Applications of stable isotope dimethyl labeling in quantitative proteomics

Mass spectrometry has proven to be an indispensable tool for protein identification, characterization, and quantification. Among the possible methods in quantitative proteomics, stable isotope labeling by using reductive dimethylation has emerged as a cost-effective, simple, but powerful method able to compete at any level with the present alternatives. In this review, we briefly introduce experimental and software methods for proteome analysis using dimethyl labeling and provide a comprehensive overview of reported applications in the analysis of (1) differential protein expression, (2) posttranslational modifications, and (3) protein interactions.     

Comparative proteomics based on stable isotope labeling and affinity selection

Disease, external stimuli (such as drugs and toxins), and mutations cause changes in the rate of protein synthesis, post-translational modification, inter-compartmental transport, and degradation of proteins in living systems. Recognizing and identifying the small number of proteins involved is complicated by the complexity of biological extracts and the fact that post-translational alterations of proteins can occur at many sites in multiple ways. It is shown here that a variety of new tools and methods based on internal standard technology are now being developed to code globally all peptides in control and experimental samples for quantification. The great advantage of these stable isotope-labeling strategies is that mass spectrometers can rapidly target those proteins that have changed in concentration for further analysis. When coupled to stable isotope quantification, targeting can be further focused through chromatographic selection of peptide classes on the basis of specific structural features. Targeting structural features is particularly useful when they are unique to types of regulation or disease. Differential displays of targeted peptides show that stimulus-specific markers are relatively easy to identify and will probably be diagnostically valuable tools.     

Quantitative carbamylation as a stable isotopic labeling method for comparative proteomics

A method was developed that uses urea to both solublize and isotopically label biological samples for comparative proteomics. This approach uses either light or heavy urea ((12)CH(4)(14)N(2)O or (13)CH(4)(15)N(2)O, respectively) at a concentration of 8 M and a pH of 7 to dissolve the samples prior to digestion. After the sample is digested using standard proteomic protocols and dried, isotopic labeling is completed by resuspending the sample in a solution of 8 M urea at a pH of 8.5, using the same isotopic species of urea as used for digestion and incubating for 4 h at 80 degrees C. Under these conditions, carbamylation occurs only on the primary amines of the peptides. The effects of complete carbamylation on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and electrospray ionization tandem mass spectrometry (ESI-MS/MS) (collision-induced dissociation (CID)) were examined. Peptides that had a C-terminal carbamylated lysine residue were found to have a reduced intensity when viewed by MALDI-TOFMS. CID of a tryptic peptide that was carbamylated on both the N-terminus and the C-terminus was found to have a more uniform distribution of b- and y-ions, as well as prominent ions from loss of water. Reversed-phase chromatography coupled to ESI-MS/MS was used to identify and quantify the isotopically labeled standard proteins, bovine serum albumin (BSA), bovine transferrin, and bovine alpha-casein. Quantitative error between theoretical and observed data ranged from 1.7-10.0%. Relative standard deviations for protein quantitation ranged from 5.2-27.8% over a dynamic range from 0.1-10 (L/H). The development of a method utilizing urea-assisted carbamylation of lysines and N-termini to globally labeled samples for comparative proteomics may prove useful for samples that require a strong chaotrope prior to proteolysis.     

RABA (Reductive Alkylation By Acetone): A novel stable isotope labeling approach for quantitative proteomics

Quantitative proteomics is challenging and various stable isotope based approaches have been developed to meet the challenge. Hereby we describe a simple, efficient, reliable, and inexpensive method named reductive alkylation by acetone (RABA) to introduce stable isotopes to peptides for quantitative analysis. The RABA method leads to alkylation of N-terminal and lysine amino groups with isopropyl moiety. Using unlabeled (d₀) and deuterium labeled (d₆) acetone, a 6 Da mass split is introduced to each isopropyl modification between the light and heavy isotope labeled peptides, which is ideally suited for quantitative analysis. The reaction specificity, stoichiometry, labeling efficiency, and linear range of the RABA method have been thoroughly evaluated in this study using standard peptides, tryptic digest of proteins, as well as human cell lysate. Reliable quantitative results have been consistently obtained in all experiments. We also applied the RABA method to quantitative analysis of proteins in spinal cords of transgenic mouse models of amyotrophic lateral sclerosis. Highly homologous proteins (transgenic human SOD1 and endogenous mouse SOD1) were distinguished and quantified using the method developed in this study. In addition, the quantitative results using the RABA approach were independently validated by Western blot.     

基于稳定同位素标记的蛋白质组学定量方法研究进展

定量蛋白质组学已经成为后基因时代的重要研究方向之一。目前该领域的研究主要采用无标记定量方法和稳定同位素标记定量法。其中,基于稳定同位素标记的蛋白质组定量方法发展非常迅速,已为生命科学研究提供了重要的技术支撑。本文分析了基于稳定同位素标记的蛋白质组学定量方法,包括相对定量方法和绝对定量方法,并对其发展进行了展望。     

Hg stable isotope analysis by the double-spike method

Recent publications suggest great potential for analysis of Hg stable isotope abundances to elucidate sources and/or chemical processes that control the environmental impact of mercury. We have developed a new MC-ICP-MS method for analysis of mercury isotope ratios using the double-spike approach, in which a solution containing enriched ¹⁹⁶Hg and ²⁰⁴Hg is mixed with samples and provides a means to correct for instrumental mass bias and most isotopic fractionation that may occur during sample preparation and introduction into the instrument. Large amounts of isotopic fractionation induced by sample preparation and introduction into the instrument (e.g., by batch reactors) are corrected for. This may greatly enhance various Hg pre-concentration methods by correcting for minor fractionation that may occur during preparation and removing the need to demonstrate 100% recovery. Current precision, when ratios are normalized to the daily average, is 0.06‰, 0.06‰, 0.05‰, and 0.05‰ (2σ) for ²⁰²Hg/¹⁹⁸Hg, ²⁰¹Hg/¹⁹⁸Hg, ²⁰⁰Hg/¹⁹⁸Hg, and ¹⁹⁹Hg/¹⁹⁸Hg, respectively. This is slightly better than previously published methods. Additionally, this precision was attained despite the presence of large amounts of other Hg isotopes (e.g., 5.0% atom percent ¹⁹⁸Hg) in the spike solution; substantially better precision could be achieved if purer ¹⁹⁶Hg were used.     

A portable automated system for trace gas sampling in the field and stable isotope analysis in the laboratory

A computer-controllable mobile system is presented which enables the automatic collection of 33 air samples in the field and the subsequent analysis for delta13C and delta18O stable isotope ratios of a carbon-containing trace gas in the laboratory, e.g. CO2, CO or CH4. The system includes a manifold gas source input for profile sampling and an infrared gas analyzer for in situ CO2 concentration measurements. Measurements of delta13C and delta18O of all 33 samples can run unattended and take less than six hours for CO2. Laboratory tests with three gases (compressed air with different pCO2 and stable isotope compositions) showed a measurement precision of 0.03 per thousand for delta13C and 0.02 per thousand for delta18O of CO2 (standard error (SE), n = 11). A field test of our system, in which 66 air samples were collected within a 24-hour period above grassland, showed a correlation of 0.99 (r2) between the inverse of pCO2 and delta13C of CO2. Storage of samples until analysis is possible for about 1 week; this can be an important factor for sampling in remote areas. A wider range of applications in the field is open with our system, since sampling and analysis of CO and CH4 for stable isotope composition is also possible. Samples of compressed air had a measurement precision (SE, n = 33) of 0.03 per thousand for delta13C and of 0.04 per thousand for delta18O on CO and of 0.07 per thousand for delta13C on CH4. Our system should therefore further facilitate research of trace gases in the context of the carbon cycle in the field, and opens many other possible applications with carbon- and possibly non-carbon-containing trace gases.     

An automated system for stable isotope and concentration analyses of CO2 from small atmospheric samples

We have developed an automated, continuous-flow isotope ratio mass spectrometry (CF-IRMS) system for the analysis of delta(13)C, delta(18)O, and CO(2) concentration (micromol mol(-1)) ([CO(2)]) from 2 mL of atmospheric air. Two replicate 1 mL aliquots of atmospheric air are sequentially sampled from fifteen 100 mL flasks. The atmospheric sample is inserted into a helium stream and sent through a gas chromatograph for separation of the gases and subsequent IRMS analysis. Two delta(13)C and delta(18)O standards and five [CO(2)] standards are run with each set of fifteen samples. We obtained a precision of 0.06 per thousand, 0.11 per thousand, and 0.48 micromol mol(-1) for delta(13)C, delta(18)O, and [CO(2)], respectively, by analyzing fifty 100 mL samples filled from five cylinders with a [CO(2)] range of 275 micromol mol(-1). Accuracy was determined by comparison with established methods (dual-inlet IRMS, and nondispersive infrared gas analysis) and found to have a mean offset of 0.00 per thousand, -0.09 per thousand, and -0.26 micromol mol(-1) for delta(13)C and delta(18)O, and [CO(2)], respectively.     

Open tube combustion method of organic samples for stable carbon isotope analysis

A simple and effective method for the conversion of organic carbon into carbon dioxide for analysis of stable carbon isotopes (delta(13)C) in samples of various organic substances, soils, sedimentary rocks, oils and volatile organic liquids is presented. The conversion of organic carbon of the samples is carried out in a quartz reactor connected to a vacuum line for CO(2) freezing and purification. A solid organic sample mixed with CuO is placed at the reactor bottom and the reactor is subsequently filled with granular CuO. One end of the CuO column is preheated to 850 degrees C while the other end of the column in contact with the sample is kept at ambient temperature. Heating of the sample (850 degrees C) and the remainder of the column is then performed. The preheated part of the column provides efficient conversion of carbon into CO(2). The reactor for the conversion of volatile liquid organic compounds is filled with granular CuO. The column of CuO is heated to 850 degrees C. Samples of volatile liquids are introduced into the reactor through a septum using a microsyringe. Complete conversion takes 10 min for solid samples and 3 min for volatile liquids. The precision of the delta(13)C analysis for solid and volatile liquid organic substances is +/-0.1 per thousand and +/-0.04 per thousand, respectively.     

An automated activation analysis data acquisition system

An automated neutron activation analysis data acquisition system has been assembled from commercially available equipment. The modifications of the components needed to make this into a working system are described in the text. The main components of the data acquisition system are a sample changer, a Ge(Li) detector, a magnetic tape deck and a minicomputer based multichannel analyzer. The sample changer has a 200-sample capacity and can handle both solid and liquid samples. Software for controlling the data acquisition system is flexible, yet simple to use. The system has operated reliably for a year and has sharply reduced the effort needed for data acquisition.     

Quantitation of phosphopeptides using affinity chromatography and stable isotope labeling

Reversible phosphorylation of proteins represents an important component of cellular signaling pathways. The isolation of phosphoproteins in complex mixtures and the determination of the level of phosphorylation have been and remain a major challenge. It has prompted the development of several strategies, including immobilized metal affinity capture to enrich for phosphorylated peptides. An improved methodology was published (Ficarro, et al., Nature Biotechnology 2002, 20, 301-305) that showed increased selectivity through esterification of amino acid side chain carboxylic groups of enzymatically digested peptides. This method was applied for relative quantitation of phosphopeptides in conjunction with the use of stable isotope labeling. The merits and limits of the approach are discussed and its application to the analysis of the effects of serum starvation on in vitro cultured human lung cells is presented.     

Error propagation in normalization of stable isotope data: a Monte Carlo analysis

A higher analytical precision of a stable isotope ratio mass spectrometer does not automatically guarantee accurate determination of the true isotope composition (δ‐value) of samples, since estimates of true δ‐values are obtained from the normalization of raw isotope data. We performed both Monte Carlo simulations and laboratory experiments to investigate aspects of error propagation during the normalization of carbon stable isotope data. We found that increasing both the number of different reference standards and the number of repetitions of each of these standards reduces the normalization error. A 50% reduction in the normalization error can be achieved over the two‐point normalization by either analyzing two standards four times each, or four standards two times each. If the true δ‐value of a sample is approximately known a priori, the normalization error may then be reduced through a targeted choice of locally optimal standards. However, the difference in improvement is minimal and, therefore, a more practical strategy is to use two or more standards covering the whole stable isotope scale. The selection of different sets of standards by different laboratories or for different batches of samples in the same laboratory may lead to significant differences in the normalized δ‐values of the same samples, leading to inconsistent results. Hence, the same set of standards should always be used for a particular element and a particular stable isotope analytical technique. Copyright © 2010 John Wiley & Sons, Ltd.     

Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation.

We have demonstrated the use of per-methyl esterification of peptides for relative quantification of proteins between two mixtures of proteins and automated de novo sequence derivation on the same dataset. Protein mixtures for comparison were digested to peptides and resultant peptides methylated using either d0- or d3-methanol. Methyl esterification of peptides converted carboxylic acids, such as are present on the side chains of aspartic and glutamic acid as well as the carboxyl terminus, to their corresponding methyl esters. The separate d0- and d3-methylated peptide mixtures were combined and the mixture subjected to microcapillary high performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS). Parent proteins of methylated peptides were identified by correlative database searching of peptide tandem mass spectra. Ratios of proteins in the two original mixtures could be calculated by normalization of the area under the curve for identical charge states of d0- to d3-methylated peptides. An algorithm was developed that derived, without intervention, peptide sequence de novo by comparison of tandem mass spectra of d0- and d3-peptide methyl esters.     

Precise proteomic identification using mass spectrometry coupled with stable isotope labeling

Stable isotope labeling (SIL) can assist mass spectrometry to improve its specificity and throughput in protein identification, de novo sequencing, and characterization of post translational modifications. This Education article summarizes the unique characteristics of stable isotope-assisted mass spectrometry for accurate protein identification without requirements for ultrahigh mass accuracy. Some applications are discussed here to demonstrate the general experimental procedures, data interpretation, and the improvements in accuracy and throughput compared to the use of mass spectrometry alone.     

A versatile method for stable carbon isotope analysis of carbohydrates by high-performance liquid chromatography/isotope ratio mass spectrometry

We have developed a method to analyze stable carbon isotope ((13)C/(12)C) ratios in a variety of carbohydrates using high-performance liquid chromatography/isotope ratio mass spectrometry (HPLC/IRMS). The chromatography is based on strong anion-exchange columns with low strength NaOH eluents. An eluent concentration of 1 mM resulted in low background signals and good separation of most of the typical plant neutral carbohydrates. We also show that more strongly bound carbohydrates such as acidic carbohydrates can be separated by inclusion of NO(3) (-) as an inorganic pusher ion in the eluent. Analyses of neutral carbohydrate concentrations and their stable carbon isotope ratios are shown for plant materials and marine sediment samples both at natural abundance and for (13)C-enriched samples. The main advantage of HPLC/IRMS analysis over traditional gas chromatography based methods is that no derivatization is needed resulting in simple sample treatment and improved accuracy and reproducibility.     

Fully automated software solution for protein quantitation by global metabolic labeling with stable isotopes

Metabolic stable isotope labeling is increasingly employed for accurate protein (and metabolite) quantitation using mass spectrometry (MS). It provides sample-specific isotopologues that can be used to facilitate comparative analysis of two or more samples. Stable Isotope Labeling by Amino acids in Cell culture (SILAC) has been used for almost a decade in proteomic research and analytical software solutions have been established that provide an easy and integrated workflow for elucidating sample abundance ratios for most MS data formats. While SILAC is a discrete labeling method using specific amino acids, global metabolic stable isotope labeling using isotopes such as (15)N labels the entire element content of the sample, i.e. for (15)N the entire peptide backbone in addition to all nitrogen-containing side chains. Although global metabolic labeling can deliver advantages with regard to isotope incorporation and costs, the requirements for data analysis are more demanding because, for instance for polypeptides, the mass difference introduced by the label depends on the amino acid composition. Consequently, there has been less progress on the automation of the data processing and mining steps for this type of protein quantitation. Here, we present a new integrated software solution for the quantitative analysis of protein expression in differential samples and show the benefits of high-resolution MS data in quantitative proteomic analyses.