Orbitrap Analyzer Research Articles

A SILAC-based Approach Identifies Substrates of Caspase-dependent Cleavage upon TRAIL-induced Apoptosis

The extracellular ligand-induced extrinsic pathway of apoptosis is executed via caspase protease cascades that activate downstream effectors by means of site-directed proteolysis. Here we identify proteome changes upon the induction of apoptosis by the cytokine tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) in a Jurkat T cell line. We detected caspase-dependent cleavage substrates by quantifying protein intensities before and after TRAIL induction in SDS gel slices. Apoptotic protein cleavage events are identified by a characteristic stable isotope labeling with amino acids in cell culture (SILAC) ratio pattern across gel slices that results from differential migration of the cleaved and uncleaved proteins. We applied a statistical test to define apoptotic substrates in the proteome. Our approach identified more than 650 of these cleaved proteins in response to TRAIL-induced apoptosis, including many previously unknown substrates and cleavage sites. Inhibitor treatment combined with triple SILAC demonstrated that the detected cleavage events were caspase dependent. Proteins located in the lumina of organelles such as mitochondria and endoplasmic reticulum were significantly underrepresented in the substrate population. Interestingly, caspase cleavage is generally observed in not only one but several members of stable complexes, but often with lower stoichiometry. For instance, all five proteins of the condensin I complex were cleaved upon TRAIL treatment. The apoptotic substrate proteome data can be accessed and visualized in the MaxQB database and might prove useful for basic and clinical research into TRAIL-induced apoptosis. The technology described here is extensible to a wide range of other proteolytic cleavage events.

Intact protein mass spectrometry and top-down proteomics

American Society for Mass Spectrometry Sanibel meeting on top-down mass spectrometrySt Pete Beach, FL, USA, 24–27 January 2013Top-down mass spectrometry involves analysis of intact proteins, typically using electrospray ionization, as multiple charging enhances dissociation and thus identification by comparison of precursor and product ion masses with protein sequence databases. Traditionally a low-throughput, precision technology performed on high-resolution Fourier-transform ion cyclotron resonance mass analyzers, top-down proteomics aims to increase throughput for whole proteome analysis while preserving the inherent value of an intact protein mass measurement. This years’ American Society for Mass Spectrometry Sanibel meeting brought together established scientists who have demonstrated the viability of the top-down approach and its applicability to virtually all segments of the proteome, mixing them with researchers from diverse areas and with the common interest of advancing top-down into the high-throughput proteomics mainstream. Advances in instrumentation including the orbitrap analyzer, ionization mechanisms, dissociation strategies and informatics, as well as a wide variety of applications, were discussed in depth, leading to the inescapable conclusion that the future for top-down is bright.

A novel UV-MALDI-MS analytical approach for determination of halogenated phenyl-containing pesticides

The paper highlighted the capability of the UV-MALDI mass spectrometry, employing the Orbitrap analyzer for solid-state assay of halogenated phenyl–pesticides in mixtures. It is successfully applied for the analysis of eighteen (1)–(18) molecular objects of Fenarimol (1) type and their condensation products (P5)–(P12). The full method and technique validation is performed using the dried droplet sample preparation technique on embedded analytes in novel organic matrix crystals of N-(1H-benzoimidazol-2-yl)-guanidine (M4) and (E)-phenyl-2-pyridyl ketone oxime (M5), resulting to successful ionization of the analytes. Since the sampling technique in the UV-MALDI method is a key step in the overall process impacting significantly the metrology through the reproducibility of the data, the crystallization of M4, M5 and matrix–analyte in situ morphology of the samples is controlled by single crystal X-ray diffraction. The achieved promising metrology of LODs, of 0.46ngkg−1 (1.53ngkg−1 LOQs), is several orders of magnitude lower than the reported ecotoxicological effect values of studied pesticides. It is confirmed by the partial validated protocol based on ESI-MS. Inasmuch that LC-MS/MS is a method of choice for foodstuffs monitoring of organic contaminations, due to its routine quantitative analytical procedures, it is often characterized with the difficulties of the chromatographic separation of the closely structured analytes at a large scale of experimental conditions, complex multi-step sampling pretreatments, which inevitably alert the variables through the systematic and random errors. In this respect, notwithstanding the complex quantitative UV-MALDI-Orbitrap-MS procedure, conceptually different from the LC-MS/MS one, its high resolving power, capability for achieving meaningful analytical qualitative, quantitative and structural information of low-molecular weight analytes, its instrumental and sampling operation flexibility, applicable for a large scale of foodstuff matrices, and operating at the analyte concentrations of up to fgg−1 make UV-MALDI-Orbitrap-MS a perspective method of choice for an extensive implementation in the foodstuffs monitoring practice for control of the most essential task related to the assessment of the human health risks from environmental and foodstuff contaminations.

Performance of the linear ion trap Orbitrap mass analyzer for qualitative and quantitative analysis of drugs of abuse and relevant metabolites in sewage water

This work illustrates the potential of liquid chromatography coupled to a hybrid linear ion trap Fourier Transform Orbitrap mass spectrometer for the simultaneous identification and quantification of 24 drugs of abuse and relevant metabolites in sewage water. The developed methodology consisted of automatic solid-phase extraction using Oasis HLB cartridges, chromatographic separation of the targeted drugs, full-scan accurate mass data acquisition under positive electrospray ionization mode over an m/z range of 50–600Da at a resolution of 30,000 FWHM and simultaneous MSn measurements to obtain information of fragment ions generated in the linear ion trap. Accurate mass of the protonated molecule, together with at least one nominal mass product ion and retention time allowed the confident identification of the compounds detected in these complex matrices. In addition to the highly reliable qualitative analysis, Orbitrap analyzer also proved to have satisfactory potential for quantification at sub-ppb analyte levels, a possibility that has been very little explored in the literature until now. The limits of quantification ranged from 4 to 68ngL−1 in influent sewage water, and from 2 to 35ngL−1 in effluent, with the exception of MDA, morphine and THC that presented higher values as a consequence of the high ionization suppression in this type of samples. Satisfactory recoveries (70–120%) and precision (<30%) for the overall procedure were obtained for all compounds with the exception of meta-chlorophenylpiperazine, methylphenidate and ketamine. Isotope-labelled internal standards were added to sewage samples as surrogates in order to correct for matrix effects and also for possible losses during sample treatment. The methodology developed was applied to sewage water samples from the Netherlands (influent and effluent), and the results were compared with those obtained by LC–MS/MS with triple quadrupole. Several drugs of abuse could be identified and quantified, mainly MDMA, benzoylecgonine, codeine, oxazepam and temazepam. Orbitrap also showed potential for retrospective investigation of ketamine metabolites in the samples without the need of additional analysis.

Liquid chromatography coupled to tandem mass spectrometry and high resolution mass spectrometry as analytical tools to characterize multi-class cytostatic compounds

Cytostatic compounds used in the treatment of cancer have emerged as a new generation of water contaminants due to the continuous amounts administered to patients and to the fact that a variable proportion is excreted unchanged. In this study, we have evaluated the performance of liquid-chromatography–tandem mass spectrometry (LC–MS/MS) and high resolution mass spectrometry using an Orbitrap analyzer (LC–HRMS) for the multiresidue determination of multi-class cytostatic compounds. In a first step, ionization conditions were tested in positive electrospray mode and optimum fragmentation patterns were determined. For LC–MS/MS, two selected reaction monitoring (SRM) transitions were optimized and for LC–HRMS, the molecular ion with 5ppm error and two product ions were defined. Following, the chromatographic conditions were optimized considering that compounds analyzed have a very different chemical structure and chromatographic behavior. The best performance was obtained with a Luna C18 column, which permitted the separation of the 26 compounds in 15min. Finally, the performance of LC–MS/MS and LC–HRMS was compared in terms of linearity, sensitivity, intra and inter-day precision and overall robustness. While LC–MS/MS provided good identification capabilities due to selective SRM transitions, LC-Orbitrap proved to be 100 times more sensitive. This study provides a comprehensive overview on the MS conditions to determine the outmost used cytostatic compounds and provides a spectral library to be used for the identification of these compounds in water or biological matrices.

Exploring an Orbitrap Analyzer for the Characterization of Intact Antibodies by Native Mass Spectrometry

Antibody profiling: native mass spectrometry analysis of intact antibodies can be achieved with improved speed, sensitivity, and mass resolution by using a modified orbitrap instrument. Complex mixtures of monoclonal antibodies can be resolved and their glycan "fingerprints" can be profiled. Noncovalent interactions are maintained, thus allowing antibody-antigen binding to be measured.

Is orbitrap quantitative? Critical aspects of its potential using natural products and synthetic drugs as models

Orbitrap analyzers represent a new exciting technology in the field of mass spectrometry as they offer unsurpassed mass accuracy (often in the sub-ppm area) along with high resolving power (up to 150.00). Its use is widespread including structure elucidation of natural products, proteomics, metabolism studies and metabolomics as well fragmentation and H/D exchange studies. Nevertheless quantitation studies using such instrumentation are rather scarce and are usually performed using the XIC mode of full scan mass spectra. This study involves a detailed study on the quantitative abilities of the instrument investigating critical factors pertaining its operation, such as the scan range, the resolution, the acquisition mode (centroid or profile) as well as the MS/MS capabilities of the instrument. Five substances (four natural products – oleuropein, hydroxytyrosol, acrovestone and hermanioside B, one semisynthetic –6-bromoindirubin-3-oxime and one synthetic drug – clopidogrel) have been used as model compounds. The evaluation of the results has been based on the statistical comparison of calibration curves constructed under the aforementioned conditions using either the extra sum-of-squares F test or the Akaike's information criterion methodologies.

Mapping Ultra-weak Protein-Protein Interactions between Heme Transporters of Staphylococcus aureus

Iron is an essential nutrient for the proliferation of Staphylococcus aureus during bacterial infections. The iron-regulated surface determinant (Isd) system of S. aureus transports and metabolizes iron porphyrin (heme) captured from the host organism. Transportation of heme across the thick cell wall of this bacterium requires multiple relay points. The mechanism by which heme is physically transferred between Isd transporters is largely unknown because of the transient nature of the interactions involved. Herein, we show that the IsdC transporter not only passes heme ligand to another class of Isd transporter, as previously known, but can also perform self-transfer reactions. IsdA shows a similar ability. A genetically encoded photoreactive probe was used to survey the regions of IsdC involved in self-dimerization. We propose an updated model that explicitly considers self-transfer reactions to explain heme delivery across the cell wall. An analogous photo-cross-linking strategy was employed to map transient interactions between IsdC and IsdE transporters. These experiments identified a key structural element involved in the rapid and specific transfer of heme from IsdC to IsdE. The resulting structural model was validated with a chimeric version of the homologous transporter IsdA. Overall, our results show that the ultra-weak interactions between Isd transporters are governed by bona fide protein structural motifs.

Super-SILAC Allows Classification of Diffuse Large B-cell Lymphoma Subtypes by Their Protein Expression Profiles

Correct classification of cancer patients into subtypes is a prerequisite for acute diagnosis and effective treatment. Currently this classification relies mainly on histological assessment, but gene expression analysis by microarrays has shown great promise. Here we show that high accuracy, quantitative proteomics can robustly segregate cancer subtypes directly at the level of expressed proteins. We investigated two histologically indistinguishable subtypes of diffuse large B-cell lymphoma (DLBCL): activated B-cell-like (ABC) and germinal-center B-cell-like (GCB) subtypes, by first developing a general lymphoma stable isotope labeling with amino acids in cell culture (SILAC) mix from heavy stable isotope-labeled cell lines. This super-SILAC mix was combined with cell lysates from five ABC-DLBCL and five GCB-DLBCL cell lines. Shotgun proteomic analysis on a linear ion trap Orbitrap mass spectrometer with high mass accuracy at the MS and MS/MS levels yielded a proteome of more than 7,500 identified proteins. High accuracy of quantification allowed robust separation of subtypes by principal component analysis. The main contributors to the classification included proteins known to be differentially expressed between the subtypes such as the transcription factors IRF4 and SPI1/PU.1, cell surface markers CD44 and CD27, as well as novel candidates. We extracted a signature of 55 proteins that segregated subtypes and contained proteins connected to functional differences between the ABC and GCB-DLBCL subtypes, including many NF-κB-regulated genes. Shortening the analysis time to single-shot analysis combined with use of the new linear quadrupole Orbitrap analyzer (Q Exactive) also clearly differentiated between the subtypes. These results show that high resolution shotgun proteomics combined with super-SILAC-based quantification is a promising new technology for tumor characterization and classification.

Proteomic Analysis of Zebrafish Caudal Fin Regeneration

The epimorphic regeneration of zebrafish caudal fin is rapid and complete. We have analyzed the biomechanism of zebrafish caudal fin regeneration at various time points based on differential proteomics approaches. The spectrum of proteome changes caused by regeneration were analyzed among controls (0 h) and 1, 12, 24, 48, and 72 h postamputation involving quantitative differential proteomics analysis based on two-dimensional gel electrophoresis matrix-assisted laser desorption/ionization and differential in-gel electrophoresis Orbitrap analysis. A total of 96 proteins were found differentially regulated between the control nonregenerating and regenerating tissues of different time points for having at least 1.5-fold changes. 90 proteins were identified as differentially regulated for regeneration based on differential in-gel electrophoresis analysis between the control and regenerating tissues. 35 proteins were characterized for its expression in all of the five regenerating time points against the control samples. The proteins identified and associated with regeneration were found to be directly allied with various molecular, biological, and cellular functions. Based on network pathway analysis, the identified proteome data set for regeneration was majorly associated in maintaining cellular structure and architecture. Also the proteins were found associated for the cytoskeleton remodeling pathway and cellular immune defense mechanism. The major proteins that were found differentially regulated during zebrafish caudal fin regeneration includes keratin and its 10 isoforms, cofilin 2, annexin a1, skeletal α1 actin, and structural proteins. Annexin A1 was found to be exclusively undergoing phosphorylation during regeneration. The obtained differential proteome and the direct association of the various proteins might lead to a new understanding of the regeneration mechanism.

Matrix-assisted laser desorption/ionization mass spectrometric analysis of herbicides in dication-containing organic crystals

The paper reported a matrix-assisted laser desorption/ionization (MALDI) mass spectrometric (MS) protocol for determination of herbicides, improving the analytical sample preparation step, making a significant contribution to the reproducibility and precision of the method. Matrix-analyte sampling is performed, employing low molecular weight (LMW) dication-containing organic crystals. Considering environmental control applications, six of the best selling herbicides, such as aclonifen (1), bifenox (2), diclofop-methyl (3), racemic mixture of diclofop (4), alachlor (5) and metolachlor (6) as well as their mixtures are quantified successively through the replacement of the polyfunctional benzoic acids with dication-containing organic matrices. The application of classical matrices for UV-MALDI-MS for the analysis of 1–6 caused their competitive chemical transformation, thus leading to spurious results and inaccurate analytical information, due to the wide variety of experimental conditions depending on the chemical, physico-chemical and physical nature of the herbicide analytes. The full method and technique validation, based on UV-MALDI-MS employing an Orbitrap analyser, are presented, achieving to our knowledge promising measurements for LMW analytes. These latter are judged by a fully validated analytical protocol based on positive electrospray ionization (ESI) mass spectrometry in a single and tandem (MS/MS) mode of operation. The chemical modifications, polymorph transformations of the UV-MALDI-MS crystal matrices and/or matrix-analyte samples, as well as ion-process formation upon solution → crystalline state and crystalline state → gas-phase transitions is controlled by joint application of unique and robust instrumental analytical methods for absolute structural determination, such as single crystal X-ray diffraction and mass spectrometry. As direct experimental qualitative, quantitative and structural evidence regarding the analytes was provided, the reported protocol is a fully validated one at each of the analytical steps. The additional quantum chemical data allowed correlation of the thermodynamic stability and MS abundances of observed ionic species in the gas-phase as well as the structure of crystals. Since environmental analysis involves a broad variety of analytes, conditions and degree of matrix complexity, only an individual certification method development may achieve meaningful analytical information. In this respect, the reported UV-MALDI-MS method for herbicides significantly impacts the field of environmental analytical chemistry, quality assurance and control; moreover the analytical protocol is constructed to deal with a real environmental problem. Therefore the reported method ensures real practical efficiency and reliability in the results for the human health safety, environmental monitoring and control programs.

Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes

Although only a few years old, the combination of a linear ion trap with an Orbitrap analyzer has become one of the standard mass spectrometers to characterize proteins and proteomes. Here we describe a novel version of this instrument family, the Orbitrap Elite, which is improved in three main areas. The ion transfer optics has an ion path that blocks the line of sight to achieve more robust operation. The tandem MS acquisition speed of the dual cell linear ion trap now exceeds 12 Hz. Most importantly, the resolving power of the Orbitrap analyzer has been increased twofold for the same transient length by employing a compact, high-field Orbitrap analyzer that almost doubles the observed frequencies. An enhanced Fourier Transform algorithm—incorporating phase information—further doubles the resolving power to 240,000 at m/z 400 for a 768 ms transient. For top-down experiments, we combine a survey scan with a selected ion monitoring scan of the charge state of the protein to be fragmented and with several HCD microscans. Despite the 120,000 resolving power for SIM and HCD scans, the total cycle time is within several seconds and therefore suitable for liquid chromatography tandem MS. For bottom-up proteomics, we combined survey scans at 240,000 resolving power with data-dependent collision-induced dissociation of the 20 most abundant precursors in a total cycle time of 2.5 s—increasing protein identifications in complex mixtures by about 30%. The speed of the Orbitrap Elite furthermore allows scan modes in which complementary dissociation mechanisms are routinely obtained of all fragmented peptides.

Identification of New Natural Sweet Compounds in Wine Using Centrifugal Partition Chromatography–Gustatometry and Fourier Transform Mass Spectrometry

Sweetness contributes notably to the taste-balance of dry wines and increases during oak-barrel aging owing to the release of natural sweeteners from wood. The search for such taste-active molecules, which are sometimes present at very low concentrations in wine or other complex matrixes, requires both reliable purification tools and powerful identification techniques. Here, we report the development of an original inductive method using centrifugal partition chromatography (CPC) and sensorial analysis. This method, called CPC-gustatometry, was implemented to isolate a sweet fraction with only four compounds from a complex oak wood extract. The recently developed Fourier transform mass spectrometry (FT-MS, Orbitrap analyzer) was used jointly with two-dimensional nuclear magnetic resonance (2D (1)H and (13)C NMR) to obtain the structural elucidation of the purified compounds. The tandem mass spectrometry (MS/MS) spectra obtained with resonant and nonresonant fragmentation modes were compared, thus providing complementary information about the molecular structure. Two oleanane-type triterpenoids substituted with galloyl and glucosyl moieties were identified, one of which exhibits sweet properties. We term these compounds which have never been reported, Quercotriterpenoside I and II.

Determination of deoxynivalenol, T-2 and HT-2 toxins in a bread model food by liquid chromatography–high resolution-Orbitrap-mass spectrometry equipped with a high-energy collision dissociation cell

A sensitive and accurate method employing a single stage high resolution mass spectrometer equipped with a high-energy collision-dissociation cell (HCD) for the simultaneous determination of deoxynivalenol (DON), T-2 toxin (T-2) and HT-2 toxin (HT-2) in a processed bread model food has been developed. Two sample pre-treatment routes for the extraction of these mycotoxins were investigated, based on Mycosep(®) column clean up or QuEChERS-like procedure, respectively. The former approach suffered less from matrix effects and allowed to achieve in bread samples LODs of 7, 12 and 17 ng/g for T-2, HT-2 and DON, respectively, with 0.5 ppm mass accuracy. Two acquisition modes, full scan MS and all ion fragmentation, exploiting the fragmentation features offered by an HCD chamber and integrated within the Orbitrap analyser, were compared for quantitative purposes. The method was applied to investigate the degradation of these mycotoxins during bread processing using a bread model food. Most T-2 hydrolyzed to HT-2 during dough preparation, and about 20-30% of HT-2 and DON was degraded during bread baking.

Identification of nitroglycerin‐induced cysteine modifications of pro‐matrix metalloproteinase‐9

Nitroglycerin (NTG), an important cardiovascular agent, has been shown recently to activate matrix metalloproteinase-9 (MMP-9) in biological systems, possibly leading to destabilization of atherosclerotic plaques. The chemical mechanism for this activation, particularly on the cysteine switch of the pro-form of MMP-9 (proMMP-9), has not been investigated and was examined here using nano-flow liquid chromatography coupled to mass spectrometry. In order to obtain high sequence coverage, two orthogonal enzymes (trypsin and GluC) were employed to digest the protein in parallel. Two complementary activation methods, collision-induced dissociation (CID) and electron-transfer dissociation (ETD), were employed for the identification of various modifications. A high-resolution Orbitrap analyzer was used to enable confident identification. Incubation of NTG with proMMP-9 resulted in the formation of an unstable thionitrate intermediate and oxidation of the cysteine switch to sulfinic and irreversible sulfonic acid derivatives. The unstable thionitrate modification was confirmed by both CID and ETD in the proteolytic peptides produced by both trypsin and GluC. Incubation of proMMP-9 with diethylenetriamine NONOate (a nitric oxide donor) led to sulfonic acid formation, but no observable sulfinic acid modification. Extensive tyrosine nitration by NTG was observed at Tyr-262, in close proximity to an oxidized Cys-256 of proMMP-9. The intramolecular interaction between these two residues toward NTG-induced oxidation was examined using a synthesized peptide representing the sequence in this domain, PWCSTTANYDTDDR, and the modification status was compared against an analog in which Cys was substituted by Ala. We observed a thionitrate product, extensive Cys oxidative modifications and enhanced tyrosine nitration with the Cys peptide but not with the Ala analog. Our results indicated that neighboring Cys and Tyr residues can facilitate each other's oxidation in the presence of NTG.

Reliable Detection of Milk Allergens in Food Using a High-Resolution, Stand-Alone Mass Spectrometer

Reliable methods are needed for detection of allergenic milk proteins in complex food matrixes. The feasibility of an LC/high-resolution MS method for the analysis of milk proteins in a thermally processed model food (incurred cookies) and in white wine spiked, respectively, with milk powder and caseinate is described. Detection of milk proteins was based on the identification of unique peptides in the tryptic digests of cookie/wine extracts using an RP-HPLC separation coupled to an Exactive nonhybrid mass spectrometer using Orbitrap technology. The extremely high mass accuracy and resolution provided by the Orbitrap analyzer allowed a fast preliminary identification of four previously proposed peptide markers of caseins using only accurate values of the m/z of their ions. No interference was observed, despite the complexity of the analyzed matrixes. Moreover, the availability of a high- energy, collisionally activated dissociation cell integrated in the mass spectrometer enabled acquisition of peptide MS/MS-like spectra through post-source fragmentation. Confirmation of peptide marker identity could then be achieved by a comparison between experimental and predicted product ions. The described method shows the great potential of Orbitrap MS as a reliable technique in the field of protein allergen detection once the peptide markers are identified.

Bottom-Up Shotgun Lipidomics by Higher Energy Collisional Dissociation on LTQ Orbitrap Mass Spectrometers

Higher energy collision dissociation (HCD) is a complementary fragmentation tool that has recently become available on mass spectrometers of the LTQ Orbitrap family. We report on a shotgun bottom-up lipidomics approach that relies on HCD of the isolated lipid precursors. HCD, together with the high mass resolution and mass accuracy of the Orbitrap analyzer, improved the confidence of molecular species assignment and accuracy of their quantification in total lipid extracts. These capabilities were particularly important for accounting for biologically interesting lipid species comprising polyunsaturated and odd numbered fatty acid moieties. We argue that now both bottom-up and top-down shotgun lipidomics could be performed on the same instrumentation platform.

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

Mass spectrometry-based proteomics has greatly benefitted from enormous advances in high resolution instrumentation in recent years. In particular, the combination of a linear ion trap with the Orbitrap analyzer has proven to be a popular instrument configuration. Complementing this hybrid trap-trap instrument, as well as the standalone Orbitrap analyzer termed Exactive, we here present coupling of a quadrupole mass filter to an Orbitrap analyzer. This “Q Exactive” instrument features high ion currents because of an S-lens, and fast high-energy collision-induced dissociation peptide fragmentation because of parallel filling and detection modes. The image current from the detector is processed by an “enhanced Fourier Transformation” algorithm, doubling mass spectrometric resolution. Together with almost instantaneous isolation and fragmentation, the instrument achieves overall cycle times of 1 s for a top10 higher energy collisional dissociation method. More than 2500 proteins can be identified in standard 90-min gradients of tryptic digests of mammalian cell lysate— a significant improvement over previous Orbitrap mass spectrometers. Furthermore, the quadrupole Orbitrap analyzer combination enables multiplexed operation at the MS and tandem MS levels. This is demonstrated in a multiplexed single ion monitoring mode, in which the quadrupole rapidly switches among different narrow mass ranges that are analyzed in a single composite MS spectrum. Similarly, the quadrupole allows fragmentation of different precursor masses in rapid succession, followed by joint analysis of the higher energy collisional dissociation fragment ions in the Orbitrap analyzer. High performance in a robust benchtop format together with the ability to perform complex multiplexed scan modes make the Q Exactive an exciting new instrument for the proteomics and general analytical communities.

Fourier Transform Mass Spectrometry

This article provides an introduction to Fourier transform-based mass spectrometry. The key performance characteristics of Fourier transform-based mass spectrometry, mass accuracy and resolution, are presented in the view of how they impact the interpretation of measurements in proteomic applications. The theory and principles of operation of two types of mass analyzer, Fourier transform ion cyclotron resonance and Orbitrap, are described. Major benefits as well as limitations of Fourier transform-based mass spectrometry technology are discussed in the context of practical sample analysis, and illustrated with examples included as figures in this text and in the accompanying slide set. Comparisons highlighting the performance differences between the two mass analyzers are made where deemed useful in assisting the user with choosing the most appropriate technology for an application. Recent developments of these high-performing mass spectrometers are mentioned to provide a future outlook.

Implementing Photodissociation in an Orbitrap Mass Spectrometer

We modified a dual pressure linear ion trap Orbitrap to permit infrared multiphoton dissociation (IRMPD) in the higher energy collisional dissociation (HCD) cell for high resolution analysis. A number of parameters, including the pressures of the C-trap and HCD cell, the radio frequency (rf) amplitude applied to the C-trap, and the HCD DC offset, were evaluated to optimize IRMPD efficiency and maintain a high signal-to-noise ratio. IRMPD was utilized for characterization of phosphopeptides, supercharged peptides, and N-terminal modified peptides, as well as for top-down protein analysis. The high resolution and high mass accuracy capabilities of the Orbitrap analyzer facilitated confident assignment of product ions arising from IRMPD.