Protein standard absolute quantification (PSAQ) method for the measurement of cellular ubiquitin pools.

The protein ubiquitin is an important post-translational modifier that regulates a wide variety of biological processes. In cells, ubiquitin is apportioned among distinct pools, which include a variety of free and conjugated species. Although maintenance of a dynamic and complex equilibrium among ubiquitin pools is crucial for cell survival, the tools necessary to quantify each cellular ubiquitin pool have been limited. We have developed a quantitative mass spectrometry approach to measure cellular concentrations of ubiquitin species using isotope-labeled protein standards and applied it to characterize ubiquitin pools in cells and tissues. Our method is convenient, adaptable and should be a valuable tool to facilitate our understanding of this important signaling molecule.

Recent developments in quantitative proteomics.

Proteomics is the study of proteins on a large scale, encompassing the many interests scientists and physicians have in their expression and physical properties. Proteomics continues to be a rapidly expanding field, with a wealth of reports regularly appearing on technology enhancements and scientific studies using these new tools. This review focuses primarily on the quantitative aspect of protein expression and the associated computational machinery for making large-scale identifications of proteins and their post-translational modifications. The primary emphasis is on the combination of liquid chromatography-mass spectrometry (LC-MS) methods and associated tandem mass spectrometry (LC-MS/MS). Tandem mass spectrometry, or MS/MS, involves a second analysis within the instrument after a molecular dissociative event in order to obtain structural information including but not limited to sequence information. This review further focuses primarily on the study of in vitro digested proteins known as bottom-up or shotgun proteomics. A brief discussion of recent instrumental improvements precedes a discussion on affinity enrichment and depletion of proteins, followed by a review of the major approaches (label-free and isotope-labeling) to making protein expression measurements quantitative, especially in the context of profiling large numbers of proteins. Then a discussion follows on the various computational techniques used to identify peptides and proteins from LC-MS/MS data. This review article then includes a short discussion of LC-MS approaches to three-dimensional structure determination and concludes with a section on statistics and data mining for proteomics, including comments on properly powering clinical studies and avoiding over-fitting with large data sets.

Consistency of a two clinical site sample collection: a proteomics study.

PURPOSE: We investigated the ability to perform a clinical proteomic study using samples collected at different times from two independent clinical sites. EXPERIMENTAL DESIGN: Label-free 2-D-LC-MS proteomic analysis was used to differentially quantify tens of thousands of peptides from human plasma. We have asked whether samples collected from two sites, when analyzed by this type of peptide profiling, reproducibly contain detectable peptide markers that are differentially expressed in the plasma of disease (advanced renal cancer) patients relative to healthy normals. RESULTS: We have demonstrated that plasma proteins enriched in disease patients are indeed detected reproducibly in both clinical collections. Regression analysis, unsupervised hierarchical clustering and PCA detected no systematic bias in the data related to site of sample collection and processing. Using a genetic algorithm, support vector machine classification method, we were able to correctly classify disease samples at 88% sensitivity and 94% specificity using the second site as an independent validation set. CONCLUSIONS AND CLINICAL RELEVANCE: We conclude that multiple site collection, when analyzed by label-free 2-D-LC-MS, generates data that are sufficiently reproducible to guide reliable biomarker discovery.

Protein biomarker identification in the CSF of patients with CNS lymphoma.

PURPOSE: Elucidation of the CSF proteome may yield insights into the pathogenesis of CNS disease. We tested the hypothesis that individual CSF proteins distinguish CNS lymphoma from benign focal brain lesions. METHODS: We used a liquid chromatography/mass spectrometry-based method to differentially quantify and identify several hundred CSF proteins in CNS lymphoma and control patients. We used enzyme-linked immunosorbent assay (ELISA) to confirm one of these markers in an additional validation set of 101 cases. RESULTS: Approximately 80 CSF proteins were identified and found to be present at significantly different concentrations, both higher and lower, in training and test studies, which were highly concordant. To further validate these observations, we defined in detail the expression of one of these candidate biomarkers, antithrombin III (ATIII). ATIII RNA transcripts were identified within CNS lymphomas, and ATIII protein was localized selectively to tumor neovasculature. Determination of ATIII concentration by ELISA was significantly more accurate (> 75% sensitivity; > 98% specificity) than cytology in the identification of cancer. Measurement of CSF ATIII levels was found to potentially enhance the ability to diagnose and predict outcome. CONCLUSION: Our findings demonstrate for the first time that proteomic analysis of CSF yields individual biomarkers with greater sensitivity in the identification of cancer than does CSF cytology. We propose that the discovery of CSF protein biomarkers will facilitate early and noninvasive diagnosis in patients with lesions not amenable to brain biopsy, as well as provide improved surrogates of prognosis and treatment response in CNS lymphoma and brain metastasis.

Global changes to the ubiquitin system in Huntington's disease.

Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder caused by expansion of CAG triplet repeats in the huntingtin (HTT) gene (also called HD) and characterized by accumulation of aggregated fragments of polyglutamine-expanded HTT protein in affected neurons. Abnormal enrichment of HD inclusion bodies with ubiquitin, a diagnostic characteristic of HD and many other neurodegenerative disorders including Alzheimer's and Parkinson's diseases, has suggested that dysfunction in ubiquitin metabolism may contribute to the pathogenesis of these diseases. Because modification of proteins with polyubiquitin chains regulates many essential cellular processes including protein degradation, cell cycle, transcription, DNA repair and membrane trafficking, disrupted ubiquitin signalling is likely to have broad consequences for neuronal function and survival. Although ubiquitin-dependent protein degradation is impaired in cell-culture models of HD and of other neurodegenerative diseases, it has not been possible to evaluate the function of the ubiquitin-proteasome system (UPS) in HD patients or in animal models of the disease, and a functional role for UPS impairment in neurodegenerative disease pathogenesis remains controversial. Here we exploit a mass-spectrometry-based method to quantify polyubiquitin chains and demonstrate that the abundance of these chains is a faithful endogenous biomarker of UPS function. Lys 48-linked polyubiquitin chains accumulate early in pathogenesis in brains from the R6/2 transgenic mouse model of HD, from a knock-in model of HD and from human HD patients, establishing that UPS dysfunction is a consistent feature of HD pathology. Lys 63- and Lys 11-linked polyubiquitin chains, which are not typically associated with proteasomal targeting, also accumulate in the R6/2 mouse brain. Thus, HD is linked to global changes in the ubiquitin system to a much greater extent than previously recognized.

Identification of short-term pharmacodynamic effects of interferon-beta-1a in multiple sclerosis subjects with broad- based phenotypic profiling.

We applied broad-based phenotypic profiling to identify pharmacodynamic markers for interferon-beta in multiple sclerosis subjects. A strong pharmacodynamic effect was observed 1.5 (short-term) vs. 6 days post weekly injection. Hundreds of differences were observed at a p-value <0.001. Most major cell populations, including neutrophils, B cells, CD4 T cells and CD8 T cells, decreased in absolute counts at 1.5 days. The striking exception was monocytes, which increased substantially. Changes in multiple monocyte-associated cell surface molecules and monocyte related soluble factors were also observed, including: HLA class II, CCR5, CD38, CD40, CD54, CD64, CD69, CD86, CD101, TLR2, TLR4 and MCP2. These results demonstrate that new hypotheses can be generated from broad molecular and cellular profiling in a clinical setting and provide an approach to identify candidate pharmacodynamic markers to evaluate new drug formulations, dosing and bioequivalence.

Quantification of proteins and metabolites by mass spectrometry without isotopic labeling.

We demonstrate the quantification capability and robustness of a new integrated liquid chromatography-mass spectrometry (LC-MS) approach for large-scale profiling of proteins and metabolites. This approach to determine differential expression relies on linearity of signal vs molecular concentration using electrospray ionization LC-MS, reproducibility of sample processing, a novel normalization strategy and associated data analysis software. No isotopic tagging or spiking of internal standards is required. The method is general and applicable to the proteome and metabolome from all biological fluids and tissues. Small or large numbers of samples can be profiled in a single experiment. Differential profiling of 6000 molecular ions per sample by one-dimensional chromatography LC-MS and 30,000 molecular ions per sample by two-dimensional chromatography LC-MS is demonstrated using rheumatoid arthritis patient samples compared with control samples. A new approach to peptide identification is described that involves building libraries of previously identified peptides, circumventing the need to acquire MS/MS data during profiling. Robustness of the platform was tested by repeating sample preparation and LC-MS differential expression analysis after 10 mo, using independent serum aliquots stored at -80 degrees C. To the best of our knowledge, this is the first demonstration of long-term robustness of a platform for quantitative proteomics and metabolomics.

Nonparametric mass calibration using hundreds of internal calibrants.

In situations where many molecular ions (>100) can be identified to the level of their elemental composition, such as in proteomics, metabolomics, and glycomics, a final mass calibration is possible for every sample without reliance on any analytical description of instrument behavior. This is achieved by applying a nonparametric calibration curve determined from the difference in observed, centroided m/z values of the known, internal calibrant molecular ions versus that calculated from their elemental compositions, over the m/z range. In examples here, proteomic data are examined for two sets of samples of complex mixtures composed of tryptic peptides from human and mouse blood proteins using high-resolution time-of-flight mass spectra from on-line liquid chromatography-mass spectrometry experiments. Resultant, postcalibration median absolute value mass errors and root-mean-square errors for peptides between 300 and 1100 m/z for many samples ranged from 3.1 to 4.4 and 5.2 to 6.9 ppm, respectively. The method may be applied to other types of mass spectrometers.

Comprehensive phenotyping in multiple sclerosis: discovery based proteomics and the current understanding of putative biomarkers.

Currently, there is no single test for multiple sclerosis (MS). Diagnosis is confirmed through clinical evaluation, abnormalities revealed by magnetic resonance imaging (MRI), and analysis of cerebrospinal fluid (CSF) chemistry. The early and accurate diagnosis of the disease, monitoring of progression, and gauging of therapeutic intervention are important but elusive elements of patient care. Moreover, a deeper understanding of the disease pathology is needed, including discovery of accurate biomarkers for MS. Herein we review putative biomarkers of MS relating to neurodegeneration and contributions to neuropathology, with particular focus on autoimmunity. In addition, novel assessments of biomarkers not driven by hypotheses are discussed, featuring our application of advanced proteomics and metabolomics for comprehensive phenotyping of CSF and blood. This strategy allows comparison of component expression levels in CSF and serum between MS and control groups. Examination of these preliminary data suggests that several CSF proteins in MS are differentially expressed, and thus, represent putative biomarkers deserving of further evaluation.

Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap.

A method is presented to quantify intermediate-abundance proteins in human serum using a single-quadrupole linear ion trap mass spectrometer-in contrast, for example, to a triple-quadrupole mass spectrometer. Stable-isotope-labeled (tryptic) peptides are spiked into digested protein samples as internal standards, aligned with the traditional isotope dilution approach. As a proof-of-concept experiment, four proteins of intermediate abundance were selected, coagulation factor V, adiponectin, C-reactive protein (CRP), and thyroxine binding globulin. Stable-isotope-labeled peptides were synthesized with one tryptic sequence from each of these proteins. The normal human serum concentration ranges of these proteins are from 1 to 30 microg/mL (or 20 to 650 pmol/mL). These labeled peptides and their endogenous counterparts were analyzed by LC-MS/MS using multiple reaction monitoring, a multiplexed form of the selected reaction monitoring technique. For these experiments, only one chromatographic dimension (on-line reversed-phase capillary column) was used. Improved limits of detection will result with multidimensional chromatographic methods utilizing more material per sample. Standard curves of the spiked calibrants were generated with concentrations ranging from 3 to 700 pmol/mL using both neat solutions and peptides spiked into the complex matrix of digested serum protein solution where ion suppression effects and interferences are common. Endogenous protein concentrations were determined by comparing MS/MS peak areas of the endogenous peptides to the isotopically labeled internal calibrants. The derived concentrations from a normal human serum pool (neglecting loss of material during sample processing) were 9.2, 110, 120, and 246 pmol/mL for coagulation factor V, adiponectin, CRP, and thyroxine binding globulin, respectively. These concentrations generally agree with the reported normal ranges for these proteins. As a measure of analytical reproducibility of this single-quadrupole assay, the coefficients of variance based on 12 repeated measurements for each of the endogenous tryptic peptides were 17.0, 25.4, 24.2, and 14.0% for coagulation factor V, adiponectin, CRP, and thyroxine binding globulin, respectively.

Azetidine-2-carboxylic acid in garden beets (Beta vulgaris).

Azetidine-2-carboxylic acid (L-Aze) is a toxic and teratogenic non-protein amino acid. In many species, including man, L-Aze is misincorporated into protein in place of proline, altering collagen, keratin, hemoglobin, and protein folding. In animal models of teratogenesis, it causes a wide range of malformations. The role of L-Aze in human disease has been unexplored, probably because the compound has not been associated with foods consumed by humans. Herein we report the presence of L-Aze in the garden or table beet (Beta vulgaris).

Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards.

A new method is presented for quantifying proteomic and metabolomic profile data by liquid chromatography-mass spectrometry (LC-MS) with electrospray ionization. This biotechnology provides differential expression measurements and enables the discovery of biological markers (biomarkers). Work presented here uses human serum but is applicable to any fluid or tissue. The approach relies on linearity of signal versus molecular concentration and reproducibility of sample processing. There is no use of isotopic labeling or chemically similar standard materials. Linear standard curves are reported for a variety of compounds introduced into human serum. As a measure of analytical reproducibility for proteome and metabolome sampling, median coefficients of variation of 25.7 and 23.8%, respectively, were determined for approximately 3400 molecular ions (not counting their numerous isotopes) from 25 independently processed human serum samples, corresponding to a total of 85000 individual molecular ion measurements.