Ultra-sensitive and quantitative characterization of proteomes

Electrospray ionization mass spectrometry combined with high efficiency capillary liquid chromatography provides high sensitivity and broad dynamic range measurements for the characterization of biological macromolecules in complex matrices, and is an increasingly powerful analytical tool for systems biology research.

Theoretical and experimental evaluation of the low m/z transmission of an electrodynamic ion funnel

The transmission of ions at low m/z can often be either necessary for an application or problematic (e.g., when large numbers of low m/z ions consume a large fraction of an ion trap's capacity). The low m/z ion transmission limit of an electrodynamic ion funnel has been characterized using both experimental and theoretical approaches. A theoretical model is developed based on a series of infinite wire conductors that represent the ring electrodes of the ion funnel. Mathematical relationships for both low and high m/z cutoffs of the idealized two-dimensional system are derived. The low m/z cutoff is also evaluated through a series of experiments that show it is influenced by both the RF frequency and the DC electric field gradient. However, unlike multipole ion guides, there is no marked dependence of the low m/z cutoff on the RF amplitude, in agreement with theoretical results. With this new understanding, ion funnels can be designed and configured to better match the m/z range requirements for various applications.

More Sensitive and Quantitative Proteomic Measurements Using Very Low Flow Rate Porous Silica Monolithic LC Columns with Electrospray Ionization-Mass Spectrometry

The sensitivity of proteomics measurements using liquid chromatography (LC) separations interfaced with electrospray ionization-mass spectrometry (ESI-MS) improves approximately inversely with liquid flow rate (for the columns having the same separation efficiency, linear velocity, and porosity), making attractive the use of smaller inner diameter LC columns. We report the development and initial application of 10 microm i.d. silica-based monolithic LC columns providing more sensitive proteomics measurements. A 50-microm-i.d. micro solid-phase extraction precolumn was used for ease of sample injection and cleanup prior to the reversed-phase LC separation, enabling the sample volume loading speed to be increased by approximately 50-fold. Greater than 10-fold improvement in sensitivity was obtained compared to analyses using more conventional capillary LC, enabling e.g. the identification of >5000 different peptides by MS/MS from 100-ng of a Shewanella oneidensis tryptic digest using an ion trap MS. The low nL/min LC flow rates provide more uniform responses for different peptides, and provided improved quantitative measurements compared to conventional separation systems without the use of internal standards or isotopic labeling. The improved sensitivity allowed LC-MS measurements of immunopurified protein phosphatase 5 that were in good agreement with quantitative Western blot analyses.

Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach

We describe the application of LC-MS without the use of stable isotope labeling for differential quantitative proteomic analysis of whole cell lysates of Shewanella oneidensis MR-1 cultured under aerobic and suboxic conditions. LC-MS/MS was used to initially identify peptide sequences, and LC-FTICR was used to confirm these identifications as well as measure relative peptide abundances. 2343 peptides covering 668 proteins were identified with high confidence and quantified. Among these proteins, a subset of 56 changed significantly using statistical approaches such as statistical analysis of microarrays, whereas another subset of 56 that were annotated as performing housekeeping functions remained essentially unchanged in relative abundance. Numerous proteins involved in anaerobic energy metabolism exhibited up to a 10-fold increase in relative abundance when S. oneidensis was transitioned from aerobic to suboxic conditions.

Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics

Central tendency, linear regression, locally weighted regression, and quantile techniques were investigated for normalization of peptide abundance measurements obtained from high-throughput liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR MS). Arbitrary abundances of peptides were obtained from three sample sets, including a standard protein sample, two Deinococcus radiodurans samples taken from different growth phases, and two mouse striatum samples from control and methamphetamine-stressed mice (strain C57BL/6). The selected normalization techniques were evaluated in both the absence and presence of biological variability by estimating extraneous variability prior to and following normalization. Prior to normalization, replicate runs from each sample set were observed to be statistically different, while following normalization replicate runs were no longer statistically different. Although all techniques reduced systematic bias to some degree, assigned ranks among the techniques revealed that for most LC-FTICR-MS analyses linear regression normalization ranked either first or second. However, the lack of a definitive trend among the techniques suggested the need for additional investigation into adapting normalization approaches for label-free proteomics. Nevertheless, this study serves as an important step for evaluating approaches that address systematic biases related to relative quantification and label-free proteomics.

Characterization of the mouse brain proteome using global proteomic analysis complemented with cysteinyl-peptide enrichment

We report a global proteomic approach for analyzing brain tissue and for the first time a comprehensive characterization of the whole mouse brain proteome. Preparation of the whole brain sample incorporated a highly efficient cysteinyl-peptide enrichment (CPE) technique to complement a global enzymatic digestion method. Both the global and the cysteinyl-enriched peptide samples were analyzed by SCX fractionation coupled with reversed phase LC-MS/MS analysis. A total of 48,328 different peptides were confidently identified (>98% confidence level), covering 7792 nonredundant proteins ( approximately 34% of the predicted mouse proteome). A total of 1564 and 1859 proteins were identified exclusively from the cysteinyl-peptide and the global peptide samples, respectively, corresponding to 25% and 31% improvements in proteome coverage compared to analysis of only the global peptide or cysteinyl-peptide samples. The identified proteins provide a broad representation of the mouse proteome with little bias evident due to protein pI, molecular weight, and/or cellular localization. Approximately 26% of the identified proteins with gene ontology (GO) annotations were membrane proteins, with 1447 proteins predicted to have transmembrane domains, and many of the membrane proteins were found to be involved in transport and cell signaling. The MS/MS spectrum count information for the identified proteins was used to provide a measure of relative protein abundances. The mouse brain peptide/protein database generated from this study represents the most comprehensive proteome coverage for the mammalian brain to date, and the basis for future quantitative brain proteomic studies using mouse models. The proteomic approach presented here may have broad applications for rapid proteomic analyses of various mouse models of human brain diseases.

"Zero-length" cross-linking in solid state as an approach for analysis of protein-protein interactions

We have developed a new approach for the analysis of interacting interfaces in protein complexes and protein quaternary structure based on cross-linking in the solid state. Protein complexes are freeze-dried under vacuum, and cross-links are introduced in the solid phase by dehydrating the protein in a nonaqueous solvent creating peptide bonds between amino and carboxyl groups of the interacting peptides. Cross-linked proteins are digested into peptides with trypsin in both H2(16)O and H(2)18O and then readily distinguished in mass spectra by characteristic 8 atomic mass unit (amu) shifts reflecting incorporation of two 18O atoms into each C terminus of proteolytic peptides. Computer analysis of mass spectrometry (MS) and MS/MS data is used to identify the cross-linked peptides. We demonstrated specificity and reproducibility of our method by cross-linking homo-oligomeric protein complexes of glutathione-S-transferase (GST) from Schistosoma japonicum alone or in a mixture of many other proteins. Identified cross-links were predominantly of amide origin, but six esters and thioesters were also found. The cross-linked peptides were validated against the GST monomer and dimer X-ray structures and by experimental (MS/MS) analyses. Some of the identified cross-links matched interacting peptides in the native 3D structure of GST, indicating that the structure of GST and its oligomeric complex remained primarily intact after freeze-drying. The pattern of oligomeric GST obtained in solid state was the same as that obtained in solution by Ru (II) Bpy(3)2+ catalyzed, oxidative "zero-length" cross-linking, confirming that it is feasible to use our strategy for analyzing the molecular interfaces of interacting proteins or peptides.

Feasibility of higher-order differential ion mobility separations using new asymmetric waveforms

Technologies for separating and characterizing ions based on their transport properties in gases have been around for three decades. The early method of ion mobility spectrometry (IMS) distinguished ions by absolute mobility that depends on the collision cross section with buffer gas atoms. The more recent technique of field asymmetric waveform IMS (FAIMS) measures the difference between mobilities at high and low electric fields. Coupling IMS and FAIMS to soft ionization sources and mass spectrometry (MS) has greatly expanded their utility, enabling new applications in biomedical and nanomaterials research. Here, we show that time-dependent electric fields comprising more than two intensity levels could, in principle, effect an infinite number of distinct differential separations based on the higher-order terms of expression for ion mobility. These analyses could employ the hardware and operational procedures similar to those utilized in FAIMS. Methods up to the 4th or 5th order (where conventional IMS is 1st order and FAIMS is 2nd order) should be practical at field intensities accessible in ambient air, with still higher orders potentially achievable in insulating gases. Available experimental data suggest that higher-order separations should be largely orthogonal to each other and to FAIMS, IMS, and MS.

It's not just what you do, it's the way that you do it: the effect of different payment card formats and survey administration on willingness to pay for health gain

A general population sample of 314 Australian respondents were randomly allocated to complete a contingent valuation survey administered by face-to-face or telephone ('phone-mail-phone') interview. Although the telephone interview was quicker to complete, no significant difference was found in values obtained through either method. Within each sub-sample, respondents were also randomly allocated to the three different versions of the payment card (PC) questionnaire format: values listed from high-to-low, values listed from low-to-high and values randomly shuffled. The high-to-low version resulted in significantly higher values than the other versions. Further analyses indicate that the randomly shuffled PC version may produce the most 'valid' values.

Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry

The enormous complexity, wide dynamic range of relative protein abundances of interest (over 10 orders of magnitude), and tremendous heterogeneity (due to post-translational modifications, such as glycosylation) of the human blood plasma proteome severely challenge the capabilities of existing analytical methodologies. Here, we describe an approach for broad analysis of human plasma N-glycoproteins using a combination of immunoaffinity subtraction and glycoprotein capture to reduce both the protein concentration range and the overall sample complexity. Six high-abundance plasma proteins were simultaneously removed using a pre-packed, immobilized antibody column. N-linked glycoproteins were then captured from the depleted plasma using hydrazide resin and enzymatically digested, and the bound N-linked glycopeptides were released using peptide-N-glycosidase F (PNGase F). Following strong cation exchange (SCX) fractionation, the deglycosylated peptides were analyzed by reversed-phase capillary liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Using stringent criteria, a total of 2053 different N-glycopeptides were confidently identified, covering 303 nonredundant N-glycoproteins. This enrichment strategy significantly improved detection and enabled identification of a number of low-abundance proteins, exemplified by interleukin-1 receptor antagonist protein (approximately 200 pg/mL), cathepsin L (approximately 1 ng/mL), and transforming growth factor beta 1 (approximately 2 ng/mL). A total of 639 N-glycosylation sites were identified, and the overall high accuracy of these glycosylation site assignments as assessed by accurate mass measurement using high-resolution liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR) is initially demonstrated.

How common is the 'prominence effect'? Additional evidence to Whynes et al

In a recent issue of Health Economics Letters, Whynes et al. report an observation not previously reported in the willingness-to-pay (WTP) literature; that when people are asked to provide an estimate using payment scales they tend to disproportionately select prominent values (that is, 1, 2, 5, 10, 20, 50, 100, etc.). However, it remains an open question just how common this prominence effect actually is. Here we present data from several additional contingent valuation (CV) studies, which suggest that although prominence occurs, it does not reach statistical significance, as found by Whynes et al. A number of reasons are outlined to explain this.

Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1

High-throughput "omic" technologies have allowed for a relatively rapid, yet comprehensive analysis of the global expression patterns within an organism in response to perturbations. In the current study, 9503 different tryptic peptides were identified with high confidence from capillary liquid chromatography-mass spectrometry analysis of 26 chemostat cultures of Shewanella oneidensis MR-1 under various conditions. Using at least one distinctive and a total of two total peptide identifications per protein, we detected the expression of 758 conserved hypothetical proteins. This included 359 such proteins previously described [Kolker, E., Picone, A.F., Galperin, M.Y., Romine, M.F., Higdon, R., Makarova, K.S., Kolker, N., Anderson, G.A., Qiu, X., Auberry, K.J., Babnigg, G., Beliaev, A.S., Edlefsen, P., Elias, D.A., Gorby, Y.A., Holzman, T., Klappenbach, J.A., Konstantinidis, K.T., Land, M.L., Lipton, M.S., McCue, L.A., Monroe, M., Pasa-Tolic, L., Pinchuk, G., Purvine, S., Serres, M.H., Tsapin, S., Zakrajsek, B.A., Zhu, W., Zhou, J., Larimer, F.W., Lawrence, C.E., Riley, M., Collart, F.R., Yates, J.R., III, Smith, R.D., Giometti, C.S., Nealson, K.H., Fredrickson, J.K., Tiedje, J.M., 2005. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A 102, 2099-2104] with an additional 399 reported herein for the first time. The latter 399 proteins ranged from 5.3 to 208.3 kDa, with 44 being of 100 amino acid residues or less. Using a combination of information including peptide detection in cells grown under specific culture conditions and predictive algorithms such as PSORT and PSORT-B, possible/plausible functions are proposed for some conserved hypothetical proteins. Such proteins were found not only to be expressed, but 19 were only expressed under certain culturing conditions, thereby providing insight into potential functions. These findings also impact the genomic annotation for S. oneidensis MR-1 by confirming that these genes code for expressed proteins. Our results indicate that 399 proteins can now be upgraded from "conserved hypothetical protein" to "expressed protein in Shewanella," 19 of which appeared to be expressed under specific culture conditions.

A macroeconomic approach to evaluating policies to contain antimicrobial resistance: a case study of methicillin-resistant Staphylococcus aureus (MRSA)

BACKGROUND

Antimicrobial resistance (AMR) is, at least in part, associated with high antimicrobial usage and causes increased morbidity, mortality and healthcare costs. However, policies to contain AMR focus on 'micro' interventions - typically in one institution (usually a hospital). Furthermore, in evaluating these interventions, economists tend to concentrate on the economic impact to the healthcare sector alone, which may give an incorrect estimation of the social costs and benefits of a disease or intervention.

METHODS

This study outlines and illustrates a macroeconomic approach to tackling AMR through the evaluation of three 'macro' policies: regulation, permits and taxes/charges. In addition to effects on the healthcare sector, the effect of AMR (and these three policies to contain it) on labour productivity, GDP, household income, government transfers, tax revenues, unemployment, inflation and social services are estimated for the UK using the specific context of methicillin-resistant Staphylococcus aureus (MRSA).

RESULTS

AMR is likely to have a far greater impact on the national economy than would be estimated by concentrating on the healthcare sector alone.

CONCLUSION

The permit system appears to offer the most efficient 'solution' to optimising antimicrobial consumption and, hence, reducing the development of resistance.

Using economic analyses for local priority setting : the population cost-impact approach

INTRODUCTION

Standard methods of economic analysis may not be suitable for local decision making that is specific to a particular population.

BACKGROUND

We describe a new three-step methodology, termed 'population cost-impact analysis', which provides a population perspective to the costs and benefits of alternative interventions. The first two steps involve calculating the population impact and the costs of the proposed interventions relevant to local conditions. This involves the calculation of population impact measures (which have been previously described but are not currently used extensively) - measures of absolute risk and risk reduction, applied to a population denominator. In step three, preferences of policy-makers are obtained. This is in contrast to the QALY approach in which quality weights are obtained as a part of the measurement of benefit.

METHODS

We applied the population cost-impact analysis method to a comparison of two interventions - increasing the use of beta-adrenoceptor antagonists (beta-blockers) and smoking cessation - after myocardial infarction in a scaled-back notional local population of 100,000 people in England. Twenty-two public health professionals were asked via a questionnaire to rank the order in which they would implement four interventions. They were given information on both population cost impact and QALYs for each intervention.

RESULTS

In a population of 100,000 people, moving from current to best practice for beta-adrenoceptor antagonists and smoking cessation will prevent 11 and 4 deaths (or gain of 127 or 42 life-years), respectively. The cost per event prevented in the next year, or life-year gained, is less for beta-adrenoceptor antagonists than for smoking cessation. Public health professionals were found to be more inclined to rank alternative interventions according to the population cost impact than the QALY approach.

DISCUSSION

The use of the population cost-impact approach allows information on the benefits of moving from current to best practice to be presented in terms of the benefits and costs to a particular population. The process for deciding between alternative interventions in a prioritisation exercise may differ according to the local context. We suggest that the valuation of the benefit is performed after the benefits have been quantified and that it takes into account local issues relevant to prioritisation. It would be an appropriate next step to experiment with, and formalise, this part of the population cost-impact analysis to provide a standardised approach for determining willingness to pay and provide a ranking of priorities.

CONCLUSION

Our method adds a new dimension to economic analysis, the ability to identify costs and benefits of potential interventions to a defined population, which may be of considerable use for policy makers working at the local level.

Thrombogenesis in experimental microvascular anastomosis

A large number of microvascular anastomoses, involving both arteriovenous and artery-artery end-to-side and end-to-end anastomoses, were carried out in the rat to develop a temporal and morphologic profile of thrombogenesis. While excellent patency rates were obtained in purely arterial preparations, significant thrombus formation occurred in the arteriovenous preparations, both at the suture line and more distally in the vein. Factors contributing to thrombogenesis in these microvascular anastomoses are discussed.

Evaluation of two-dimensional electrophoresis and liquid chromatography--tandem mass spectrometry for tissue-specific protein profiling of laser-microdissected plant samples

Laser microdissection (LM) allows the collection of homogeneous tissue- and cell-specific plant samples. The employment of this technique with subsequent protein analysis has thus far not been reported for plant tissues, probably due to the difficulties associated with defining a reasonable cellular morphology and, in parallel, allowing efficient protein extraction from tissue samples. The relatively large sample amount needed for successful proteome analysis is an additional issue that complicates protein profiling on a tissue- or even cell-specific level. In contrast to transcript profiling that can be performed from very small sample amounts due to efficient amplification strategies, there is as yet no amplification procedure for proteins available. In the current study, we compared different tissue preparation techniques prior to LM/laser pressure catapulting (LMPC) with respect to their suitability for protein retrieval. Cryo-sectioning was identified as the best compromise between tissue morphology and effective protein extraction. After collection of vascular bundles from Arabidopsis thaliana stem tissue by LMPC, proteins were extracted and subjected to protein analysis, either by classical two-dimensional gel electrophoresis (2-DE), or by high-efficiency liquid chromatography (LC) in conjunction with tandem mass spectrometry (MS/MS). Our results demonstrate that both methods can be used with LMPC collected plant material. But because of the significantly lower sample amount required for LC-MS/MS than for 2-DE, the combination of LMPC and LC-MS/MS has a higher potential to promote comprehensive proteome analysis of specific plant tissues.

Comparison of Normal and Breast Cancer Cell Lines Using Proteome, Genome, and Interactome Data

Normal and cancer cell line proteomes were profiled using high throughput mass spectrometry techniques. Application of protein-level and peptide-level sample fractionation combined with LC-MS/MS analysis enabled identification of 2235 unmodified proteins representing a broad range of functional and compartmental classes. An iterative multistep search strategy was used to identify post-translational modifications, revealing several proteins that are preferentially modified in cancer cells. Information regarding both unmodified and modified protein forms was combined with publicly available gene expression and protein-protein interaction data. The resulting integrated dataset revealed several functionally related proteins that are differentially regulated between normal and cancer cell lines.

Making Broad Proteome Protein Measurements in 1−5 min Using High-Speed RPLC Separations and High-Accuracy Mass Measurements

The throughput of proteomics measurements that provide broad protein coverage is limited by the quality and speed of both the separations as well as the subsequent mass spectrometric analysis; at present, analysis times can range anywhere from hours (high throughput) to days or longer (low throughput). We have explored the basis for proteomics analyses conducted on the order of minutes using high-speed capillary RPLC combined through on-line electrospray ionization interface with high-accuracy mass spectrometry (MS) measurements. Short 0.8-microm porous C18 particle-packed 50-microm-i.d. capillaries were used to speed the RPLC separations while still providing high-quality separations. Both time-of-flight (TOF) and Fourier transform ion cyclotron resonance (FTICR) MS were applied for identifying peptides using the accurate mass and time (AMT) tag approach. Peptide RPLC relative retention (elution) times that were generated by solvent gradients that differed by at least 25-fold were found to provide relative elution times that agreed to within 5%, which provides the basis for using peptide AMT tags for higher throughput proteomics measurements. For fast MS acquisition speeds (e.g., 0.2 s for TOF and either approximately 0.3 or approximately 0.6 s for FTICR), peptide mass measurement accuracies of better than +/-15 ppm were obtained with the high-speed RPLC separations. The ability to identify peptides and the overall proteome coverage was determined by factors that include the separation peak capacity, the sensitivity of the MS (with fast scanning), and the accuracy of both the mass measurements and the relative RPLC peptide elution times. The experimental RPLC relative elution time accuracies of 5% (using high-speed capillary RPLC) and mass measurement accuracies of better than +/-15 ppm allowed for the confident identification of >2800 peptides and >760 proteins from >13,000 different putative peptides detected from a Shewanellaoneidensis tryptic digest. Initial results for both RPLC-ESI-TOF and RPLC-ESI-FTICR MS were similar, with approximately 2000 different peptides from approximately 600 different proteins identified within 2-3 min. For <120-s proteomic analysis, TOF MS analyses were more effective, while FTICR MS was more effective for the >150-s analysis due to the improved mass accuracies attained using longer spectrum acquisition times.

Development and evaluation of a micro- and nanoscale proteomic sample preparation method

Challenges associated with the efficient and effective preparation of micro- and nanoscale (micro- and nanogram) clinical specimens for proteomic applications include the unmitigated sample losses that occur during the processing steps. Herein, we describe a simple "single-tube" preparation protocol appropriate for small proteomic samples using the organic cosolvent, trifluoroethanol (TFE) that circumvents the loss of sample by facilitating both protein extraction and protein denaturation without requiring a separate cleanup step. The performance of the TFE-based method was initially evaluated by comparisons to traditional detergent-based methods on relatively large scale sample processing using human breast cancer cells and mouse brain tissue. The results demonstrated that the TFE-based protocol provided comparable results to the traditional detergent-based protocols for larger, conventionally sized proteomic samples (>100 microg protein content), based on both sample recovery and numbers of peptide/protein identifications. The effectiveness of this protocol for micro- and nanoscale sample processing was then evaluated for the extraction of proteins/peptides and shown effective for small mouse brain tissue samples (approximately 30 microg total protein content) and also for samples of approximately 5000 MCF-7 human breast cancer cells (approximately 500 ng total protein content), where the detergent-based methods were ineffective due to losses during cleanup and transfer steps.

Assessing the macroeconomic impact of a healthcare problem: the application of computable general equilibrium analysis to antimicrobial resistance

There is a positive relationship between the health of a nation and its economic prosperity. However, in evaluating health care, economists typically concentrate on the economic impact only to the health (care) sector, which may mis-specify the social costs and benefits of a disease or intervention. This paper demonstrates the value of using a macroeconomic approach to modelling a major health problem, using the context of antimicrobial resistance and the application of the computable general equilibrium technique. This approach is described in detail and its 'added value' demonstrated in the case of AMR.

Utilizing human blood plasma for proteomic biomarker discovery

Candidate proteomic biomarker discovery from human plasma holds both incredible clinical potential as well as significant challenges. The dynamic range of proteins within plasma is known to exceed 10(10), and many potential biomarkers are likely present at lower protein abundances. At present, proteomic based MS analyses provide a dynamic range typically not exceeding approximately 10(3) in a single spectrum, and approximately 10(4)-10(6) when combined with on-line separations (e.g., reversed-phase gradient liquid chromatography), and thus are generally insufficient for low level biomarker detection directly from human plasma. This limitation is providing an impetus for the development of experimental methodologies and strategies to increase the possible number of detections within this biofluid. Discussed is the diversity of available approaches currently used by our laboratory and others to utilize human plasma as a viable medium for biomarker discovery. Various separation, depletion, enrichment, and quantitative efforts as well as recent improvements in MS capabilities have resulted in measurable improvements in the detection and identification of lower abundance proteins (by approximately 10-10(2)). Despite these improvements, further advances are needed to provide a basis for discovery of candidate biomarkers at very low levels. Continued development of depletion and enrichment techniques, coupled with improved pre-MS separations (both at the protein and peptide level) holds promise in extending the dynamic range of proteomic analysis.

A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy

Characterization of the human blood plasma proteome is critical to the discovery of routinely useful clinical biomarkers. We used an accurate mass and time (AMT) tag strategy with high-resolution mass accuracy cLC-FT-ICR MS to perform a global proteomic analysis of pilot study samples as part of the HUPO Plasma Proteome Project. HUPO reference serum and citrated plasma samples from African Americans, Asian Americans, and Caucasian Americans were analyzed, in addition to a Pacific Northwest National Laboratory reference serum and plasma. The AMT tag strategy allowed us to leverage two previously published "shotgun" proteomics experiments to perform global analyses on these samples in triplicate in less than 4 days total analysis time. A total of 722 (22% with multiple peptide identifications) International Protein Index redundant proteins, or 377 protein families by ProteinProphet, were identified over the six individual HUPO serum and plasma samples. The samples yielded a similar number of identified redundant proteins in the plasma samples (average 446 +/- 23) as found in the serum samples (average 440 +/- 20). These proteins were identified by an average of 956 +/- 35 unique peptides in plasma and 930 +/- 11 unique peptides in serum. In addition to this high-throughput analysis, the AMT tag approach was used with a Z-score normalization to compare relative protein abundances. This analysis highlighted both known differences in serum and citrated plasma such as fibrinogens, and reproducible differences in peptide abundances from proteins such as soluble activin receptor-like kinase 7b and glycoprotein m6b. The AMT tag strategy not only improved our sample throughput but also provided a basis for estimated quantitation.

Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans

The results of previous studies indicated that D. radiodurans mounts a regulated protective response to heat shock, and that expression of more than 130 genes, including classical chaperones such as the groESL and dnaKJ operons and proteases such as clpB are induced in response to elevated temperature. In addition, previous qualitative whole-cell mass spectrometric studies conducted under heat shock conditions indicated global changes in the D. radiodurans proteome. To enable the discovery of novel heat shock inducible proteins as well as gain greater biological insight into the classical heat shock response at the protein level, we undertook the global whole-cell FTICR mass spectrometric proteomics study reported here. We have greatly increased the power of this approach by conducting a large number of replicate experiments in addition to taking a semiquantitative approach to data analysis, finding good reproducibility between replicates. Through this analysis, we have identified with high confidence a core set of classical heat shock proteins whose expression increases dramatically and reproducibly in response to elevated temperature. In addition, we have found that the heat shock proteome includes a large number of induced proteins that have not been identified previously as heat responsive, and have therefore been designated as candidate responders. Finally, our results are consistent with the hypothesis that elevated temperature stress could lead to cross-protection against other related stresses.

Characterization of purified c-type heme-containing peptides and identification of c-type heme-attachment sites in Shewanella oneidenis cytochromes using mass spectrometry

We describe methods for mass spectrometric identification of heme-containing peptides from c-type cytochromes that contain the CXXCH (X=any amino acid) sequence motif. The heme fragment ion yielded the most abundant MS/MS peak for standard heme-containing peptides with one amino acid difference for both 2+ and 3+ peptide charge states; both sequence and charge affect the extent of heme loss. Application to Shewanella oneidenis demonstrated the utility of this approach for identifying c-type heme-containing peptides from complex proteome samples.