Proteomics by FTICR mass spectrometry: top down and bottom up

Top-down mass analysis of protein tyrosine nitration: comparison of electron capture dissociation with "slow-heating" tandem mass spectrometry methods

Tyrosine nitration in proteins is an important post-translational modification (PTM) linked to various pathological conditions. When multiple potential sites of nitration exist, tandem mass spectrometry (MS/MS) methods provide unique tools to locate the nitro-tyrosine(s) precisely. Electron capture dissociation (ECD) is a powerful MS/MS method, different in its mechanisms to the "slow-heating" threshold fragmentation methods, such as collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD). Generally, ECD provides more homogeneous cleavage of the protein backbone and preserves labile PTMs. However recent studies in our laboratory demonstrated that ECD of doubly charged nitrated peptides is inhibited by the large electron affinity of the nitro group, while CID efficiency remains unaffected by nitration. Here, we have investigated the efficiency of ECD versus CID and IRMPD for top-down MS/MS analysis of multiply charged intact nitrated protein ions of myoglobin, lysozyme, and cytochrome c in a commercial Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. CID and IRMPD produced more cleavages in the vicinity of the sites of nitration than ECD. However the total number of ECD fragments was greater than those from CID or IRMPD, and many ECD fragments contained the site(s) of nitration. We conclude that ECD can be used in the top-down analysis of nitrated proteins, but precise localization of the sites of nitration may require either of the "slow-heating" methods.

Protein- versus peptide fractionation in the first dimension of two-dimensional high-performance liquid chromatography-matrix-assisted laser desorption/ionization tandem mass spectrometry for qualitative proteome analysis of tissue samples

The availability of robust and highly efficient separation methods represents a major requirement for proteome analysis. This study investigated the characteristics of two different gel-free proteomic approaches to the fractionation of proteolytic peptides and intact proteins, respectively, in a first separation dimension. Separation and mass spectrometric detection by matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS) were performed at the peptide level in both methods. Bottom-up analysis (BU) was carried out employing well established peptide fractionation in the first separation dimension by strong cation-exchange chromatography (SCX), followed by ion-pair reversed-phase chromatography (IP-RPC) in the second dimension. In the semi-top-down approach (STD), which involved intact protein fractionation in the first dimension, the separation mode in both dimensions was IP-RPC utilizing monolithic columns. Application of the two approaches to the proteome analysis of proteins extracted from a tumor tissue revealed that the BU method identified more proteins (1245 in BU versus 920 in STD) while STD analysis offered higher sequence coverage (14.8% in BU versus 17.5% in STD on average). The identification of more basic and larger proteins was slightly favored in the BU approach, most probably due to higher losses of these proteins during intact protein handling and separation in the STD method. A significant degree of complementarity was revealed by an approximately 33% overlap between one BU and STD replicate, while 33% each of the protein identifications were unique to both methods. In the STD method, peptides obtained upon digestion of the proteins contained in fractions of the first separation dimension covered a broad elution window in the second-dimension separation, which demonstrates a high degree of "pseudo-orthogonality" of protein and peptide separation by IP-RPC in both separation dimensions.

Functional analysis of proteins and protein species using shotgun proteomics and linear mathematics

Covalent post-translational modification of proteins is the primary modulator of protein function in the cell. It greatly expands the functional potential of the proteome compared to the genome. In the past few years shotgun proteomics-based research, where the proteome is digested into peptides prior to mass spectrometric analysis has been prolific in this area. It has determined the kinetics of tens of thousands of sites of covalent modification on an equally large number of proteins under various biological conditions and uncovered a transiently active regulatory network that extends into diverse branches of cellular physiology. In this review, we discuss this work in light of the concept of protein speciation, which emphasizes the entire post-translationally modified molecule and its interactions and not just the modification site as the functional entity. Sometimes, particularly when considering complex multisite modification, all of the modified molecular species involved in the investigated condition, the protein species must be completely resolved for full understanding. We present a mathematical technique that delivers a good approximation for shotgun proteomics data.

Quantitative top-down proteomics of SILAC labeled human embryonic stem cells

Human embryonic stem cells (hESCs) are self-renewing pluripotent cells with relevance to treatment of numerous medical conditions. However, a global understanding of the role of the hESC proteome in maintaining pluripotency or triggering differentiation is still largely lacking. The emergence of top-down proteomics has facilitated the identification and characterization of intact protein forms that are not readily apparent in bottom-up studies. Combined with metabolic labeling techniques such as stable isotope labeling by amino acids in cell culture (SILAC), quantitative comparison of intact protein expression under differing experimental conditions is possible. Herein, quantitative top-down proteomics of hESCs is demonstrated using the SILAC method and nano-flow reverse phase chromatography directly coupled to a linear-ion-trap Fourier transform ion cyclotron resonance mass spectrometer (nLC-LTQ-FT-ICR-MS). In this study, which to the best of our knowledge represents the first top-down analysis of hESCs, we have confidently identified 11 proteins by accurate intact mass, MS/MS, and amino acid counting facilitated by SILAC labeling. Although quantification is challenging due to the incorporation of multiple labeled amino acids (i.e., lysine and arginine) and arginine to proline conversion, we are able to quantitatively account for these phenomena using a mathematical model.

Structural characterization of intact proteins is enhanced by prevalent fragmentation pathways rarely observed for peptides

While collisionally activated dissociation (CAD) pathways for peptides are well characterized, those of intact proteins are not. We systematically assigned CAD product ions of ubiquitin, myoglobin, and bovine serum albumin generated using high-yield, in-source fragmentation. Assignment of >98% of hundreds of product ions implies that the fragmentation pathways described are representative of the major pathways. Protein dissociation mechanisms were found to be modulated by both source declustering potential and precursor ion charge state. Like peptides, higher charge states of proteins fragmented at lower energies next to Pro, via mobile protons, while lower charge states fragmented at higher energies after Asp and Glu, via localized protons. Unlike peptides, however, predominant fragmentation channels of proteins occurred at intermediate charge states via non-canonical mechanisms and produced extensive internal fragmentation. The non-canonical mechanisms include prominent cleavages C-terminal to Pro and Asn, and N-terminal to Ile, Leu, and Ser; these cleavages, along with internal fragments, led to a 45% increase in sequence coverage, improving the specificity of top-down protein identification. Three applications take advantage of the different mechanisms of protein fragmentation. First, modulation of declustering potential selectively fragments different charge states, allowing the source region to be used as the first stage of a low-resolution tandem mass spectrometer, facilitating pseudo-MS(3) of product ions with known parent charge states. Second, development and integration of automated modulation of ion funnel declustering potential allows users access to a particular fragmentation mechanism, yielding facile cleavage on a liquid chromatography timescale. Third, augmentation of a top-down search engine improved protein characterization.

A review of current applications of mass spectrometry for neuroproteomics in epilepsy

The brain is unquestionably the most fascinating organ, and the hippocampus is crucial in memory storage and retrieval and plays an important role in stress response. In temporal lobe epilepsy (TLE), the seizure origin typically involves the hippocampal formation. Despite tremendous progress, current knowledge falls short of being able to explain its function. An emerging approach toward an improved understanding of the complex molecular mechanisms that underlie functions of the brain and hippocampus is neuroproteomics. Mass spectrometry has been widely used to analyze biological samples, and has evolved into an indispensable tool for proteomics research. In this review, we present a general overview of the application of mass spectrometry in proteomics, summarize neuroproteomics and systems biology-based discovery of protein biomarkers for epilepsy, discuss the methodology needed to explore the epileptic hippocampus proteome, and also focus on applications of ingenuity pathway analysis (IPA) in disease research. This neuroproteomics survey presents a framework for large-scale protein research in epilepsy that can be applied for immediate epileptic biomarker discovery and the far-reaching systems biology understanding of the protein regulatory networks. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of epilepsy on society.

Artificial neural networks for the prediction of peptide drift time in ion mobility mass spectrometry

Background

There is an increasing usage of ion mobility-mass spectrometry (IMMS) in proteomics. IMMS combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS). It separates and detects peptide ions on a millisecond time-scale. IMS separates peptide ions based on drift time that is determined by the collision cross-section of each peptide ion in a given experiment condition. A peptide ion's collision cross-section is related to the ion size and shape resulted from the peptide amino acid sequence and their modifications. This inherent relation between the drift time of peptide ion and peptide sequence indicates that the drift time of peptide ions can be used to infer peptide sequence and therefore, for peptide identification.

Results

This paper describes an artificial neural networks (ANNs) regression model for the prediction of peptide ion drift time in IMMS. Each peptide in this work was represented using three descriptors (i.e., molecular weight, sequence length and a two-dimensional sequence index). An ANN predictor consisting of four input nodes, three hidden nodes and one output node was constructed for peptide ion drift time prediction. For the model training and testing, a 10-fold cross-validation strategy was employed for three datasets each containing different charge states. Dataset one contains 212 singly-charged peptide ions, dataset two has 306 doubly-charged peptide ions, and dataset three has 77 triply-charged peptide ions. Our proposed method achieved 94.4%, 93.6% and 74.2% prediction accuracy for singly-, doubly- and triply-charged peptide ions, respectively.

Conclusions

An ANN-based method has been developed for predicting the drift time of peptide ions in IMMS. The results achieved here demonstrate the effectiveness and efficiency of the prediction model. This work can enhance the confidence of protein identification by combining with current database search approaches for protein identification.

Genomics and bioinformatics resources for crop improvement

Recent remarkable innovations in platforms for omics-based research and application development provide crucial resources to promote research in model and applied plant species. A combinatorial approach using multiple omics platforms and integration of their outcomes is now an effective strategy for clarifying molecular systems integral to improving plant productivity. Furthermore, promotion of comparative genomics among model and applied plants allows us to grasp the biological properties of each species and to accelerate gene discovery and functional analyses of genes. Bioinformatics platforms and their associated databases are also essential for the effective design of approaches making the best use of genomic resources, including resource integration. We review recent advances in research platforms and resources in plant omics together with related databases and advances in technology.

Deconvoluting the 'omics' for organ transplantation

PURPOSE OF REVIEW

The desire for biomarkers for diagnosis and prognosis of diseases has never been greater. With the availability of genome data and an increased availability of proteome data, the discovery of biomarkers has become increasingly feasible. This article reviews some recent applications of the many evolving 'omic technologies to organ transplantation.

RECENT FINDINGS

With the advancement of many high-throughput 'omic techniques such as genomics, metabolomics, antibiomics, peptidomics, and proteomics, efforts have been made to understand potential mechanisms of specific graft injuries and develop novel biomarkers for acute rejection, chronic rejection, and operational tolerance.

SUMMARY

The translation of potential biomarkers from the laboratory bench to the clinical bedside is not an easy task and will require the concerted effort of the immunologists, molecular biologists, transplantation specialists, geneticists, and experts in bioinformatics. Rigorous prospective validation studies will be needed using large sets of independent patient samples. The appropriate and timely exploitation of evolving 'omic technologies will lay the cornerstone for a new age of translational research for organ transplant monitoring.

Integrated platform for proteome analysis with combination of protein and peptide separation via online digestion

An integrated platform with the combination of protein and peptide separation was established via online protein digestion, by which proteins were first separated by a microcolumn packed with mixed weak anion and weak cation exchange (WAX/WCX) particles under a series of salt steps, online digested by a trypsin immobilized microenzymatic reactor (IMER), trapped and desalted by two parallel C8 precolumns, separated by microreversed-phase liquid chromatography (muRPLC) under a linear gradient of organic modifier concentration, and finally identified by electrospray ionization-MS/MS (ESI-MS/MS). To evaluate the performance of such a platform, a mixture of myoglobin, cytochrome c, bovine serum albumin (BSA), and alpha-casein, with mass ranging from 25 ng to 2 microg, was analyzed. Compared to the methods by off-line protein fractionation and shotgun based strategy, the analysis time, including sample preparation, digestion, desalting, separation, and detection, was shortened from ca. 30 to 5 h, and cytochrome c with abundance of 25 ng could be identified with improved sequence coverage. Furthermore, such an integrated platform was successfully applied into the analysis of proteins extracted from human lung cancer cells. Compared with the results obtained by the shotgun approach, the identified protein number was increased by 30%. All these results demonstrated that such an integrated approach would be an attractive alternative to commonly applied approaches for proteome research.

Activated-electron photodetachment dissociation for the structural characterization of protein polyanions

Multiply deprotonated anions [M - nH](n-) of large peptide mellitin, ubiquitin, and beta-casein proteins were subjected to laser irradiation at 260 nm in a quadrupole ion trap. For all compounds, the predominant event consecutive to laser irradiation was the detachment of an electron. The subsequent isolation and collisional activation of the oxidized [M - nH]((n-1)-*) resulted in extensive fragmentation of the peptide backbone. For mellitin peptide, nearly a complete series of c(*), z, and a(*), x product ions were observed. Applied to proteins, this technique, coined as activated-electron photodetachment dissociation (activated-EPD), achieved much more extensive sequence coverage than regular collision activated dissociation (CAD) on the even-electron components. Furthermore, the activated-EPD spectrum of beta-casein displayed phosphorylated fragment ions which suggest that the method is able to preserve part of the labile bonds of post-translational modifications. Activated-EPD is, therefore, a promising complementary technique to other dissociation techniques governed by radicals, i.e., electron capture dissociation (ECD), electron transfer dissociation (ETD), and electron detachment dissociation (EDD), for the structural characterization of large peptides and small proteins.

Proteomics of brain extracellular fluid (ECF) and cerebrospinal fluid (CSF)

Mass spectrometry has become the gold standard for the identification of proteins in proteomics. In this review, I will discuss the available literature on proteomic experiments that analyze human cerebrospinal fluid (CSF) and brain extracellular fluid (ECF), mostly obtained by cerebral microdialysis. Both materials are of high diagnostic value in clinical neurology, for example, in cerebrovascular disorders like stroke, neurodegenerative diseases like Alzheimer's Disease, Parkinson's Disease, amyotrophic lateral sclerosis (ALS), traumatic brain injury and cerebral infectious and inflammatory disease, such as multiple sclerosis. Moreover, there are standard procedures for sampling. In a number of studies in recent years, biomarkers have been proposed in CSF and ECF for improved diagnosis or to control therapy, based on proteomics and mass spectrometry. I will also discuss the needs for a transition of research-based experimental screening with mass spectrometry to fast and reliable diagnostic instrumentation for clinical use.

Precursor ion independent algorithm for top-down shotgun proteomics

We present a precursor ion independent top-down algorithm (PIITA) for use in automated assignment of protein identifications from tandem mass spectra of whole proteins. To acquire the data, we utilize data-dependent acquisition to select protein precursor ions eluting from a C4-based HPLC column for collision induced dissociation in the linear ion trap of an LTQ-Orbitrap mass spectrometer. Gas-phase fractionation is used to increase the number of acquired tandem mass spectra, all of which are recorded in the Orbitrap mass analyzer. To identify proteins, the PIITA algorithm compares deconvoluted, deisotoped, observed tandem mass spectra to all possible theoretical tandem mass spectra for each protein in a genomic sequence database without regard for measured parent ion mass. Only after a protein is identified, is any difference in measured and theoretical precursor mass used to identify and locate post-translation modifications. We demonstrate the application of PIITA to data generated via our wet-lab approach on a Salmonella typhimurium outer membrane extract and compare these results to bottom-up analysis. From these data, we identify 154 proteins by top-down analysis, 73 of which were not identified in a parallel bottom-up analysis. We also identify 201 unique isoforms of these 154 proteins at a false discovery rate (FDR) of <1%.

Modifying the charge state distribution of proteins in electrospray ionization mass spectrometry by chemical derivatization

Electrospray ionization (ESI) of denatured proteins produces a broad distribution of multiply-charged ions leading to multiple peaks in the mass spectrum. We investigated changes in the positive-mode ESI charge state distribution produced by several chemical modifications of denatured proteins. Capping carboxylic acid groups with neutral functional groups yields little change in charge state distribution compared with unmodified proteins. The results indicate that carboxyl groups do not play a significant role in the positive charging of denatured proteins in ESI. The modification of proteins with additional basic sites or fixed positive charges generates substantially higher charge states, providing evidence that the number of ionizable sites, rather than molecular size and shape, determines ESI charging for denatured proteins. Fixed charge modification also significantly reduces the number of protons acquired by a protein, in that the charge state envelope is not increased by the full number of fixed charges appended. This result demonstrates that Coulombic repulsion between positive charges plays a significant role in determining charge state distribution by affecting the gas-phase basicity of ionizable sites. Addition of fixed-charge moieties to a protein is a useful approach for shifting protein charge state distributions to higher charge states, and with further work, it may help limit the distribution of protein ions to fewer charge states.

Identification of active compounds and their metabolites by high-performance liquid chromatography/electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry from Xiao-xu-ming decoction (XXMD)

Xiao-xu-ming decoction (XXMD) prescription is a traditional Chinese prescription that has been widely used to treat theoplegia and the sequela of theoplegia. Modern pharmacological research has also indicated that the active fraction from XXMD is able to treat cardiovascular diseases and Alzheimer's disease. In the study reported here, high-performance liquid chromatography coupled with Fourier transform ion cyclotron resonance mass spectrometry (HPLC/FTICR-MS) was developed to identify active compounds and their metabolites after oral administration of active fraction from Xiao-xu-ming decoction to rats, using parent mass list triggered data-dependent multiple-stage mass analysis at a resolving power of 100,000 in the external calibration mode. The mass accuracies obtained for full-scan MS were within 2 ppm in most cases. Fifteen constituents were identified in the active fraction from XXMD and the biological samples of rats. The fragmentation behaviors of these constituents were summarized which would be helpful for structural characterization. The profiles of the constituents in the active fraction and biological samples of rats were obtained which provided us with much information for a better understanding of the chemical basis of the pharmacologic actions of XXMD.

An integrated serum proteomic approach capable of monitoring the low molecular weight proteome with sequencing of intermediate to large peptides

The low-abundance, low molecular weight serum proteome has high potential for the discovery of new biomarkers using mass spectrometry (MS). Because the serum proteome is large and complex, defining relative quantitative differences for a molecular species between comparison groups requires an approach with robust separation capability, high sensitivity, as well as high mass resolution. Capillary liquid chromatography (cLC)/MS provides both the necessary separation technique and the sensitivity to observe many low-abundance peptides. Subsequent identification of potential serum peptide biomarkers observed in the cLC/MS step can in principle be accomplished by in series cLC/MS/MS without further sample preparation or additional instrumentation. In this report a novel cLC/MS/MS method for peptide sequencing is described that surpasses previously reported size limits for amino acid sequencing accomplished by collisional fragmentation using a tandem time-of-flight MS instrument. As a demonstration of the approach, two low-abundance peptides with masses of approximately 4000-5000 Da were selected for MS/MS sequencing. The multi-channel analyzer (MCA) was used in a novel way that allowed for summation of 120 fragmentation spectra for each of several customized collision energies, providing more thorough fragmentation coverage of each peptide with improved signal to noise. The peak list from this composite analysis was submitted to Mascot for identification. The two index peptides, 4279 Da and 5061 Da, were successfully identified. The peptides were a 39 amino acid immunoglobulin G heavy chain variable region fragment and a 47 amino acid fibrin alpha isoform C-terminal fragment. The method described here provides the ability both to survey thousands of serum molecules and to couple that with markedly enhanced cLC/MS/MS peptide sequencing capabilities, providing a promising technique for serum biomarker discovery.

Synergistic design of electric field and membrane in facilitating continuous adsorption for cleanup and enrichment of proteins in direct ESI-MS analysis

We designed and fabricated a novel microdevice to facilitate continuous adsorption phenomena for biological sample preparation. Using the device, we also developed an online, highly integrated, multifunctional strategy, with a promise of accepting a large volume of crude tissue extracts with the end point generation of a reliable MS identification within 20 min. Under an external electric field, charged membranes can adsorb multiple layers of proteins, which exceed the capacity limit of common resins or membranes. It enlarges sample loading and trapping efficiency, thus bypasses the tradeoff between sample capacity and downstream detection sensitivity. This integrated approach, formed by synergistic utilization among electric field, membrane, and fluidic handling at the microscale, reduces the overall complexity of crude samples in one step for direct MS analysis. The sample preparation goals, including enrichment, desalting, removal of noncharged contaminants, and initial fractionation, can be rapidly performed in a single device. The strategy facilitates reproducible MS quantification by circumventing traditional laborious and time-consuming sample preparation steps. In addition, MEPD extended the ion trap linear dynamic range from 2 to at least 4 orders of magnitude by eliminating ion suppression effect, enriching target analyte(s), and decreasing sample loss during integrated sample preparation.

Interpreting the proteome and peptidome in transplantation

Publication of the human proteome has prompted efforts to develop high-throughput techniques that can catalogue and quantify proteins and peptides present in different tissue types. The field of proteomics aims to identify, quantify, analyze, and functionally define a large number of proteins in cellular processes in different disease states on a global scale. Peptidomics, a newer name in the -omics world, measures and identifies naturally occurring low molecular weight peptides, also providing an insight into enzymatic processes and molecular events occurring in the system of interest. One area of major interest is the use of proteomics to identify diagnostic and prognostic biomarkers for different diseases as well as for various clinical phenotypes in organ transplantation that can advance targeted therapy for various forms of graft injury. Outcomes in organ transplantation can be potentially improved by identifying noninvasive biomarkers that will serve as triggers that predate graft injury, and can offer a means to customize patient treatment by differentiating among causes of acute and chronic graft injury. Proteomic and peptidomic strategies can be harnessed for frequent noninvasive measurements in tissue fluids, allowing for serial monitoring of organ disease. In this review, we describe the basic techniques used in proteomic and peptidomic approaches, point out special considerations in using these methods, and discuss their applications in recently published studies in organ transplantation.

Shotgun proteomics in neuroscience

Mass spectrometry-based proteomics is increasingly used to address basic and clinical questions in biomedical research through studies of differential protein expression, protein-protein interactions, and posttranslational modifications. The complex structural and functional organization of the human brain warrants the application of high-throughput, systematic approaches to understand the functional alterations under normal physiological conditions and the perturbations of neurological diseases. This primer focuses on shotgun-proteomics-based tandem mass spectrometry for the identification of proteins in a complex mixture. It describes the basic concepts of protein differential expression analysis and posttranslational modification analysis and discusses several strategies to improve the coverage of the proteome.

Perspectives for imaging mass spectrometry in the proteomics landscape

A number of techniques are used in the field of proteomics that can be combined to get the most molecular information from a specific biological sample, fluid or tissue. Imaging techniques are often used to obtain local information from tissue samples. However, imaging experiments are often staining experiments, which rely on specific or aspecific interactions between fluorescent markers and pre-defined (families of) peptide or protein. Therefore, imaging is often used as a screening or validation tool for the local presence of proteins that have been identified by other means. Imaging mass spectrometry (IMS) combines the advantages of MS and microscopy in a single experiment. It is a technique that does not require any labeling of the analytes and provides a high multiplexing capability combined with the potential for analyte identification. It enables simultaneous detection of potentially all peptides and proteins present at a tissue surface and is used for the determination and identification of tissue-specific disease markers. The workflows of IMS experiments closely resemble those of conventional proteomics. In this review, we describe IMS experiments step-by-step to position and evaluate the role of IMS in a comparative proteomics landscape. We illustrate in a concise review that IMS is a true discovery oriented tool for proteomics that seamlessly integrates in conventional proteomics workflows and can be perceived as either an alternative or complementary proteomics technique.

Mass measurement and top-down HPLC/MS analysis of intact monoclonal antibodies on a hybrid linear quadrupole ion trap-Orbitrap mass spectrometer

Mass and top-down analyses of 150-kDa monoclonal immunoglobulin gamma (IgG) antibodies were performed on an Orbitrap analyzer. Three different sample delivery methods were tested including (1) infusion of an off-line desalted IgG sample using nano-electrospray; (2) on-line desalting followed by a step elution with a high percentage of organic solvent; and (3) reversed-phase HPLC separation and on-line mass and top-down analyses of disulfide isoforms of an IgG2 antibody. The accuracy of mass measurements of intact antibody was within +/-2 Da (15 ppm). The glycoforms of intact IgG antibodies separated by 162 Da were baseline resolved. In-source fragmentation of the intact antibodies produced mainly 115 residue fragments including N-terminal variable domains of heavy and light chains. The sequence coverage (the number of cleavages) was greatly increased after reduction of disulfide bonds and HPLC/MS/MS analysis of light and heavy chains using collision-induced dissociation in the ion trap of the LTQ-Orbitrap. This is an attractive alternative to peptide mapping for characterization and monitoring of post-translational modifications attributed to minimal sample preparation, high speed of the mass/top-down analysis, and relatively minor method-induced sample modifications.

An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications

We present an integrated top-down and bottom-up approach that is facilitated by concurrent liquid chromatography-mass spectrometry (LC-MS) analysis and fraction collection for comprehensive high-throughput intact protein profiling. The approach employs high-resolution, reversed-phase (RP) LC separations coupled on-line with a 12 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer to profile and tentatively identify modified proteins, using detected intact protein masses in conjunction with bare protein identifications from the bottom-up analysis of the corresponding LC fractions. Selected identifications are incorporated into a target ion list for subsequent off-line gas-phase fragmentation that uses an aliquot of the original fraction used for bottom-up analysis. In a proof-of-principle demonstration, this comprehensive strategy was applied to identify protein isoforms arising from various amino acid modifications (e.g., acetylation, phosphorylation) and genetic variants (e.g., single nucleotide polymorphisms, SNPs). This strategy overcomes major limitations of traditional bottom-up (e.g., inability to characterize multiple unexpected protein isoforms and genetic variants) and top-down (e.g., low throughput) approaches.

Structures, energetics, and dynamics of gas phase ions studied by FTICR and HPMS

Both Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and high-pressure mass spectrometry (HPMS) are very powerful tools in the field of gas phase ion chemistry. Many experimental method developments based on FTICR-MS and HPMS are summarized, including the coupling of a high-pressure external ion source to a FTICR mass spectrometer, blackbody infrared radiative dissociation (BIRD), coupling laser desorption ionization with HPMS, infrared multiple photon dissociation (IRMPD), radiative association and bimolecular routes to gas phase cluster ion formation. An abundance of thermochemical data, such as proton affinities, gas phase acidities, methyl cation affinities and metal cation affinities, have been obtained. Some of these data are the basis of the standard data listed in the NIST thermochemical databases. Ion-molecule interactions, energetics, reactivities, and structures of molecules have been extensively investigated using the methods developed based on HPMS and FTICR mass spectrometric techniques.

Urinary protein profiles in a rat model for diabetic complications

Diabetes mellitus is estimated to affect approximately 24 million people in the United States and more than 150 million people worldwide. There are numerous end organ complications of diabetes, the onset of which can be delayed by early diagnosis and treatment. Although assays for diabetes are well founded, tests for its complications lack sufficient specificity and sensitivity to adequately guide these treatment options. In our study, we employed a streptozotocin-induced rat model of diabetes to determine changes in urinary protein profiles that occur during the initial response to the attendant hyperglycemia (e.g. the first two months) with the goal of developing a reliable and reproducible method of analyzing multiple urine samples as well as providing clues to early markers of disease progression. After filtration and buffer exchange, urinary proteins were digested with a specific protease, and the relative amounts of several thousand peptides were compared across rat urine samples representing various times after administration of drug or sham control. Extensive data analysis, including imputation of missing values and normalization of all data was followed by ANOVA analysis to discover peptides that were significantly changing as a function of time, treatment and interaction of the two variables. The data demonstrated significant differences in protein abundance in urine before observable pathophysiological changes occur in this animal model and as function of the measured variables. These included decreases in relative abundance of major urinary protein precursor and increases in pro-alpha collagen, the expression of which is known to be regulated by circulating levels of insulin and/or glucose. Peptides from these proteins represent potential biomarkers, which can be used to stage urogenital complications from diabetes. The expression changes of a pro-alpha 1 collagen peptide was also confirmed via selected reaction monitoring.

Advances in Nutrigenomics research: novel and future analytical approaches to investigate the biological activity of natural compounds and food functions

In recent years, nutrition research has moved from classical epidemiology and physiology to molecular biology and genetics. Following this trend, Nutrigenomics has emerged as a novel and multidisciplinary research field in nutritional science that aims to elucidate how diet can influence human health. It is already well known that bioactive food compounds can interact with genes affecting transcription factors, protein expression and metabolite production. The study of these complex interactions requires the development of advanced analytical approaches combined with bioinformatics. Thus, to carry out these studies Transcriptomics, Proteomics and Metabolomics approaches are employed together with an adequate integration of the information that they provide. In this article, an overview of the current methodologies and a thorough revision of the advances in analytical technologies and their possibilities for future developments and applications in the field of Nutrigenomics is provided.

A novel Fourier transform ion cyclotron resonance mass spectrometer with improved ion trapping and detection capabilities

A novel Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer has been developed for improved biomolecule analysis. A flared metal capillary and an electrodynamic ion funnel were installed in the source region of the instrument for improved ion transmission. The transfer quadrupole is divided into 19 segments, with the capacity for independent control of DC voltage biases for each segment. Restrained ion population transfer (RIPT) is used to transfer ions from the ion accumulation region to the ICR cell. The RIPT ion guide reduces mass discrimination that occurs as a result of time-of-flight effects associated with gated trapping. Increasing the number of applied DC bias voltages from 8 to 18 increases the number of ions that are effectively trapped in the ICR cell. The RIPT ion guide with a novel voltage profile applied during ion transfer provides a 3- to 4-fold increase in the number of ions that are trapped in the ICR cell compared with gated trapping for the same ion accumulation time period. A novel ICR cell was incorporated in the instrument to reduce radial electric field variation for ions with different z-axis oscillation amplitudes. With the ICR cell, called trapping ring electrode cell (TREC), we can tailor the shape of the trapping electric fields to reduce dephasing of coherent cyclotron motion of an excited ion packet. With TREC, nearly an order of magnitude increase in sensitivity is observed. The performance of the instrument with the combination of RIPT, TREC, flared inlet, and ion funnel is presented.

Peptide fragmentation induced by radicals at atmospheric pressure

A novel ion dissociation technique, which is capable of providing an efficient fragmentation of peptides at essential atmospheric pressure conditions, is developed. The fragmentation patterns observed often contain c-type fragments that are specific to electron capture dissociation/electron transfer dissociation (ECD/ETD), along with the y-/b-type fragments that are specific to collision-activated dissociation (CAD). In the presented experimental setup, ion fragmentation takes place within a flow reactor located in the atmospheric pressure region between the ion source and the mass spectrometer. According to a proposed mechanism, the fragmentation results from the interaction of ESI-generated analyte ions with the gas-phase radical species produced by a corona discharge source.

Accessing natural product biosynthetic processes by mass spectrometry

Two important classes of natural products are made by nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). With most biosynthetic intermediates covalently tethered during biogenesis, protein mass spectrometry (MS) has proven invaluable for their interrogation. New mass spectrometric assay formats (such as selective cofactor ejection and proteomics style LC-MS) are showcased here in the context of functional insights into new breeds of NRPS/PKS enzymes, including the first characterization of an 'iterative' PKS, the biosynthesis of the enediyne antitumor antibiotics, the study of a new strategy for PKS initiation via a GNAT-like mechanism, and the analysis of branching strategies in the so-called 'AT-less' NRPS/PKS hybrid systems. The future of MS analysis of NRPS and PKS biosynthetic pathways lies in adoption and development of methods that continue bridging enzymology with proteomics as both fields continue their post-genomic acceleration.

Top-down proteomics on a high-field Fourier transform ion cyclotron resonance mass spectrometer

Mass spectrometry is the tool of choice for sequencing peptides and determining the sites of posttranslational modifications; however, this bottom-up approach lacks in providing global information about the modification states of proteins including the number and types of isoforms and their stoichiometry. Recently, various techniques and mass spectrometers, such as high-field Fourier Transform Ion Cyclotron Resonance (FTICR) mass spectrometers, have been developed to study intact proteins (top-down proteomics). While the protein molecular mass and the qualitative and quantitative information about protein isoforms can be revealed by FTICR-MS analysis, their primary structure (including the identification of modifications and their exact locations in the amino acid sequence) can directly be determined using the MS/MS capability offered by the FTICR mass spectrometer. The distinct advantage of top-down methods are that modifications can be determined for a specific protein isoform rather than for peptides belonging to one or several isoforms. In this chapter, we describe different top-down proteomic approaches enabled by high-field (7, 9.4, and 12 T) FTICR mass spectrometers, and their applicability to answer biological and biomedical questions. We also describe the use of the free flow electrophoresis (FFE) to separate proteins prior to top-down mass spectrometric characterization.

Label-free relative quantitation of prokaryotic proteomes using the accurate mass and time tag approach

Prokaryotic protein expression changes in detectable amounts due to the environmental stimuli encountered by the organism. To understand the underlying mechanisms involved it is necessary to comprehensively detect both the proteins present and their relative abundance under the growth conditions of interest. LC-MS based accurate mass and time (AMT) tag method along with the use of clustering software can provide a visual and more comprehensive understanding of significant protein abundance increases and decreases. These data then can be effectively used to pin-point proteins of interest for further genetic and physiological studies. This method allows for the identification and quantitation of thousands of proteins in a single mass spectrometric analysis and is more comprehensive than two dimensional electrophoresis and shotgun approaches.

Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-down mass spectrometry

Top-down and bottom-up mass spectrometry methods can generate gas phase fragments and use these to identify proteins. Top-down methods, in addition, can provide the mass of the protein itself and therefore additional structural information. Despite the conceptual advantage of top-down methods, the market share advantage belongs to bottom-up methods as a result of their more robust sample preparation, fragmentation, and data processing methods. Here we report improved fragmentation and data processing methods for top-down mass spectrometry. Specifically we report the use of funnel-skimmer dissociation, a variation of nozzle-skimmer dissociation, and compare its performance with electron capture dissociation. We also debut BIG Mascot, an extended version of Mascot with incorporated top-down MS(2) search ability and the first search engine that can perform both bottom-up and top-down searches. Using BIG Mascot, we demonstrated the ability to identify proteins 1) using only intact protein MS(1), 2) using only MS(2), and 3) using the combination of MS(1) and MS(2). We correctly identified proteins with a wide range of masses, including 13 amyotrophic lateral sclerosis-associated variants of the protein Cu/Zn-superoxide dismutase, and extended the upper mass limit of top-down protein identification to 669 kDa by identifying thyroglobulin.