Quantitative Workflow Research Articles

Online Peptide Fractionation Using a Multiphasic Microfluidic Liquid Chromatography Chip Improves Reproducibility and Detection Limits for Quantitation in Discovery and Targeted Proteomics*[S

Comprehensive proteomic profiling of biological specimens usually requires multidimensional chromatographic peptide fractionation prior to mass spectrometry. However, this approach can suffer from poor reproducibility because of the lack of standardization and automation of the entire workflow, thus compromising performance of quantitative proteomic investigations. To address these variables we developed an online peptide fractionation system comprising a multiphasic liquid chromatography (LC) chip that integrates reversed phase and strong cation exchange chromatography upstream of the mass spectrometer (MS). We showed superiority of this system for standardizing discovery and targeted proteomic workflows using cancer cell lysates and nondepleted human plasma. Five-step multiphase chip LC MS/MS acquisition showed clear advantages over analyses of unfractionated samples by identifying more peptides, consuming less sample and often improving the lower limits of quantitation, all in highly reproducible, automated, online configuration. We further showed that multiphase chip LC fractionation provided a facile means to detect many N- and C-terminal peptides (including acetylated N terminus) that are challenging to identify in complex tryptic peptide matrices because of less favorable ionization characteristics. Given as much as 95% of peptides were detected in only a single salt fraction from cell lysates we exploited this high reproducibility and coupled it with multiple reaction monitoring on a high-resolution MS instrument (MRM-HR). This approach increased target analyte peak area and improved lower limits of quantitation without negatively influencing variance or bias. Further, we showed a strategy to use multiphase LC chip fractionation LC-MS/MS for ion library generation to integrate with SWATH(TM) data-independent acquisition quantitative workflows. All MS data are available via ProteomeXchange with identifier PXD001464.

Validation of a novel shotgun proteomic workflow for the discovery of protein-protein interactions: focus on ZNF521.

The study of protein-protein interactions is increasingly relying on mass spectrometry (MS). The classical approach of separating immunoprecipitated proteins by SDS-PAGE followed by in-gel digestion is long and labor-intensive. Besides, it is difficult to integrate it with most quantitative MS-based workflows, except for stable isotopic labeling of amino acids in cell culture (SILAC). This work describes a fast, flexible and quantitative workflow for the discovery of novel protein-protein interactions. A cleavable cross-linker, dithiobis[succinimidyl propionate] (DSP), is utilized to stabilize protein complexes before immunoprecipitation. Protein complex detachment from the antibody is achieved by limited proteolysis. Finally, protein quantitation is performed via (18)O labeling. The workflow has been optimized concerning (i) DSP concentration and (ii) incubation times for limited proteolysis, using the stem cell-associated transcription cofactor ZNF521 as a model target. The interaction of ZNF521 with the core components of the nuclear remodelling and histone deacetylase (NuRD) complex, already reported in the literature, was confirmed. Additionally, interactions with newly discovered molecular partners of potentially relevant functional role, such as ZNF423, Spt16, Spt5, were discovered and validated by Western blotting.

An MRM-based workflow for absolute quantitation of lysine-acetylated metabolic enzymes in mouse liver.

As a key post-translational modification mechanism, protein acetylation plays critical roles in regulating and/or coordinating cell metabolism. Acetylation is a prevalent modification process in enzymes. Protein acetylation modification occurs in sub-stoichiometric amounts; therefore extracting biologically meaningful information from these acetylation sites requires an adaptable, sensitive, specific, and robust method for their quantification. In this work, we combine immunoassays and multiple reaction monitoring-mass spectrometry (MRM-MS) technology to develop an absolute quantification for acetylation modification. With this hybrid method, we quantified the acetylation level of metabolic enzymes, which could demonstrate the regulatory mechanisms of the studied enzymes. The development of this quantitative workflow is a pivotal step for advancing our knowledge and understanding of the regulatory effects of protein acetylation in physiology and pathophysiology.

Improvement of the performance of targeted LC-MS assays through enrichment of histidine-containing peptides.

Mass spectrometric-based quantification using targeted methods has matured during the past decade and is now commonly used in proteomics. However, the reliability of protein quantification in complex matrixes using selected reaction monitoring is often impaired by interfering signals arising from coelution of nontargeted components. Sample preparation methods resulting in the reduction of the number of peptides present in the mixture minimizes this effect. One solution consists in the selective capture of peptides containing infrequent amino acids. The enrichment of histidine-containing peptides via immobilized metal-ion affinity chromatography loaded with Cu(2+) ions (IMAC-Cu) was applied in a quantitative workflow and found to be a simple and cost effective method for the reduction of sample complexity with high recovery and selectivity. When applied to a series of depleted human plasma digests, the method decreased nonspecific signals, resulting in a more precise and robust protein quantification. The method was also shown to be an alternative to HSA/IgG depletion during plasma protein analysis. This method, used in conjunction with recent improvements in the instrument's peak capacity, addresses a bottleneck generally encountered in quantitative proteomics studies by providing the robustness and throughput required for the analysis of large sample series without compromising the number of proteins monitored.

Information Processing in Computer-Assisted Interventions: 4th International Conference, 2013.

Information Processing in Computer-Assisted Interventions: 4th International Conference, 2013.

Quantitative label-free redox proteomics of reversible cysteine oxidation in red blood cell membranes

Reversible oxidation of cysteine residues is a relevant posttranslational modification of proteins. However, the low activation energy and transitory nature of the redox switch and the intrinsic complexity of the analysis render quite challenging the aim of a rigorous high-throughput screening of the redox status of redox-sensitive cysteine residues. We describe here a quantitative workflow for redox proteomics, where the ratio between the oxidized forms of proteins in the control vs treated samples is determined by a robust label-free approach. We critically present the convenience of the procedure by specifically addressing the following aspects: (i) the accurate ratio, calculated from the whole set of identified peptides rather than just isotope-tagged fragments; (ii) the application of a robust analytical pipeline to frame the most consistent data averaged over the biological variability; (iii) the relevance of using stringent criteria of analysis, even at the cost of losing potentially interesting but statistically uncertain data. The pipeline has been assessed on red blood cell membrane challenged with diamide as a model of a mild oxidative condition. The cluster of identified proteins encompassed components of the cytoskeleton more oxidized. Indirectly, our analysis confirmed the previous observation that oxidized hemoglobin binds to membranes while oxidized peroxiredoxin 2 loses affinity.

Condenser: A statistical aggregation tool for multi-sample quantitative proteomic data from Matrix Science Mascot Distiller™

We describe Condenser, a freely available, comprehensive open-source tool for merging multidimensional quantitative proteomics data from the Matrix Science Mascot Distiller Quantitation Toolbox into a common format ready for subsequent bioinformatic analysis. A number of different relative quantitation technologies, such as metabolic (15)N and amino acid stable isotope incorporation, label-free and chemical-label quantitation are supported. The program features multiple options for curative filtering of the quantified peptides, allowing the user to choose data quality thresholds appropriate for the current dataset, and ensure the quality of the calculated relative protein abundances. Condenser also features optional global normalization, peptide outlier removal, multiple testing and calculation of t-test statistics for highlighting and evaluating proteins with significantly altered relative protein abundances. Condenser provides an attractive addition to the gold-standard quantitative workflow of Mascot Distiller, allowing easy handling of larger multi-dimensional experiments. Source code, binaries, test data set and documentation are available at http://condenser.googlecode.com/.

Pitfalls in prestack inversion of merged seismic surveys

Modern 3D seismic surveys are often of such good quality and 3D interpretation packages so user-friendly that seismic interpretation is no longer exclusively carried out by geophysicists. This ease-of-use has also been extended to more quantitative workflows, such as 3D prestack inversion, putting it in the hands of the “nonexpert” — be it geologist, engineer, or new-hire geophysicist. Indeed, given good quality input seismic data, almost any interpreter who can generate good well ties and define an accurate background model of P-impedance, S-impedance, and density can generate a quality prestack inversion. Two of the authors are new geophysicists who fell into the prestack inversion “pit.” Fortunately, they were able to recognize that something was wrong. We applied prestack inversion to gathers that were carefully reprocessed by a major service company. The problem, however, was not with the processing, but with our lack of understanding of the input legacy data that formed part of a larger “megamerge” survey. Not all of the surveys that were merged had the same offset range. In the migration step, gaps in long offsets of the older surveys were not muted. Migration noise from newer surveys was allowed to fill this space. We share our initial workflow and suspicious results. We also clarify the meaning of “fold” and “offset” for prestack-migrated gathers. In addition to presenting some QC tools useful in analyzing megamerge surveys, we show how, by limiting the offsets used in our prestack inversion, we obtain less aggressive but still useful results.

LC-MS3 quantification of O-glycopeptides in human serum.

Quantitative analysis of site-specific glycosylation of proteins is a challenging part of glycoproteomic research. Multiple enrichment steps are typically required in the analytical workflows to achieve adequate characterization of the site-specific glycoforms. In spite of recent advances, quantitative workflows need further development. Here, we report a selective and sensitive MS2 followed by further fragmentation in the linear IT-MS analyzer (MS3) multiple reaction monitoring workflow mass spectrometric method for direct analysis of O-glycopeptides in difficult matrix such as serum. Method optimization was performed using two serum glycoproteins, hemopexin (HPX) and sex hormone binding globulin. With the optimized MS3 workflow, we were able to analyze major glycoforms of HPX directly in human serum. Quantification of the minor glycoforms of HPX and glycoforms of sex hormone binding globulin required enrichment of the protein because these analytes were below the sensitivity of the 4000 quadrupole ion trap hybrid mass spectrometer in the complex serum background. In conclusion, we present a quantitative method for site-specific analysis of O-glycosylation with general applicability to mucin-type glycoproteins. Our results document reliable application of the optimized MS3 multiple reaction monitoring workflow to the relative quantification of O-glycosylation microheterogeneity of HPX in human serum. Introduction of isotopically labeled standards would be desirable to achieve absolute quantification of the analytes. The possibility to analyze serum samples directly represents a significant improvement of the quantitative glycopeptide workflows with the potential for use in clinical applications.

Quantitative Assessment of In-solution Digestion Efficiency Identifies Optimal Protocols for Unbiased Protein Analysis

The majority of mass spectrometry-based protein quantification studies uses peptide-centric analytical methods and thus strongly relies on efficient and unbiased protein digestion protocols for sample preparation. We present a novel objective approach to assess protein digestion efficiency using a combination of qualitative and quantitative liquid chromatography-tandem MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein fractions. We evaluated nine trypsin-based digestion protocols, based on standard in-solution or on spin filter-aided digestion, including new optimized protocols. We investigated various reagents for protein solubilization and denaturation (dodecyl sulfate, deoxycholate, urea), several trypsin digestion conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents before analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative liquid chromatography-tandem MS workflow quantified over 3700 distinct peptides with 96% completeness between all protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows for efficient, unbiased generation and recovery of peptides from all protein classes, including membrane proteins. This deoxycholate-assisted protocol was also optimal for spin filter-aided digestions as compared with existing methods.

High-Resolution MS: First Choice for Peptide Quantification?

Janssen Research & Development, a Division of Janssen Pharmaceutica N.V., Belgium The role of MS in peptide quantification For quantitative analysis of small-molecule drugs, LC–MS is considered the gold standard. However, focusing on peptide drugs, the majority of peptide development programs still rely on immunoassays for evaluation of exposure of the peptide drug in study samples. The advantages of these assays are the unrivaled sensitivity and the high throughput. Selectivity issues and method development times are, on the other hand, often rate-limiting. LC–MS technology can offer an alternative to improve selectivity and reduce method development time (no reagent preparation needed), but at the expense of lower sensitivity and throughput. Therefore, in our portfolio, for early peptide drug programs, quantitative workflows with LC–MS are preferred to address the short cycle times requested at this stage. In development and also with the aim to evaluate anti-drug antibody response, immunological assays are primarily preferred. An LC–MS assay can then be requested as an orthogonal assay to confirm the selectivity of the immunoassay or to address specific issues. In rare cases, the immunological assay is confronted with considerable challenges and LC–MS(/MS) can be developed faster and with more confidence to support the program.

Additions to the Human Plasma Proteome via a Tandem MARS Depletion iTRAQ-Based Workflow

Robust platforms for determining differentially expressed proteins in biomarker and discovery studies using human plasma are of great interest. While increased depth in proteome coverage is desirable, it is associated with costs of experimental time due to necessary sample fractionation. We evaluated a robust quantitative proteomics workflow for its ability (1) to provide increased depth in plasma proteome coverage and (2) to give statistical insight useful for establishing differentially expressed plasma proteins. The workflow involves dual-stage immunodepletion on a multiple affinity removal system (MARS) column, iTRAQ tagging, offline strong-cation exchange chromatography, and liquid chromatography tandem mass spectrometry (LC-MS/MS). Independent workflow experiments were performed in triplicate on four plasma samples tagged with iTRAQ 4-plex reagents. After stringent criteria were applied to database searched results, 689 proteins with at least two spectral counts (SC) were identified. Depth in proteome coverage was assessed by comparison to the 2010 Human Plasma Proteome Reference Database in which our studies reveal 399 additional proteins which have not been previously reported. Additionally, we report on the technical variation of this quantitative workflow which ranges from ±11 to 30%.

Abstract 5036: MicroRNA expression profiling potential for human breast cancer diagnosis using a bead-based microRNA-specific capturing method

Abstract MicroRNAs (miRNAs), a family of small, endogenous, non-coding (∼17-24 nucleotides) nucleic acids, were initially discovered in 1993, but the discovery of a second miRNA led to their use as molecular markers of disease and potential therapeutic targets. MiRNAs regulate RNA translation, play a role in cell proliferation, control timing of organism development, and are associated with carcinogenesis. Because of their regulatory function in cell differentiation and renewal during physiologic and malignant conditions, miRNAs are emerging as a new class of effective biomarkers for cancer research. The miRNA expression profiling of tumor cells will allow for the identification of prognostic markers to indicate potential targets for patient- or disease-specific therapies. Three criteria important for profiling miRNAs are ease of use, simplicity and sensitivity. We have designed and developed a new method to quickly extract and purify specific miRNAs for detection using our current reverse transcription and real-time quantitative PCR workflows. The method involved 1μm-diameter magnetic beads conjugated with anti-miRNA oligoncleotides to capture these select miRNA targets from blood, plasma, and other tissues. The miRNAs were then transcribed into cDNA and subsequently used as templates for TaqMan® qRT-PCR analysis. We used this method to evaluate the miRNA signatures from normal and cancerous human breast modeled by cell lines and represented by formalin-fixed, paraffin-embedded tissues. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5036. doi:1538-7445.AM2012-5036

An MRM-based workflow for quantifying cardiac mitochondrial protein phosphorylation in murine and human tissue

The regulation of mitochondrial function is essential for cardiomyocyte adaptation to cellular stress. While it has long been understood that phosphorylation regulates flux through metabolic pathways, novel phosphorylation sites are continually being discovered in all functionally distinct areas of the mitochondrial proteome. Extracting biologically meaningful information from these phosphorylation sites requires an adaptable, sensitive, specific and robust method for their quantification. Here we report a multiple reaction monitoring-based mass spectrometric workflow for quantifying site-specific phosphorylation of mitochondrial proteins. Specifically, chromatographic and mass spectrometric conditions for 68 transitions derived from 23 murine and human phosphopeptides, and their corresponding unmodified peptides, were optimized. These methods enabled the quantification of endogenous phosphopeptides from the outer mitochondrial membrane protein VDAC, and the inner membrane proteins ANT and ETC complexes I, III and V. The development of this quantitative workflow is a pivotal step for advancing our knowledge and understanding of the regulatory effects of mitochondrial protein phosphorylation in cardiac physiology and pathophysiology. This article is part of a Special Issue entitled: Translational Proteomics.

Driving efficiency in a high-throughput metabolic stability assay through a generic high-resolution accurate mass method and automated data mining

Improving analytical throughput is the focus of many quantitative workflows being developed for early drug discovery. For drug candidate screening, it is common practice to use ultra-high performance liquid chromatography (U-HPLC) coupled with triple quadrupole mass spectrometry. This approach certainly results in short analytical run time; however, in assessing the true throughput, all aspects of the workflow needs to be considered, including instrument optimization and the necessity to re-run samples when information is missed. Here we describe a high-throughput metabolic stability assay with a simplified instrument set-up which significantly improves the overall assay efficiency. In addition, as the data is acquired in a non-biased manner, high information content of both the parent compound and metabolites is gathered at the same time to facilitate the decision of which compounds to proceed through the drug discovery pipeline.

COMPASS: A suite of pre‐ and post‐search proteomics software tools for OMSSA

Here we present the Coon OMSSA Proteomic Analysis Software Suite (COMPASS): a free and open-source software pipeline for high-throughput analysis of proteomics data, designed around the Open Mass Spectrometry Search Algorithm. We detail a synergistic set of tools for protein database generation, spectral reduction, peptide false discovery rate analysis, peptide quantitation via isobaric labeling, protein parsimony and protein false discovery rate analysis, and protein quantitation. We strive for maximum ease of use, utilizing graphical user interfaces and working with data files in the original instrument vendor format. Results are stored in plain text comma-separated value files, which are easy to view and manipulate with a text editor or spreadsheet program. We illustrate the operation and efficacy of COMPASS through the use of two LC-MS/MS data sets. The first is a data set of a highly annotated mixture of standard proteins and manually validated contaminants that exhibits the identification workflow. The second is a data set of yeast peptides, labeled with isobaric stable isotope tags and mixed in known ratios, to demonstrate the quantitative workflow. For these two data sets, COMPASS performs equivalently or better than the current de facto standard, the Trans-Proteomic Pipeline.

Shell's integrated quantitative interpretation workflow

Shell Development Australia is a major asset holder in the Browse Basin and the Carnarvon Basin in the North West Shelf of Australia. In 2007, Shell Development Australia embarked on an integrated quantitative seismic interpretation project related to the Triassic Mungaroo Formation in the Carnarvon Basin. The main objective was to constrain the uncertainties in using seismic data as a predictor for rock and fluid properties of fields and prospects in the basin. This project followed a workflow that has been proven in other basins around the world, whereby the vertical and lateral variability of rock properties of both reservoir and non-reservoir lithologies are captured in general trends. The calculated trends are based on well log extractions of end member lithologies and the input of petrographic information and forward modelling. In combination with a regionally consistent 3D burial model for the estimation of remaining porosity, these established rock trends then allow for a prediction of various acoustic responses of reservoir and pore fill properties. The comparisons between the pre-drill predicted rock properties and the properties encountered after drilling at different reservoir levels have lead to a general confidence that the reservoir properties can be derived from seismic data where well data are not abundant. This increased confidence will play a major part in Shell’s attitude towards appraisal activities and decisions on various development options.

Use of Enthalpy and Gibbs Free Energy to Evaluate the Risk of Amorphous Formation

The control of crystalline and amorphous phases is important during the development of a new drug candidate. Our approach begins with an understanding of the thermodynamics of these two phases. We have developed a quantitative yet practical work flow consisting of three steps towards the analysis of the risk of amorphous material formation. First, we derive the thermodynamic equations to calculate the enthalpy, Gibbs free energy, and the solubility of each phase and their differences as a function of temperature. The enthalpy for each crystalline drug substance at its melting point is selected as the reference state to enable a consistent approach for all analysis. Second, we use data from DSC measurements and the derived thermodynamic equations to construct the enthalpy, Gibbs free energy and solubility diagrams so as to compare the characteristics of these two phases. Finally, we use the results of these calculations to evaluate the potential risk of crystalline-to-amorphous phase conversion during processing of either the drug substance or the drug product. In addition, the impact of amorphous formation on solubility is evaluated. Two drug candidates are used to illustrate this workflow for risk analysis.

Mass spectrometry analysis of soybean seed proteins: optimization of gel-free quantitative workflow

For high-throughput quantitative mass spectrometry (MS) analysis of soybean seed proteins, a method that avoids gel fractionation is advantageous. We developed and optimized a workflow from protein isolation to MS-based quantitation without polyacrylamide matrices. The objective was to quantitatively compare extraction methods to reproducibly arrive at the highest yield and proteome coverage. Beginning with mature soybean seed, we compared four proteinextraction methods, employing either TCA/acetone, urea, urea/thiourea, or phenol. Soybean proteins were extracted, quantified for total protein content, and comparatively visualized by Coomassie–SDS-PAGE. The phenolextraction method yielded protein concentrations 2 to 7-fold higher than other extraction methods. Comparison of trypsin to protein ratios (1 : 25, 1 : 50, 1 : 75, and 1 : 100) revealed a near linear increase in spectral counts by MS with increasing trypsin levels. In-solution digestion procedures were also compared to determine optimal resuspension and digestion conditions for peptideextraction and quantitation. A resuspension buffer that contained 50 mM Tris–HCl of pH 8.0 and 5 M urea showed the highest spectral counts and protein identifications. The results of this study show the time-honored phenolextraction method consistently and unequivocally yielded the highest amounts of protein from mature soybean seed, and that buffered urea is sufficient for optimal resuspension of precipitated proteins for tryptic digestion and mass spectrometry.

Plasminogen-activator-producing tumour.

In a patient with giant-cell carcinoma of the lung a secondary tumour deposit in the arm was incised and bled for three weeks. Investigations showed the tumour to be rich in plasminogen activator. Haemostasis in the tumour was achieved with aminocaproic acid therapy. For a period the plasminogen-activator properties were retained in cell culture of the tumour.