Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer

Online liquid chromatography-mass spectrometric (LC-MS) analysis of intact proteins (i.e., top-down proteomics) is a growing area of research in the mass spectrometry community. A major advantage of top-down MS characterization of proteins is that the information of the intact protein is retained over the vastly more common bottom-up approach that uses protease-generated peptides to search genomic databases for protein identification. Concurrent to the emergence of top-down MS characterization of proteins has been the development and implementation of the stable isotope labeling of amino acids in cell culture (SILAC) method for relative quantification of proteins by LC-MS. Herein we describe the qualitative and quantitative top-down characterization of proteins derived from SILAC-labeled Aspergillus flavus using nanoflow reversed-phase liquid chromatography directly coupled to a linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (nLC-LTQ-FTICR-MS). A. flavus is a toxic filamentous fungus that significantly impacts the agricultural economy and human health. SILAC labeling improved the confidence of protein identification, and we observed 1318 unique protein masses corresponding to 659 SILAC pairs, of which 22 were confidently identified. However, we have observed some limiting issues with regard to protein quantification using top-down MS/MS analyses of SILAC-labeled proteins. The role of SILAC labeling in the presence of competing endogenously produced amino acid residues and its impact on quantification of intact species are discussed in detail.     

Tandem mass tag protein labeling for top-down identification and quantification

Top-down mass spectrometry holds tremendous potential for characterization and quantification of intact proteins. So far, however, very few studies have combined top-down proteomics with protein quantification. In view of the success of isobaric mass tags in quantitative bottom-up proteomics, we applied the tandem mass tag (TMT) technology to label intact proteins and examined the feasibility to directly quantify TMT-labeled proteins. A top-down platform encompassing separation via ion-pair reversed-phase liquid chromatography using monolithic stationary phases coupled online to an LTQ-Orbitrap Velos electron-transfer dissociation (ETD) mass spectrometer (MS) was established to simultaneously identify and quantify TMT-labeled proteins. The TMT-labeled proteins were found to be readily dissociated under high-energy collision dissociation (HCD) activation. The liberated reporter ions delivered expected ratios over a wide dynamic range independent of the protein charge state. Furthermore, protein sequence tags generated either by low-energy HCD or ETD activation along with the intact protein mass information allow for confident identification of small proteins below 35 kDa. We conclude that the approach presented in this pilot study paves the way for further developments and numerous applications for straightforward, accurate, and multiplexed quantitative analysis in protein chemistry and proteomics.     

Precolumn isotope dilution analysis in nanoHPLC-ICPMS for absolute quantification of sulfur-containing peptides

A novel generic approach based on precolumn isotope dilution nanoHPLC-ICPMS analysis was developed for the accurate absolute quantification of sulfur-containing peptides. A 34S-labeled, species-unspecific sulfur spike (sulfate), noninteracting with analyte peptides under the optimized HPLC condition, was added directly to the chromatographic eluents. Thus a generic sulfur standard permanently present during analysis was used for peptide quantification. Interference-free detection of the 32S and 34S isotopes in ICPMS was achieved by eliminating O2+ ions in a collision cell using Xe gas at 130 microL min-1. The detection limit for sulfur was 45 microg L-1 which corresponded to 1-2 pmol of individual peptides. The method was validated by the analysis of a standard peptide solution showing high accuracy (recovery 103%) and good precision (RSD 2.1%). The combination of nanoHPLC-ICP IDMS with nanoHPLC-ESI MS/MS allowed the precise quantification and identification of sulfur-containing peptides in tryptic digests of human serum albumin and salt-induced yeast protein (SIP18) at the picomole level.     

Top-down and bottom-up mass spectrometric characterization of human myoglobin-centered free radicals induced by oxidative damage

In an effort to determine the utility of top-down mass spectrometric methodologies for the characterization of protein radical adducts, top-down approaches were investigated and compared to the traditional bottom-up approaches. Specifically, the nature of the radicals on human myoglobin induced by the addition of hydrogen peroxide and captured by the spin trap 5,5-dimethyl-1-pyrroline N-oxide (DMPO) was investigated. The most abundant ion observed in the electrospray mass spectrum of this reaction mixture corresponds in mass to the human myoglobin plus one DMPO molecule. In addition, a second ion of lower abundance is observed, which corresponds to a second DMPO molecule being trapped on myoglobin. Top-down analyses using Fourier transform ion cyclotron resonance mass spectrometry can be used to characterize proteins and, thus, were performed on several different charge-state ions of both the native and the mono-DMPO nitrone adduct of human myoglobin. Data produced from the top-down analyses are very complex yet information rich. In the case of DMPO-modified human myoglobin, the top-down data localized the DMPO spin trap to residues 97-110 of the myoglobin. The observation of the y43+5 fragment ion arising from C-terminal cleavage to the cysteine-110 residue in the MS/MS spectrum of DMPO-modified myoglobin and not in the unmodified myoglobin implicates a change to this residue, specifically, DMPO adduction. On the other hand, using the traditional bottom-up approach of peptide mapping and MS sequencing methodologies, two DMPO radical adducts on human myoglobin were identified, Cys-110 and Tyr-103. The bottom-up approach is more proven and robust than the top-down methodologies. Nonetheless, the bottom-up and top-down approaches to protein characterization are complementary rather than competitive approaches with each having its own utility.     

Rapid quantification of clostridial epsilon toxin in complex food and biological matrixes by immunopurification and ultraperformance liquid chromatography-tandem mass spectrometry

Epsilon toxin (ETX) is one of the most lethal toxins produced by Clostridium species and is considered as a potential bioterrorist weapon. Here, we present a rapid mass spectrometry-based method for ETX quantification in complex matrixes. As a prerequisite, naturally occurring prototoxin and toxin species were first structurally characterized by top-down and bottom-up experiments, to identify the most pertinent peptides for quantification. Following selective ETX immunoextraction and trypsin digestion, two proteotypic peptides shared by all the toxin forms were separated by ultraperformance liquid chromatography (UPLC) and monitored by ESI-MS (electrospray ionization-mass spectrometry) operating in the multiple reaction monitoring mode (MRM) with collision-induced dissociation. Thorough protocol optimization, i.e., a 15 min immunocapture, a 2 h enzymatic digestion, and an UPLC-MS/MS detection, allowed the whole quantification process including the calibration curve to be performed in less than 4 h, without compromising assay robustness and sensitivity. The assay sensitivity in milk and serum was estimated at 5 ng·mL(-1) for ETX, making this approach complementary to enzyme linked immunosorbent assay (ELISA) techniques.     

Consequences of vapor enhancement on selenium speciation analysis by HPLC/ICPMS

Recent work has shown the presence of volatile selenium metabolites in human urine and suggested that these compounds could compromise quantitative selenium analyses by ICPMS. We show that with a commonly used sample introduction system (pneumatic nebulizer and spray chamber), two volatile selenium species recently identified in urine, namely, dimethyl selenide and dimethyl diselenide, gave greatly increased ICPMS responses (up to 58-fold) relative to selenite, an effect related to their volatilization in the spray chamber resulting in enhanced transport to the plasma. The quantitative consequences of this effect were demonstrated by measurement of total selenium and selenium species in certified reference material, NIES CRM 18 human urine. Direct flow injection analysis of the urine gave a total selenium concentration more than 2-fold higher than the certified value. These data suggested that NIES CRM 18 may contain part of its selenium as volatile species, and subsequent reversed-phase HPLC/ICPMS showed the presence of dimethyl selenide in addition to selenosugars and trimethylselenonium ion. Although the practice of quantifying unidentified chromatographic peaks against those of known compounds is common in speciation analysis, this approach when applied to NIES CRM 18 gave a value for the sum of selenium species which was twice the certified total selenium concentration. This work shows that the presence of volatile selenium species in urine precludes the use of flow injection analysis for total selenium measurements and imposes severe restrictions on the quantification of urinary selenium metabolites. In addition, it raises broader issues of the validity of the "dilute and shoot" approach to the determination of metals in clinical analysis of biological fluids.     

Absolute quantification of the G protein-coupled receptor rhodopsin by LC/MS/MS using proteolysis product peptides and synthetic peptide standards

Methods for the absolute quantification of a membrane protein are described using isotopically labeled or unlabeled synthetic peptides as standards. Synthetic peptides are designed to mimic peptides that are cleaved from target analyte proteins by proteolytic or chemical digestion, and the peptides selected serve as standards for quantification by LC/MS/MS on a triple quadrupole mass spectrometer. The technique is complementary to relative quantification techniques in widespread use by providing absolute quantitation of selected targets with greater sensitivity, dynamic range, and precision. Proteins that are found to be of interest by global proteome searches can be selected as targets for quantitation by the present method. This method has a much shorter analytical cycle time (minutes versus hours for the global proteome experiments), making it well suited for high-throughput environments. The present approach using synthetic peptides as standards, in conjunction with proteolytic or chemical cleavage of target proteins, allows mass spectrometry to be used as a highly selective detector for providing absolute quantification of proteins for which no standards are available. We demonstrate that quantification is simple and reliable for the integral membrane protein rhodopsin with reasonable recoveries for replicate experiments using low-micromolar solutions of rhodopsin from rod outer segments.     

Trace analyses of arsenic in drinking water by inductively coupled plasma mass spectrometry: high resolution versus hydride generation

A magnetic sector inductively coupled plasma mass spectrometer (ICPMS) was applied to the determination of arsenic in drinking water samples using standard liquid sample introduction in the high-resolution mode (M/delta M = 7800) and hydride generation in the low-resolution mode (M/delta M = 300). Although high mass resolution ICPMS allowed the spectral separation of the argon chloride interference, the accompanying reduction in sensitivity at high resolution compromised detection and determination limits to 0.3 and 0.7 microgram/L, respectively. Therefore, a hydride generation sample introduction method, utilizing a new membrane gas-liquid separator design, was developed to overcome the chloride interference. Due to the high transport efficiency and the 50-100 times higher sensitivity at M/delta M = 300, the HG-ICPMS method resulted in an over 2000-fold increase in relative sensitivity. The routine detection and quantification limits were 0.3 and 0.5 ng/L, respectively. The results for both methods applied to the analysis of over 400 drinking water samples showed very good agreement at concentrations above 1 microgram/L. For concentrations between 0.01 and 1 microgram/L, only HG-ICPMS provided accurate quantitative results. Membrane desolvation, mixed-gas plasmas, and the addition of organic solvents for the reduction of the ArCl+ interference were also investigated and evaluated for trace As determination.     

Development of isotope dilution cold vapor inductively coupled plasma mass spectrometry and its application to the certification of mercury in NIST standard reference materials

An isotope dilution cold vapor inductively coupled plasma mass spectrometry (ID-CV-ICPMS) method featuring gaseous introduction of mercury via tin chloride reduction has been developed and applied to the quantification and certification of mercury in various NIST standard reference materials: SRM 966 Toxic Metals in Bovine Blood (30 ng x mL(-1)); SRM 1641d Mercury in Water (1.6 microg x mL(-1)); and SRM 1946 Lake Superior Fish Tissue (436 ng x g(-1)). Complementary mercury data were generated for SRMs and NIST quality control standards using cold vapor atomic absorption spectroscopy (CVAAS). Certification results for the determination of mercury in SRM 1641d using two independent methods (ID-CV-ICPMS and CVAAS) showed a degree of agreement of 0.3% between the methods. Gaseous introduction of mercury into the ICPMS resulted in a single isotope sensitivity of 2 x 10(6) counts x s(-1)/ng x g(-1) for 201Hg and significantly reduced the memory and washout effects traditionally encountered in solution nebulization ICPMS. Figures of merit for isotope ratio accuracy and precision were evaluated at dwell times of 10, 20, 40, 80, and 160 ms using SRM 3133 Mercury Spectrometric Solution. The optimum dwell time of 80 ms yielded a measured 201Hg/202Hg isotope ratio within 0.13% of the theoretical natural value and a measurement precision of 0.34%, on the basis of three replicate injections of SRM 3133.     

Absolute quantification of proteins in solutions and in polyacrylamide gels by mass spectrometry

A combination of nanoelectrospray tandem mass spectrometry and (18)O-labeled peptide internal standards was applied for the absolute quantification of proteins from their in-solution and in-gel tryptic digests. Although absolute quantification from in-solution digests was accurate, we observed that in-gel digestion compromised the quantification accuracy by affecting the recovery of individual peptides and, therefore, the provided estimates might be strongly influenced by the selection of reference peptides. Under optimized experimental conditions, it was possible to provide a semiquantitative estimate of the absolute amount of gel separated proteins within better than 50% error margin.     

Multielement analysis of polyethylene using solid sampling electrothermal vaporization ICP mass spectrometry

Next to laser ablation (LA) also electrothermal vaporization (ETV) from a graphite furnace as a means of sample introduction opens possibilities for direct analysis of solid samples using inductively coupled plasma mass spectrometry (ICPMS). In this paper, it is demonstrated that solid sampling ETV-ICPMS is very well suited for the determination of metal traces in polyethylene. A limited multielement capability is often cited as an important drawback of ETV-ICPMS. However, by studying the effect of monitoring an increasing number of mass-to-charge ratios on the signal profile (integrated signal intensity and repeatability) of selected analyte elements, the multielement capability of (solid sampling) ETV-ICPMS was systematically evaluated, and the results obtained suggest that, with a quadrupole-based ICPMS instrument, at least 11 elements can be determined "simultaneously" (from the same vaporization step), in essence without compromising the sensitivity or the precision of the results obtained. In this work, the "simultaneous" determination of Al, Ba, Cd, Cu, Mn, Pb, and Ti in a polyethylene candidate reference material has been accomplished, despite the large variation in analyte concentration (from 5 ng/g for Mn to 500 microg/g for Ti) and in furnace behavior (volatility) they exhibit. To avoid premature losses of Cd during thermal pretreatment of the samples, Pd was used as a chemical modifier. Two different calibration methods--external calibration using an aqueous standard solution and single standard addition--were studied and the results obtained were compared with those obtained using neutron activation analysis (NAA) and/or with the corresponding (candidate) certified values (if available). Single standard addition was shown to be preferable (average deviation between ICPMS result and reference value < 3%), although--except for Ba--acceptable results could also be obtained with external calibration.     

Species-specific GC/ICP-IDMS for trimethyllead determinations in biological and environmental samples

An accurate and sensitive species-specific isotope dilution GC/ICPMS method was developed for the determination of trimethyllead (Me3Pb+) in biological and environmental samples. A trimethyllead spike was synthesized from 206Pb-enriched metallic lead by reaction of lead halide with methyllithium and subsequent formation of trimethyllead iodide. The isotopic composition of the spike solution was determined by GC/ICPMS after derivatization with tetraethylborate, and its concentration was determined by reverse isotope dilution analysis. The species-specific GC/ICP-IDMS method was validated by reference material CRM 605 (urban dust) certified for Me3Pb+. The method was also applied to determine the Me3Pb+ content in six biological reference materials (DORM 2, CRM 278, CRM 422, CRM 463, CRM 477, MURST-ISS-A2) and one sediment reference material (CRM 580) for which no certified values of this species exist. The Me3Pb+ concentrations in the biological reference materials vary in the range of 0.3-17 ng g(-1) (as Pb) except for the Antarctic Krill (MURST-ISS-A2), where the concentration was less than the detection limit of 0.09 ng g(-1), which was also found for the sediment. Up to 20% of total lead was methylated in the biological reference materials, whereas much higher methylation fractions were found for mercury. The method was also applied to seafood samples purchased from a supermarket with Me3Pb+ concentrations in the limited range of 0.3-0.7 ng g(-1). On the contrary, the portion of methylated lead in these samples varied over more than 2 orders of magnitude from 0.02 to 7.5%.     

Protein and proteome phosphorylation stoichiometry analysis by element mass spectrometry

Protein phosphorylation stoichiometry was assessed by two analytical strategies. Both are based on element mass spectrometry (ICPMS, inductively coupled plasma mass spectrometry) and simultaneous monitoring of (31)P and (34)S. One strategy employs a combination of 1D gel electrophoresis, in-gel digestion, and final microLC-ICPMS analysis (microLC = capillary liquid chromatography). The other strategy uses the combination of 1D gel electrophoresis, protein blotting, and imLA-ICPMS (imLA = imaging laser ablation). The two methods were evaluated with standard phosphoproteins and were applied to the analysis of the cytoplasmatic proteome of bacterial cells (Corynebacterium glutamicum) and eukaryotic cells (Mus musculus). The eukaryotic proteome was found to exhibit a significantly higher phosphorylation degree (approximately 0.8 mol of P/mol of protein) compared to the bacterial proteome (approximately 0.01 mol of P/mol of protein). Both analytical strategies revealed consistent quantitative results, with the microLC-ICPMS approach providing the higher sensitivity. In summary, two ICPMS-based methods for quantitative estimation of the phosphorylation degree of a cellular proteome are presented which access the native proteome state and do not require any type of label introduction or derivatization.     

On-line 1D and 2D porous layer open tubular/LC-ESI-MS using 10-microm-i.d. poly(styrene-divinylbenzene) columns for ultrasensitive proteomic analysis

Following on our recent work, on-line one-dimensional (1D) and two-dimensional (2D) porous layer open tubular/liquid chromatography-electrospray ionization-mass spectrometry (PLOT/LC-ESI-MS) platforms using 3.2 mx10 microm i.d. poly(styrene-divinylbenzene) (PS-DVB) PLOT columns have been developed to provide robust, high-performance, and ultrasensitive proteomic analysis. With the use of a PicoClear tee, the dead volume connection between a 50 microm i.d. PS-DVB monolithic micro-SPE column and the PLOT column was minimized. The micro-SPE/PLOT column assembly provided a separation performance similar to that obtained with direct injection onto the PLOT column at a mobile phase flow rate of 20 nL/min. The trace analysis potential of the platform was evaluated using an in-gel tryptic digest sample of a gel fraction (15-40 kDa) of a cervical cancer (SiHa) cell line. As an example of the sensitivity of the system, approximately 2.5 ng of protein in 2 microL of solution, an amount corresponding to 20 SiHa cells, was subjected to on-line micro-SPE-PLOT/LC-ESI-MS/MS analysis using a linear ion trap MS. A total of 237 peptides associated with 163 unique proteins were identified from a single analysis when using stringent criteria associated with a false positive rate of less than 1%. The number of identified peptides and proteins increased to 638 and 343, respectively, as the injection amount was raised to approximately 45 ng of protein, an amount corresponding to 350 SiHa cells. In comparison, only 338 peptides and 231 unique proteins were identified (false positive rate again less than 1%) from 750 ng of protein from the identical gel fraction, an amount corresponding to 6000 SiHa cells, using a typical 15 cmx75 microm i.d. packed capillary column. The greater sensitivity, higher recovery, and higher resolving power of the PLOT column resulted in the increased number of identifications from only approximately 5% of the injected sample amount. The resolving power of the micro-SPE/PLOT assembly was further extended by 2D chromatography via combination of the high-efficiency reversed-phase PLOT column with strong cation-exchange chromatography (SCX). As an example, 1071 peptides associated with 536 unique proteins were identified from 75 ng of protein from the same gel fraction, an amount corresponding to 600 cells, using five ion-exchange fractions in on-line 2D SCX-PLOT/LC-MS. The 2D system, implemented in an automated format, led to simple and robust operation for proteomic analysis. These promising results demonstrate the potential of the PLOT column for ultratrace analysis.     

Determination of triclosan as its pentafluorobenzoyl ester in human plasma and milk using electron capture negative ionization mass spectrometry

A sensitive method for the determination of triclosan in plasma and milk is presented. Following hydrolysis of possible conjugates, triclosan is extracted with n-hexane/acetone, partitioned into alcoholic potassium hydroxide, and converted into its pentafluorobenzoyl ester. After sulfuric acid cleanup, sample extracts are analyzed by gas chromatography/electron capture negative ionization mass spectrometry. The limit of quantification was 0.009 ng/g for a 5-g plasma sample and 0.018 ng/g for a 3-g milk sample. The coefficient of variation for the method was 6%. The method was tested on more than 70 human plasma and milk samples, of which all plasma samples and more than half of the milk samples were above the limit of quantification. The presented method has lowered the limit of quantification for triclosan in human matrixes significantly as compared to previous methods and makes possible the analysis of triclosan in humans under normal exposure conditions.     

An immunoassay for Leu-enkephalin based on a C-terminal aequorin-peptide fusion

Recently we demonstrated that the fusion of an octapeptide to the C-terminus of a cysteine-free mutant of aequorin showed no inhibitory effect on the luminescence activity of the photoprotein. This observation is of particular importance when the use of aequorin as a label in the development of immunoassays for peptides whose activity lies in their C-terminal region or the epitope for antibody recognition is at their C-terminus is desired. In the case of opioid peptides, antibodies are directed toward their C-terminus as they differ from each other at this terminus. The goal of this study was to develop an immunoassay for Leu-enkephalin, a mammalian opioid peptide, using a C-terminal aequorin-peptide fusion protein. For that, the N-terminus of Leu-enkephalin was genetically fused to the C-terminus of a cysteine-free mutant of aequorin. It was observed that the C-terminal conjugated aequorin maintained its luminescence activity. An immunoassay for Leu-enkephalin was then developed using the aequorin-Leu-enkephalin fusion protein as a labeled analyte in a competitive as well as in a sequential binding mode. It was demonstrated that aequorin can be used as a label in peptide assays in which it is critical that the peptide's C-terminus be free for activity and/or for antibody recognition.     

Top-down approaches for measuring expression ratios of intact yeast proteins using Fourier transform mass spectrometry

The extension of quantitation methods for small peptides to ions above 5 kDa, and eventually to global quantitative proteomics of intact proteins, will require extensive refinement of current analytical approaches. Here we evaluate postgrowth Cys-labeling and 14N/15N metabolic labeling strategies for determination of relative protein expression levels and their posttranslational modifications using top-down mass spectrometry (MS). We show that intact proteins that are differentially alkylated with acrylamide (+71 Da) versus iodoacetamide (+57 Da) have substantial chromatographic shifts during reversed-phase liquid chromatography separation (particularly in peak tails), indicating a requirement for stable isotopes in alkylation tags for top-down MS. In the 14N/15N metabolic labeling strategy, we achieve 98% 15N incorporation in yeast grown 10 generations under aerobic conditions and determine 50 expression ratios using Fourier transform ion cyclotron resonance MS in comparing these cells to anaerobically grown control (14N) cells. We devise quantitative methods for top-down analyses, including a correction factor for accurate protein ratio determination based upon the signal-to-noise ratio. Using a database of 200 yeast protein forms identified previously by top-down MS, we verify the intact mass tag concept for protein identification without tandem MS. Overall, we find that top-down MS promises work flows capable of large-scale proteome profiling using stable isotope labeling and the determination of >5 protein ratios per spectrum.     

PICquant: a quantitative platform to measure differential peptide abundance using dual-isotopic labeling with 12C6- and 13C6-phenyl isocyanate

We have developed a complete system for the isotopic labeling, fractionation, and automated quantification of differentially expressed peptides that significantly facilitates candidate biomarker discovery. We describe a new stable mass tagging reagent pair, (12)C(6)- and (13)C(6)-phenyl isocyanate (PIC), that offers significant advantages over currently available tags. Peptides are labeled predominantly at their amino termini and exhibit elution profiles that are independent of label isotope. Importantly, PIC-labeled peptides have unique neutral-mass losses upon CID fragmentation that enable charge state and label isotope identification and, thereby, decouple the sequence identification from the quantification of candidate biomarkers. To exploit these properties, we have coupled peptide fractionation protocols with a Thermo LTQ-XL LC-MS(2) data acquisition strategy and a suite of automated spectrum analysis software that identifies quantitative differences between labeled samples. This approach, dubbed the PICquant platform, is independent of protein sequence identification and excludes unlabeled peptides that otherwise confound biomarker discovery. Application of the PICquant platform to a set of complex clinical samples showed that the system allows rapid identification of peptides that are differentially expressed between control and patient groups.     

Quantitative analysis of metal impurities in carbon nanotubes: efficacy of different pretreatment protocols for ICPMS spectroscopy

Metal impurities in carbon nanotubes (CNTs) are undesirable for their uses in diverse applications, for instance, they may potentially have a negative health impact when using in biomedical fields. However, so far there is a lack of analysis methods able to quantify metallic impurities in CNTs. In this paper, using the neutron activation analysis (NAA) technique as a nondestructive standard quantification method and inductively coupled plasma mass spectrometry (ICPMS) as a practical approach, we established an analytical method for quantitative determination of metallic impurities in CNTs. ICPMS, one of the most sensitive analytical techniques used for coincident multielement measurements, has become a common tool in many laboratory, and thus it is easily available and a good selection for determining the metal impurities in CNTs. However, because of their extremely stable structure and the encapsulated metals in the defect structure, CNTs must undergo special pretreatments before ICPMS. We investigated different sample pretreatment procedures for ICPMS analysis, including dry ashing coupled with acid extraction, wet digestion, and a combination of dry ashing with acid digestion. With the reference data from the nondestructive analytical method of NAA, we found that the quantitative determination of metal impurities in CNTs is highly dependent on the sample pretreatment in which the conditions are largely different from those used for conventional biological samples or environmental materials. This paper not only provides the practical method and analysis conditions for quantifying the metal impurities of CNTs but also the first protocol for pretreatment processes of CNT samples.     

Top-down proteomics on a chromatographic time scale using linear ion trap fourier transform hybrid mass spectrometers

Proteomics has grown significantly with the aid of new technologies that consistently are becoming more streamlined. While processing of proteins from a whole cell lysate is typically done in a bottom-up fashion utilizing MS/MS of peptides from enzymatically digested proteins, top-down proteomics is becoming a viable alternative that until recently has been limited largely to offline analysis by tandem mass spectrometry. Here we describe a method for high-resolution tandem mass spectrometery of intact proteins on a chromatographic time scale. In a single liquid chromatography-tandem mass spectrometry (LC-MS/MS) run, we have identified 22 yeast proteins with molecular weights from 14 to 35 kDa. Using anion exchange chromatography to fractionate a whole cell lysate before online LC-MS/MS, we have detected 231 metabolically labeled (14N/15N) protein pairs from Saccharomyces cerevisiae. Thirty-nine additional proteins were identified and characterized from LC-MS/MS of selected anion exchange fractions. Automated localization of multiple acetylations on Histone H4 was also accomplished on an LC time scale from a complex protein mixture. To our knowledge, this is the first demonstration of top-down proteomics (i.e., many identifications) on linear ion trap Fourier transform (LTQ FT) systems using high-resolution MS/MS data obtained on a chromatographic time scale.