, 1D gel separation, transmission electron microscopy, Western blotting, and high‐resolution LC‐MS/MS analysis. It was found that a five‐cycle repetition of UC or centrifugation is necessary for successful removal of nonexosomal proteins in the enrichment of exosomes from human serum. More significantly, 5× centrifugation enrichment was found to provide similar or better performance than 5× UC enrichment in terms of enriched exosome protein amount, Western blot band intensity for detection of CD‐63, and numbers of identified exosome‐related proteins and cluster of differentiation (CD) proteins. A total of 478 proteins were identified in the LC‐MS/MS analyses of exosome proteins obtained from 5× UCs and 5× centrifugations including many important CD membrane proteins. The presence of previously reported exosome‐related proteins including key exosome protein markers demonstrates the utility of this method for analysis of proteins in human serum.     

From Chemistry to Translational Medicine: The Application of Proteomics to Cancer Biomarker Discovery and Diagnosis

The study of complex protein mixtures and their interactions in cells and tissues has been difficult due to the tedious process involved in their characterization and analysis. The recent emergence of fast‐evolving and state‐of‐the‐art proteomics methodologies has provided a rapid and scalable platform for understanding the comprehensive proteome profiles from complex whole tissues or cells of various biological sources. Therefore, proteomics has been increasingly valuable to examine real‐time changes in protein expression of various tissues or body fluids from patients with various diseases, especially cancer, resulting in the identification of clinically useful biomarkers for diagnosis, prognosis and disease staging. In this review, we focus on potential biomarkers for (1) Helicobacter pylori‐associated gastric cancer, (2) hepatocellular carcinoma (HCC), and (3) renal cell carcinoma (RCC). In addition to the conventional gel‐based proteomics (1‐D or 2‐D gels), we have utilized a more advanced proteomic approach by incorporating stable isotope dimethyl labelling and shotgun proteomics strategy in combination with nanoliquid chromatography and tandem mass spectrometry (nanoLC‐MS/MS) to better characterize the biomarkers in several cancer tissues. By establishing a high‐throughput proteomics platform based on multiple reaction monitoring (MRM), we have successfully detected and analyzed potential protein markers at low concentrations in various normal and tumor tissues. This platform not only highlights the utility of proteomics for biomarker discovery but also can be uniquely applied to disease‐oriented translational medicine for diagnosis of diverse types of cancers and other diseases.     

MSQ: a tool for quantification of proteomics data generated by a liquid chromatography/matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry based targeted quantitative proteomics platform

Mass spectrometry (MS)‐based quantitative proteomics has become a critical component of biological and clinical research for identification of biomarkers that can be used for early detection of diseases. In particular, MS‐based targeted quantitative proteomics has been recently developed for the detection and validation of biomarker candidates in complex biological samples. In such approaches, synthetic reference peptides that are the stable isotope labeled version of proteotypic peptides of proteins to be quantitated are used as internal standards enabling specific identification and absolute quantification of targeted peptides. The quantification of targeted peptides is achieved using the intensity ratio of a native peptide to the corresponding reference peptide whose spike‐in amount is known. However, a manual calculation of the ratios can be time‐consuming and labor‐intensive, especially when the number of peptides to be tested is large. To establish a liquid chromatography/matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry (LC/MALDI TOF/TOF)‐based targeted quantitative proteomics pipeline, we have developed a software named Mass Spectrometry based Quantification (MSQ). This software can be used to automate the quantification and identification of targeted peptides/proteins by the MALDI TOF/TOF platform. MSQ was applied to the detection of a selected group of targeted peptides in pooled human cerebrospinal spinal fluid (CSF) from patients with Alzheimer's disease (AD) in comparison with age‐matched control (OC). The results for the automated quantification and identification of targeted peptides/proteins in CSF were in good agreement with results calculated manually. Copyright © 2010 John Wiley & Sons, Ltd.     

微流控技术在外泌体分离分析中的研究进展

外泌体是一类由细胞分泌的含有脂质、蛋白、核酸等多种物质的纳米级囊泡,主要参与细胞间的物质交换及信息传导,与多种疾病的发生发展密切相关。对外泌体进行深入研究,理解其生物学功能,对疾病诊断与治疗具有重要意义。由于外泌体尺寸较小且密度和体液接近,想要对复杂生物样本中的外泌体进行分离与分析十分困难。传统的外泌体分离方法如超速离心、超滤等大都需要借助大型仪器设备,且耗时长、操作复杂。因此迫切需要开发高效、便捷的外泌体分离检测手段。微流控技术因其微型化、高通量、可集成等特点,为外泌体的分离分析提供了一个新的平台。该文主要对近年来微流控技术在外泌体分离分析相关领域的研究进展进行了综述。重点从外泌体物理特性和生化特性两个角度出发,介绍了微流控芯片技术用于外泌体分离领域的主要原理、策略和方法。此外,还介绍了微流控技术与荧光、电化学传感、表面等离子体共振等多模态检测方法结合,实现外泌体一体化分析的新进展。最后,该文分析了目前微流控技术用于外泌体分离检测存在的挑战,并对其发展趋势和前景进行了展望。随着微流控外泌体分离分析装置的不断微型化、集成化、自动化,微流控芯片技术将在外泌体分离、生化检测、机制研究等方面将发挥越来越重要的作用。     

A comparative analysis of human plasma and serum proteins by combining native PAGE,whole‐gel slicing and quantitative LC‐MS/MS: Utilizing native MS‐electropherograms in proteomic analysis for discovering structure and interaction‐correlated differences

MS identification has long been used for PAGE‐separated protein bands, but global and systematic quantitation utilizing MS after PAGE has remained rare and not been reported for native PAGE. Here we reported on a new method combining native PAGE, whole‐gel slicing and quantitative LC‐MS/MS, aiming at comparative analysis on not only abundance, but also structures and interactions of proteins. A pair of human plasma and serum samples were used as test samples and separated on a native PAGE gel. Six lanes of each sample were cut, each lane was further sliced into thirty‐five 1.1 mm × 1.1 mm squares and all the squares were subjected to standardized procedures of in‐gel digestion and quantitative LC‐MS/MS. The results comprised 958 data rows that each contained abundance values of a protein detected in one square in eleven gel lanes (one plasma lane excluded). The data were evaluated to have satisfactory reproducibility of assignment and quantitation. Totally 315 proteins were assigned, with each protein assigned in 1–28 squares. The abundance distributions in the plasma and serum gel lanes were reconstructed for each protein, named as “native MS‐electropherograms”. Comparison of the electropherograms revealed significant plasma‐versus‐serum differences on 33 proteins in 87 squares (fold difference > 2 or < 0.5, p < 0.05). Many of the differences matched with accumulated knowledge on protein interactions and proteolysis involved in blood coagulation, complement and wound healing processes. We expect this method would be useful to provide more comprehensive information in comparative proteomic analysis, on both quantities and structures/interactions.     

Characterization of chemical constituents and absorbed components,screening the active components of gelanxinning capsule and an evaluation of therapeutic effects by ultra‐high performance liquid chromatography with quadrupole time of flight mass spectrometry

We revealed the potential biomarker and pathway of gelanxinning capsule on rat model with coronary heart disease, which aims to clarify holistic therapeutic effect and predict quality‐markers of gelanxinning capsule. Ultra‐high performance liquid chromatography coupled with mass spectrometry based on metabolomics technique was used to find the biomarkers and related metabolic pathways of coronary heart disease model, which evaluates the intervention effect of gelanxinning capsule. Using serum pharmacochemistry of traditional Chinese medicine and Pearson correlation analysis, effective ingredients in serum is analyzed to characterize the activity of gelanxinning capsule on coronary heart disease under valid state. A total of 20 biomarkers from coronary heart disease were identified and 12 of them were regulated by gelanxinning capsule treatment, which is mainly involved in sphingolipid metabolism and glycerophospholipid metabolism. With the high sensitivity liquid chromatography coupled with mass spectrometry technology, a total of 46 compounds from gelanxinning capsule were identified in vitro and 25 of them were absorbed in blood. The correlation analysis of serum biomarkers and absorbed components was used to find 11 compounds as quality‐markers to be responsible for the efficacy of gelanxinning capsule. This strategy was successfully applied to screening of potential mechanism and quality‐markers from herbal medicine.      

A soluble pH-responsive host-guest-based nanosystem for homogeneous exosomes capture with high-efficiency

Exosomes offer ideal biomarkers for liquid biopsies. However, high-efficient capture of exosomes has been proven to be extreme challenging. Here, we report a soluble pH-responsive host-guest-based nanosystem (pH-HGN) for homogeneous isolation of exosomes around physiological pH. The pH-HGN consists of two specifically functionalized modules. First, a pH-responsive module, poly-dimethylaminoethyl methacrylate, provides homogeneous capture circumstances and sharp pH-triggered self-assembly separation in aqueous solution to improve capture efficiency and reduce nonspecific adsorption. Second, a host-guest module, poly-acrylamide azobenzene and β-cyclodextrin linked with exosomes-specific antibody, could act as the "cleavable bridge" to specific capture and subsequent rapid release of captured exosomes through host-guest interaction between β-cyclodextrin and AAAB moieties. The pH-HGN offered high capture efficiencies for exosomes from two different cell lines, which were 90.2% ± 0.28% and 87.0% ± 4.6% for H1299 and MCF-7 cell-derived exosomes, respectively. The purity of isolated exosomes was (1.49 ± 0.71) × 10¹¹ particles/µg, which was 4.1 times higher compared with the gold standard ultracentrifugation (UC) method. Furthermore, the isolated exosomes via the pH-HGN can preserve well integrity and biological activity. The developed pH-HGN was further successfully applied to differentiate lung cancer patients from healthy persons. These findings indicated that pH-HGN is a promising strategy in exosomes-based research and downstream applications.     

Analysis of the complex formation of heparin with protamine by light scattering and analytical ultracentrifugation: implications for blood coagulation management

Heparin, a linear glycosaminoglycan, is used in different forms in anticoagulation treatment. Protamine, a highly positive charged peptide containing about 32 amino acids, acts as an antagonist for heparin to restore normal blood coagulation. The complex formation of protamine with heparin was analyzed by a combination of analytical ultracentrifugation and light scattering. Titration of heparin with protamine in blood plasma preparations results in a drastic increase of turbidity, indicating the formation of nanoscale particles. A similar increase of turbidity was observed in physiological saline solution with or without human serum albumin (HSA). Particle size analysis by analytical ultracentrifugation revealed a particle radius of approximately 30 nm for unfractionated heparin and of approximately 60 nm for low molecular weight heparin upon complexation with excess protamine, in agreement with atomic force microscopy data. In the absence of HSA, larger and more heterogeneous particles were observed. The particles obtained were found to be stable for hours. The particle formation kinetics was analyzed by light scattering at different scattering angles and was found to be complete within several minutes. The time course of particle formation suggests a condensation reaction, with sigmoidal traces for low heparin concentrations and quasi-first-order reaction for high heparin concentrations. Under all conditions, the final scattering intensity reached after several minutes was found to be proportional to the amount of heparin in the blood plasma or buffer solution, provided that excess protamine was available and no multiple scattering occurred. On the basis of a direct relation between particle concentration and the heparin concentration present before protaminization, a light scattering assay was developed which permits the quantitative analysis of the heparin concentration in blood plasma and which could complement or even replace the activated clotting time test, which is currently the most commonly used method for blood coagulation management.     

Exploring metabolic syndrome serum profiling based on gas chromatography mass spectrometry and random forest models

Metabolic syndrome (MetS) is a constellation of the most dangerous heart attack risk factors: diabetes and raised fasting plasma glucose, abdominal obesity, high cholesterol and high blood pressure. Analysis and representation of the variances of metabolic profiles is urgently needed for early diagnosis and treatment of MetS. In current study, we proposed a metabolomics approach for analyzing MetS based on GC–MS profiling and random forest models. The serum samples from healthy controls and MetS patients were characterized by GC–MS. Then, random forest (RF) models were used to visually discriminate the serum changes in MetS based on these GC–MS profiles. Simultaneously, some informative metabolites or potential biomarkers were successfully discovered by means of variable importance ranking in random forest models. The metabolites such as 2-hydroxybutyric acid, inositol and d-glucose, were defined as potential biomarkers to diagnose the MetS. These results obtained by proposed method showed that the combining GC–MS profiling with random forest models was a useful approach to analyze metabolites variances and further screen the potential biomarkers for MetS diagnosis.     

New method for prefractionation of plasma for proteomic analysis

The depth of proteome analysis is severely limited in complex samples with a wide dynamic range of protein abundance such as plasma. Removal of high‐abundance proteins should reveal the signal of lower abundance plasma proteins. However, smaller proteins may be part of larger protein complexes and hence the removal of proteins involved in complexes with high‐abundance proteins such as albumin may inhibit the search for disease biomarkers. Prefractionation of a sample divides it into fractions of reduced complexity, allowing improved detection of lower abundance proteins. Using a prefractionation device, which employs Gradiflow? technology, we were able to separate small volume plasma samples into multiple fractions based on the molecular weight and/or charge. The resulting samples of reduced complexity were directly compatible with 2‐DE. The use of this prefractionation machine may therefore be useful in the hunt for disease biomarkers.     

UPLC-ESI-QTOF/MS and multivariate data analysis for blood plasma and serum metabolomics: Effect of experimental artefacts and anticoagulant

Clotting and anticoagulation of blood samples may give rise to different metabolic profiles of serum and plasma samples, respectively. The anticoagulant used for blood plasma preparation may affect the resulting metabolic profile due to different mechanisms involved in anticoagulation by various agents, e.g. heparin, EDTA and citrate. In the present study, we looked into metabolite and other differences in matched serum and plasma samples and different plasma preparations by using untargeted UPLC-ESI-QTOF/MS profiling and multivariate data analysis (PCA and OPLS-DA). Metabolite differences between serum and plasma samples were mainly related to small peptides reflecting presence or absence of coagulation. Only subtle metabolite differences between the different plasma preparations were noticed, which were primarily related to ion suppression or enhancement caused by citrate and EDTA anticoagulants. For the first time, we also report that anticoagulant counter cation (Na+ or K+) in Na-citrate and K-EDTA plasma can make some metabolites more dominant in ESI-MS. Polymeric material residues originating from blood collection tubes for serum preparation were observed only in serum samples. Hypoxanthine and xanthine were found at higher levels in serum than in plasma samples, possibly due to release from the clot. Mass spectral features of sodium formate and potassium formate ion clusters were detected in citrate and EDTA plasma samples, respectively, originating from formate in mobile phase and Na⁺ (in Na-citrate tubes) and K⁺ (in K-EDTA tubes). Among the anticoagulants, heparin is recommended for plasma samples used for LC-ESI/MS-based metabolomics of hydrophilic compounds because no plasma interferences or matrix effects were noticed for this polarity range. Citrate and EDTA should be avoided since interferences and serious matrix effects were encountered on some co-eluting polar metabolites. Serum is recommended as a second choice and an alternative to plasma. In conclusion, heparin plasma or serum should be the order of best choice for LC-ESI/MS-based metabolomics research.     

Potentiometric Biosensor System Based on Recombinant Urease and Creatinine Deiminase for Urea and Creatinine Determination in Blood Dialysate and Serum

A biosensor system for simultaneous determination of creatinine and urea in blood serum and dialysate samples was developed. It consisted of creatinine and urea biosensors based on a potentiometric transducers with two identical pH‐sensitive field‐effect transistors. In creatinine biosensor, creatinine deiminase immobilized via photopolymerization in PVA/SbQ polymer on one transistor served as a biorecognition element, while bovine serum albumin in PVA/SbQ polymer placed on the second transistor was used for reference. The urea biosensor was created in the same way but recombinant urease was used instead of creatinine deiminase. The linear ranges of creatinine and urea measurement were 0.02–2 mM and 0.5–15 mM, correspondingly, which allowed simultaneous determination of the metabolites. Response time of the biosensor system was 2–3 min; RSD of responses did not exceeded 5 %. The biosensors demonstrated absence of non‐selective response towards components of blood dialysate and serum. Urea and creatinine concentrations were determined in 20 samples of blood dialysate and serum. The results correlated well with traditional methods of analysis. Creatinine and urea biosensors were stable during five months of storage (during this time the responses decreased by about 10 %). The proposed biosensor system can be effectively used for analysis of serum samples and for hemodialysis control.     

Searching for serum tumor markers for colorectal cancer using a 2‐D DIGE approach

Identification of specific protein markers for colorectal cancer (CRC) could provide a basis for its early diagnosis and detection, as well as clues to the molecular mechanisms governing cancer progression. In the present study, 2‐D DIGE coupled with MS was used to screen for biomarker candidates in the serum proteome of ten human CRC samples and ten healthy control samples. After pooling identical amounts of serum proteins (based on total protein concentration), albumin/IgG was depleted under partially denaturing conditions. Subsequently, the serum samples were labeled with three different CyDyes, and separated by 2‐D DIGE. After analysis with the biological variation analysis module of the DeCyder software, only three spots were found to be significantly elevated in all patient groups (with ratios from 1.52 to 9.08), whereas five spots were significantly down‐regulated in patients (with ratios from ?1.23 to ?10.21) (t‐test; p<0.05). Finally, two potential biomarkers, Transaldolase 1 and thyroid receptor interactor, were chosen for validation and analysis by ELISA with the serum of 30 CRC patients and 30 healthy controls. The serum levels of the two proteins correlated well with the 2‐D DIGE results. Thus, 2‐D DIGE approaches show great promise for biomarker discovery in CRC.     

Assessing the suitability of capillary electrophoresis‐mass spectrometry for biomarker discovery in plasma‐based metabolomics

The actual utility of capillary electrophoresis‐mass spectrometry (CE‐MS) for biomarker discovery using metabolomics still needs to be assessed. Therefore, a simulated comparative metabolic profiling study for biomarker discovery by CE‐MS was performed, using pooled human plasma samples with spiked biomarkers. Two studies have been carried out in this work. Focus of study I was on comparing two sets of plasma samples, in which one set (class I) was spiked with five isotope‐labeled compounds, whereas another set (class II) was spiked with six different isotope‐labeled compounds. In study II, focus was also on comparing two sets of plasma samples, however, the isotope‐labeled compounds were spiked to both class I and class II samples but with concentrations which differ by a factor two between both classes (with one compound absent in each class). The aim was to determine whether CEMS‐based metabolomics could reveal the spiked biomarkers as the main classifiers, applying two different data analysis software tools (MetaboAnalyst and Matlab). Unsupervised analysis of the recorded metabolic profiles revealed a clear distinction between class I and class II plasma samples in both studies. This classification was mainly attributed to the spiked isotope‐labeled compounds, thereby emphasizing the utility of CE‐MS for biomarker discovery.     

Isotope coded protein label quantification of serum proteins—Comparison with the label-free LC-MS and validation using the MRM approach

Protein quantification based upon mass spectrometry is gaining ground in diverse applications of biological and clinical relevance. The present article focuses on one of the most complex biological fluids - serum - and provides a novel ICPL based quantification protocol. The results are compared to a label-free (data independent alternate scanning) absolute quantification method. The validation is performed using MRM based protein quantification technique. Regarding the ICPL approach, serum samples used in this study were depleted of high abundant proteins, labeled with ICPL and fractionated according to their respective pI (3-5, 5-7 and 7-12). The samples were further subjected to tryptic digestion followed by treatment with the Glu-C enzyme. The peptides were analyzed on a 2D-nano-LC system using four different concentrations of salt injections (45, 75, 150 and 500 mM ammonium acetate). The LC system was connected on-line with the electrospray ion-trap mass spectrometer. For the label-free quantification the serum samples were depleted and digested with trypsin. A proteome-wide comparison was performed using highly reproducible LC and data independent alternate scanning in conjunction with a high mass accuracy orthogonal time-of-flight mass spectrometer. Selected proteins, found by both methods, were validated using the MRM approach. For this purpose non-depleted tryptically digested serum samples were analyzed by LC coupled with a triple-quadrupole MS. The relative protein quantification using ICPL and mass spectrometry allowed for the detection of approximately 200 proteins, whereas about 2/3 of those contained the ICPL label and could therefore be quantified. Label-free approach used no fractionation, less sample and was able to identify and quantify over 110 proteins. The identified proteins covered generally 3-4 orders of magnitude of protein concentration in human serum. Changes in relative abundance of eight proteins were validated using MRM. This study, for the first time, shows the ability of the relative protein quantification based upon ICPL and 2D-LC-MS/MS to quantify serum biomarkers. It provides two additional label-free approaches that could validate and bring additional value to the label-based results, offering a starting point for comprehensive proteomics studies aiming at revealing biomarkers of clinical relevance.     

Quantitative analysis of the low molecular weight serum proteome using 18O stable isotope labeling in a lung tumor xenograft mouse model

With advancements in the analytical technologies and methodologies in proteomics, there is great interest in biomarker discovery in biofluids such as serum and plasma. Current hypotheses suggest that the low molecular weight (LMW) serum proteome possesses an archive of clipped and cleaved protein fragments that may provide insight into disease development. Though these biofluids represent attractive samples from which new and more accurate disease biomarkers may be found, the intrinsic person-to-person variability in these samples complicates their discovery. Mice are one of the most extensively used animal models for studying human disease because they represent a highly controllable experimental model system. In this study, the LMW serum proteome was compared between xenografted tumor-bearing mice and control mice by differential labeling utilizing trypsin-mediated incorporation of the stable isotope of oxygen, 18O. The digestates were combined, fractionated by strong cation exchange chromatography, and analyzed by nanoflow reversed-phase liquid chromatography coupled online with tandem mass spectrometry, resulting in the identification of 6003 proteins identified by at least a single, fully tryptic peptide. Almost 1650 proteins were identified and quantitated by two or more fully tryptic peptides. The methodology adopted in this work provides the means for future quantitative measurements in comparative animal models of disease and in human disease cohorts.