Proteomics analysis of bodily fluids in pancreatic cancer

Proteomics study of pancreatic cancer using bodily fluids emphasizes biomarker discovery and clinical application, presenting unique prospect and challenges. Depending on the physiological nature of the bodily fluid and its proximity to pancreatic cancer, the proteomes of bodily fluids, such as pancreatic juice, pancreatic cyst fluid, blood, bile, and urine, can be substantially different in terms of protein constitution and the dynamic range of protein concentration. Thus, a comprehensive discovery and specific detection of cancer‐associated proteins within these varied fluids is a complex task, requiring rigorous experiment design and a concerted approach. While major challenges still remain, fluid proteomics studies in pancreatic cancer to date have provided a wealth of information in revealing proteome alterations associated with pancreatic cancer in various bodily fluids.     

Analysis of host-cell proteins in biotherapeutic proteins by comprehensive online two-dimensional liquid chromatography/mass spectrometry

Assays for identification and quantification of host-cell proteins (HCPs) in biotherapeutic proteins over 5 orders of magnitude in concentration are presented. The HCP assays consist of two types: HCP identification using comprehensive online two-dimensional liquid chromatography coupled with high resolution mass spectrometry (2D-LC/MS), followed by high-throughput HCP quantification by liquid chromatography, multiple reaction monitoring (LC-MRM). The former is described as a “discovery” assay, the latter as a “monitoring” assay. Purified biotherapeutic proteins (e.g., monoclonal antibodies) were digested with trypsin after reduction and alkylation, and the digests were fractionated using reversed-phase (RP) chromatography at high pH (pH 10) by a step gradient in the first dimension, followed by a high-resolution separation at low pH (pH 2.5) in the second dimension. As peptides eluted from the second dimension, a quadrupole time-of-flight mass spectrometer was used to detect the peptides and their fragments simultaneously by alternating the collision cell energy between a low and an elevated energy (MSE methodology). The MSE data was used to identify and quantify the proteins in the mixture using a proven label-free quantification technique (“Hi3” method). The same data set was mined to subsequently develop target peptides and transitions for monitoring the concentration of selected HCPs on a triple quadrupole mass spectrometer in a high-throughput manner (20 min LC-MRM analysis). This analytical methodology was applied to the identification and quantification of low-abundance HCPs in six samples of PTG1, a recombinant chimeric anti-phosphotyrosine monoclonal antibody (mAb). Thirty three HCPs were identified in total from the PTG1 samples among which 21 HCP isoforms were selected for MRM monitoring. The absolute quantification of three selected HCPs was undertaken on two different LC-MRM platforms after spiking isotopically labeled peptides in the samples. Finally, the MRM quantitation results were compared with TOF-based quantification based on the Hi3 peptides, and the TOF and MRM data sets correlated reasonably well. The results show that the assays provide detailed valuable information to understand the relative contributions of purification schemes to the nature and concentrations of HCP impurities in biopharmaceutical samples, and the assays can be used as generic methods for HCP analysis in the biopharmaceutical industry.     

An improved radioimmunoassay for myelin basic protein-like immunoreactive material in cerebrospinal fluid

A modified radioimmunoassay protocol is described which can measure elevated levels of myelin basic protein-like immunoreactive material in the cerebrospinal fluid of some patients with multiple sclerosis or head injury and in rats developing an acute demyelinating form of experimental allergic encephalomyelitis. The assay uses synthetic peptides that differ in their sequences from natural myelin basic protein for both standard and radioligand, but in apparent contrast to previously published assays serial dilutions of samples produce the expected dose estimates when interpolated from the standard curve. A second radioimmunoassay was produced with high sensitivity and specificity for myelin basic protein peptides with a carboxyl terminus at phenylalanine 89. This assay was used in attempts to detect the myelin basic protein-like immunoreactivity recently reported to occur in human urine. This radioimmunoassay failed to detect specific immunoreactivity in urine samples from control and multiple sclerosis donors. The specificities of both assays were studied using a wide range of synthetic peptides and the importance of this information to the design of future assays is addressed. Our work reinforces that of others in suggesting the complex situation involved in the design of assays for MBP fragments in body fluids. We are willing to distribute the reagents for use in our CSF assay to researchers who request them.     

Toward a standardized urine proteome analysis methodology

Urine is an easily accessible bodily fluid particularly suited for the routine clinical analysis of disease biomarkers. Actually, the urinary proteome is more diverse than anticipated a decade ago. Hence, significant analytical and practical issues of urine proteomics such as sample collection and preparation have emerged, in particular for large-scale studies. We have undertaken a systematic study to define standardized and integrated analytical protocols for a biomarker development pipeline, employing two LC-MS analytical platforms, namely accurate mass and time tags and selected reaction monitoring, for the discovery and verification phase, respectively. Urine samples collected from hospital patients were processed using four different protocols, which were evaluated and compared on both analytical platforms. Addition of internal standards at various stages of sample processing allowed the estimation of protein extraction yields and the absolute quantification of selected urinary proteins. Reproducibility of the entire process and dynamic range of quantification were also evaluated. Organic solvent precipitation followed by in-solution digestion provided the best performances and was thus selected as the standard method common to the discovery and verification phases. Finally, we applied this protocol for platforms' cross-validation and obtained excellent consistency between urinary protein concentration estimates by both analytical methods performed in parallel in two laboratories.     

Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays

The identification of clinically relevant biomarkers represents an important challenge in oncology. This problem can be addressed with biomarker discovery and verification studies performed directly in tumor samples using formalin-fixed paraffin-embedded (FFPE) tissues. However, reliably measuring proteins in FFPE samples remains challenging. Here, we demonstrate the use of liquid chromatography coupled to multiple reaction monitoring mass spectrometry (LC-MRM/MS) as an effective technique for such applications. An LC-MRM/MS method was developed to simultaneously quantify hundreds of peptides extracted from FFPE samples and was applied to the targeted measurement of 200 proteins in 48 triple-negative, 19 HER2-overexpressing, and 20 luminal A breast tumors. Quantitative information was obtained for 185 proteins, including known markers of breast cancer such as HER2, hormone receptors, Ki-67, or inflammation-related proteins. LC-MRM/MS results for these proteins matched immunohistochemistry or chromogenic in situ hybridization data. In addition, comparison of our results with data from the literature showed that several proteins representing potential biomarkers were identified as differentially expressed in triple-negative breast cancer samples. These results indicate that LC-MRM/MS assays can reliably measure large sets of proteins using the analysis of surrogate peptides extracted from FFPE samples. This approach allows to simultaneously quantify the expression of target proteins from various pathways in tumor samples. LC-MRM/MS is thus a powerful tool for the relative quantification of proteins in FFPE tissues and for biomarker discovery.     

Quantification of cyanuric acid residue in human urine using high performance liquid chromatography–tandem mass spectrometry

Concern has increased about the resulting health effects of exposure to melamine and its metabolic contaminant, cyanuric acid, after infants in China were fed baby formula milk products contaminated with these compounds. We have developed a selective and sensitive analytical method to quantify the amount of cyanuric acid in human urine. The sample preparation involved extracting free-form cyanuric acid in human urine using anion exchange solid phase extraction. Cyanuric acid was separated from its urinary matrix components on the polymeric strong anion exchange analytical column; the analysis was performed by high performance liquid chromatography–tandem mass spectrometry using negative mode electrospray ionization interface. Quantification was performed using isotope dilution calibration covering the concentration range of 1.00–200 ng/mL. The limit of detection was 0.60 ng/mL and the relative standard deviations were 2.8–10.5% across the calibration range. The relative recovery of cyanuric acid was 100–104%. Our method is suitable to detect urinary concentrations of cyanuric acid caused by either environmental exposures or emerging poisoning events.     

Mass spectrometric quantitation of C-reactive protein using labeled tryptic peptides

Given the extensive efforts applied toward proteomics and research in biomarkers, methods for the simultaneous measurement of proteins, peptides, metabolic intermediates, hormones, etc. in a complex sample may be required in the foreseeable future. Assays based on mass spectrometric detection may be suitable for meeting the demands of such complex samples with sensitivity and specificity. An analytical method for the quantitation of C-reactive protein (CRP), a well-known marker of inflammation, is described. Exact quantities of two synthetic (13)C-labeled CRP tryptic peptides were added as internal standards directly to the sample prior to chemical treatment, trypsinization, and liquid chromatography/mass spectrometry quantitation. C-reactive protein levels based on isotopic response ratios were measured. Intact C-reactive protein was spiked into blank rat urine for chemical and enzymatic treatment, producing linear response ratios of labeled to unlabeled peptides. For rigorous quantitation, standard curves, and quality control samples were prepared in rat urine with highly purified labeled and unlabeled peptides over the 50 pg-5 ng/muL concentration range. Using the same chemical and enzymatic treatment used for digestion of intact CRP, data from these samples demonstrated excellent analytical performance. The method was successfully applied toward the quantitation of urinary C-reactive protein from a study of drug-induced nephrotoxicity.     

Cross validation and ruggedness testing of analytical methods used for the quantification of urinary phthalate metabolites

Since the publication of our first analytical method in 2000 to detect and quantify phthalate metabolites in human urine, we have modified the method several times to improve performance, reduce the volume of matrix and solvents used, and to increase the number of analytes in one analytical run. We performed cross method validation and ruggedness testing after each modification to ensure that the analytical method adopted is robust and produces accurate and reproducible data when compared to the previously used method. Here, we present the results from the evaluation of the ruggedness of our analytical approach under variable experimental conditions, using the current analytical method. Minor deviations of the standard experimental conditions, i.e., pH, incubation time, amount of deconjugation enzyme, and incubation temperature, had no effect on final analyte concentrations. Furthermore, we validated the method to ensure accuracy at concentrations beyond the highest calibration standard. The concentrations obtained by using a lower volume of urine agreed well with original levels, suggesting broad linear calibration range as well as complete hydrolysis of the glucuronide conjugates with the standard amount of beta-glucuronidase used for deglucuronidation; also, the time of incubation (90 min) was adequate regardless of the amount of glucuronide present. We also summarize the precision of concentration data acquired by the five different analytical approaches we have used since 2000. The correlation plots of concentration data for each analyte obtained from split sample analysis, using three of these approaches, produced linear curves (R(2)>0.98) with slopes and intercepts that were not statistically different (p>0.05) from 1 and 0, respectively. These results suggest that the data are reproducible and accurate, regardless of the analytical method used. Furthermore, analysis of quality control urine samples made over the years confirmed the stability of the phthalate metabolites in urine at -70 degrees C for several years and the consistency of the analytical measurements obtained by using various methodological approaches over time.     

Analysis of host-cell proteins in biotherapeutic proteins by comprehensive online two-dimensional liquid chromatography/mass spectrometry

Assays for identification and quantification of host-cell proteins (HCPs) in biotherapeutic proteins over 5 orders of magnitude in concentration are presented. The HCP assays consist of two types: HCP identification using comprehensive online two-dimensional liquid chromatography coupled with high resolution mass spectrometry (2D-LC/MS), followed by high-throughput HCP quantification by liquid chromatography, multiple reaction monitoring (LC-MRM). The former is described as a “discovery” assay, the latter as a “monitoring” assay. Purified biotherapeutic proteins (e.g., monoclonal antibodies) were digested with trypsin after reduction and alkylation, and the digests were fractionated using reversed-phase (RP) chromatography at high pH (pH 10) by a step gradient in the first dimension, followed by a high-resolution separation at low pH (pH 2.5) in the second dimension. As peptides eluted from the second dimension, a quadrupole time-of-flight mass spectrometer was used to detect the peptides and their fragments simultaneously by alternating the collision cell energy between a low and an elevated energy (MS^E methodology). The MS^E data was used to identify and quantify the proteins in the mixture using a proven label-free quantification technique (“Hi3” method). The same data set was mined to subsequently develop target peptides and transitions for monitoring the concentration of selected HCPs on a triple quadrupole mass spectrometer in a high-throughput manner (20 min LC-MRM analysis). This analytical methodology was applied to the identification and quantification of low-abundance HCPs in six samples of PTG1, a recombinant chimeric anti-phosphotyrosine monoclonal antibody (mAb). Thirty three HCPs were identified in total from the PTG1 samples among which 21 HCP isoforms were selected for MRM monitoring. The absolute quantification of three selected HCPs was undertaken on two different LC-MRM platforms after spiking isotopically labeled peptides in the samples. Finally, the MRM quantitation results were compared with TOF-based quantification based on the Hi3 peptides, and the TOF and MRM data sets correlated reasonably well. The results show that the assays provide detailed valuable information to understand the relative contributions of purification schemes to the nature and concentrations of HCP impurities in biopharmaceutical samples, and the assays can be used as generic methods for HCP analysis in the biopharmaceutical industry.Key words: host cell proteins, protein quantification, biotherapeutic proteins, mAbs, HCP     

Discrimination of bovine estrus-related odors by mice

The present investigation was carried out (1) to evaluate whether the mouse is able to discriminate vaginal and other bovine body fluids and (2) to determine which bodily fluid will most efficiently be used to detect estrus. The time spent by the male mice in investigating the different bovine odorant samples clearly demonstrated the mouses ability to discriminate between estrus and non-estrus fluid samples. Estrus vaginal fluid was found to be the most attractive followed by saliva, feces and milk. Thus estrus vaginal fluid may act as an additional/secondary factor along with urine in eliciting copulatory behavior in bulls. The results of this study revealed that bodily fluids such as saliva, feces and milk also have estrus-related odors and that these may be involved in bovine biocommunication.This revised version was published online in March 2005 with corrections to the contact informations of the corresponding author.     

High-performance liquid chromatographic determination of tazobactam and piperacillin in human plasma and urine

A high-performance liquid chromatographic (HPLC) method with ultraviolet (UV) absorbance was developed for the analysis of piperacillin-tazobactam (tazocillin), in plasma and urine. The detection was performed at 218 nm for tazobactam and 222 nm for piperacillin. The procedure for assay of these two compounds in plasma and of piperacillin in urine involves the addition of an internal standard (ceftazidime for tazobactam and benzylpenicillin for piperacillin) followed by a treatment of the samples with acetonitrile and chloroform. To quantify tazobactam in urine, diluted samples were analysed using a column-switching technique without internal standard. The HPLC column, LiChrosorb RP-select B, was equilibrated with an eluent mixture composed of acetonitrile-ammonium acetate (pH 5). The proposed technique is reproducible, selective, and reliable. The method has been validated, and stability tests under various conditions have been performed. Linear detector responses were observed for the calibration curve standards in the ranges 5–60 μg/ml for tazobactam, and 1–100 μg/ml for piperacillin and spans what is currently though to be the clinically relevant range for tazocillin concentrations in body fluids. The limit of quantification was 3 μg/ml for tazobactam and 0.5 μg/ml for piperacillin in plasma and urine. Extraction recoveries from plasma proved to be more than 85%. Precision, expressed as C.V., was in the range 0.4–18%.     

Comparative urine protein phenotyping using mass spectrometric immunoassay

Reported here, human urine samples were analyzed for beta-2-microglobulin (beta2m), transthyretin (TTR), cystatin C, urine protein 1 (UP1), retinol binding protein (RBP), albumin, transferrin, and human neutrophil defensin peptides (HNP) using mass spectrometric immunoassay (MSIA). MSIA is a unique analytical technique, which allows for the generation of distinct protein profiles of specific target proteins from each subject, which may be subsequently used in comparative protein expression profiling between all subjects. Comparative profiling allows for the rapid identification of variations within individual protein expression profiles. Although the majority of analyses performed in this study revealed homology between study participants, roughly one-quarter showed variation in the protein profiles. Some of these observed variants included a point mutation in TTR, absence of wild-type RBP, monomeric forms UP1, a novel beta2m glycated end product and altered HNP ratios. MSIA has been previously used in the analysis of blood proteins, but this study shows how MSIA easily transitions to the analysis, of urine samples. This study displays how qualitative urine protein differentiation is readily achievable with MSIA and is useful in identifying proteomic differences between subjects that might be otherwise overlooked with other analytical techniques due to complexity of the resulting data or insufficient sensitivity.     

Targeted proteome investigation via selected reaction monitoring mass spectrometry

Due to the enormous complexity of proteomes which constitute the entirety of protein species expressed by a certain cell or tissue, proteome-wide studies performed in discovery mode are still limited in their ability to reproducibly identify and quantify all proteins present in complex biological samples. Therefore, the targeted analysis of informative subsets of the proteome has been beneficial to generate reproducible data sets across multiple samples. Here we review the repertoire of antibody- and mass spectrometry (MS) -based analytical tools which is currently available for the directed analysis of predefined sets of proteins. The topics of emphasis for this review are Selected Reaction Monitoring (SRM) mass spectrometry, emerging tools to control error rates in targeted proteomic experiments, and some representative examples of applications. The ability to cost- and time-efficiently generate specific and quantitative assays for large numbers of proteins and posttranslational modifications has the potential to greatly expand the range of targeted proteomic coverage in biological studies. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.     

Peptides and proteins in plasma and cerebrospinal fluid as biomarkers for the prediction, diagnosis, and monitoring of therapeutic efficacy of Alzheimer's disease

Alzheimer's disease (AD) affects millions of persons worldwide. Earlier detection and/or diagnosis of AD would permit earlier intervention, which conceivably could delay progression of this dementing disorder. In order to accomplish this goal, reliable and specific biomarkers are needed. Biomarkers are multidimensional and have the potential to aid in various facets of AD such as diagnostic prediction, assessment of disease stage, discrimination from normally cognitive controls as well as other forms of dementia, and therapeutic efficacy of AD drugs. To date, biomarker research has focused on plasma and cerebrospinal fluid (CSF), two bodily fluids believed to contain the richest source of biomarkers for AD. CSF is the fluid surrounding the central nervous system (CNS), and is the most indicative obtainable fluid of brain pathology. Blood plasma contains proteins that affect brain processes from the periphery, as well as proteins/peptides exported from the brain; this fluid would be ideal for biomarker discovery due to the ease and non-invasive process of sample collection. However, it seems reasonable that biomarker discovery will result in combinations of CSF, plasma, and other fluids such as urine, to serve the aforementioned purposes. This review focuses on proteins and peptides identified from CSF, plasma, and urine that may serve as biomarkers in AD.     

基于液相色谱质谱联用的蛋白质组非标记定量研究策略的建立及应用

定量蛋白质组研究是蛋白质组研究的热点和难点,而液相色谱质谱技术已经被广泛地应用于蛋白质的定性和定量研究.该研究建立和优化了一种基于液相色谱质谱联用技术的蛋白质组非标记定量方法,并对两种肽段质谱检测计数的归一化算法进行了比较,结果发现ASC法要优于Rsc法.最后,将建立的方法应用于肝癌细胞模型HepG2和HepG2-HBx细胞系的差异蛋白质组表达研究.质谱鉴定结果用聚类分析软件cluster3.0进行分析,最后鉴定出107个重叠蛋白,其中9个蛋白质表达上调(Ratio>1.75),6个蛋白质表达下调(Ratio<0.5),这些蛋白质均与肝癌发生和恶化密切相关.结果表明,该技术操作简单、方便,具有较高的灵敏度和动态范围,利用该方法进行差异蛋白质组研究和发现生物标志物在理论和临床上具有十分重要的意义.     

Reverse-Phase Protein Array: Technology,Application, Data Processing,and Integration

Reverse-phase protein array (RPPA) is a high-throughput antibody-based targeted proteomics platform that can quantify hundreds of proteins in thousands of samples derived from tissue or cell lysates, serum, plasma, or other body fluids. Protein samples are robotically arrayed as microspots on nitrocellulose-coated glass slides. Each slide is probed with a specific antibody that can detect levels of total protein expression or post-translational modifications, such as phosphorylation as a measure of protein activity. Here we describe workflow protocols and software tools that we have developed and optimized for RPPA in a core facility setting that includes sample preparation, microarray mapping and printing of protein samples, antibody labeling, slide scanning, image analysis, data normalization and quality control, data reporting, statistical analysis, and management of data. Our RPPA platform currently analyzes ∼240 validated antibodies that primarily detect proteins in signaling pathways and cellular processes that are important in cancer biology. This is a robust technology that has proven to be of value for both validation and discovery proteomic research and integration with other omics data sets.     

High-performance liquid chromatographic determination of cefepime in human plasma and in urine and dialysis fluid using a column-switching technique

A high-performance liquid chromatographic method with UV absorbance was developed for the analysis of cefepime in human plasma and urine, and in dialysis fluid. Detection was performed at 280 nm. The assay procedure for cefepime in plasma involves the addition of an internal standard (cefpirome) followed by treatment of the samples with trichloracetic acid, acetonitrile and dichloromethane. To quantify cefepime in diluted urine (1:20) and in the dialysis fluid, samples spiked with the internal standard (cefpirome) were analysed using a column-switching technique. The HPLC column, Nucleosil C₁₈, was equilibrated with an eluent mixture composed of acetonitrile–ammonium acetate (pH 4). Linear detector responses were observed for the calibration curve standards in the range 0.5 to 100 μg/ml, which spans what is currently thought to be the clinically relevant range for cefepime concentrations in body fluids. The limit of quantification was 0.5 μg/ml in the three matrices. Extraction recoveries proved to be more than 84%. Precision, expressed as %RSD, was in the range 1.5 to 9%. Accuracy ranged from 93 to 105%. This method was used to follow the time course of the concentration of cefepime in plasma, urine and dialysate outlet samples after a 10-min infusion period of 2 g of this drug in patients with acute renal failure undergoing hemodiafiltration.     

Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry

A main objective of proteomics research is to systematically identify and quantify proteins in a given proteome (cells, subcellular fractions, protein complexes, tissues or body fluids). Protein labeling with isotope-coded affinity tags (ICAT) followed by tandem mass spectrometry allows sequence identification and accurate quantification of proteins in complex mixtures, and has been applied to the analysis of global protein expression changes, protein changes in subcellular fractions, components of protein complexes, protein secretion and body fluids. This protocol describes protein-sample labeling with ICAT reagents, chromatographic fractionation of the ICAT-labeled tryptic peptides, and protein identification and quantification using tandem mass spectrometry. The method is suitable for both large-scale analysis of complex samples including whole proteomes and small-scale analysis of subproteomes, and allows quantitative analysis of proteins, including those that are difficult to analyze by gel-based proteomics technology.     

Computational prediction of proteotypic peptides

Evaluation of: Mallick P, Schirle M, Chen SS et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25(1), 125–131 (2007).

Mass spectrometry, the driving analytical force behind proteomics, is primarily used to identify and quantify as many proteins in a complex biological mixture as possible. While there are many ways to prepare samples, one aspect that is common to a vast majority of bottom-up proteomic studies is the digestion of proteins into tryptic peptides prior to their analysis by mass spectrometry. As correctly highlighted by Mallick and colleagues, only a few peptides are repeatedly and consistently identified for any given protein within a complex mixture. While the existence of these proteotypic peptides (to borrow the authors’ terminology) is well known in the proteomics community, there has never been an empirical method to recognize which peptides may be proteotypic for a given protein. In this study, the investigators discovered over 16,000 proteotypic peptides from a collection of over 600,000 peptide identifications obtained from four different analytical platforms. The study examined a number of physicochemical parameters of these peptides to determine which properties were most relevant in defining a proteotypic peptide. These characteristic properties were then used to develop computational tools to predict proteotypic peptides for any given protein within an organism.