3D Ion Research Articles

DC potentials applied to an end-cap electrode of a 3D ion trap for enhanced MS n functionality

The effects of the application of various DC magnitudes and polarities to an end-cap of a 3D quadrupole ion trap throughout a mass spectrometry experiment were investigated. Application of a monopolar DC field was achieved by applying a DC potential to the exit end-cap electrode, while maintaining the entrance end-cap electrode at ground potential. Control over the monopolar DC magnitude and polarity during time periods associated with ion accumulation, mass analysis, ion isolation, ion/ion reaction, and ion activation can have various desirable effects. Included amongst these are increased ion capture efficiency, increased ion ejection efficiency during mass analysis, effective isolation of ions using lower AC resonance ejection amplitudes, improved temporal control of the overlap of oppositely charged ion populations, and the performance of “broad-band” collision induced dissociation (CID). These results suggest general means to improve the performance of the 3D ion trap in a variety of mass spectrometry and tandem mass spectrometry experiments.

Rapid separation, identification, and quantification of coumarins in Peucedanum ostruthium by high-performance liquid chromatography with diode-array detection and mass spectrometry

The genus Peucedanum (Apiaceae) contains over 120 species. Various coumarins are typical for its family and, therefore, can be used to distinguish between closely related species [1]. As the rhizomes of Peucedanum ostruthium are traditionally used in the alpine region as herbal drug and as ingredient of liqueurs and bitters [2], there is a need for quality control of this drug (“Radix Imperatoriae“). A high performance liquid chromatography-diode array detector-mass spectrometry (HPLC-DAD-MS) method has been developed for the simultaneous separation and identification of the six main coumarins, Oxypeucedanin-hydrate, Oxypeucedanin, Ostruthol, Imperatorin, Isoimperatorin, and Ostruthin, in the dichloromethane extract of the dried rhizomes of Peucedanum ostruthium. Fast HPLC separation of the (furano)coumarins could be achieved on a Aquasil C18 column (150×2,1, particle size: 3µm) using a mobile phase gradient of acetonitrile-water modified with 0,01% acetic acid. Peak assignment and purity control were obtained by multistage LC-MS using a 3D quadrupole ion trap instrument equipped with an orthogonal electrospray ionisation source. The identity of the main compounds was confirmed either by comparison with reference compounds (Oxypeucedanin, Imperatorin and Isoimperatorin), or by isolation (Oxypeucedaninhydrate, Ostruthol and Ostruthin) and structural characterization by NMR and MS. Moreover, the content of the main coumarins was quantified in various batches of commercial and field-collected rhizomes of Peucedanum ostruthium by this newly established HPLC-DAD method. Hence, it can be used for performing a fast profiling and quantification of the main coumarins in samples of “Radix Imperatoriae“.

Study of the performance of three LC-MS/MS platforms for analysis of perfluorinated compounds

The analytical suitabilities of three different liquid chromatography-tandem mass spectrometry (LC-MS/MS) systems, (1) triple quadrupole (QqQ), (2) conventional 3D ion trap (IT), and (3) quadrupole-linear IT (QqLIT), to determine trace levels of perfluorinated compounds (PFCs) in fish and shellfish were compared. Sample preparation was performed using alkaline extraction and solid-phase-extraction cleanup. This evaluation was focused on both quantitative (sensitivity, precision, and accuracy) and qualitative (identification capabilities) aspects. In the three instruments, the former facet was evaluated using selected reaction monitoring (SRM), which is the standard mode for quantitative LC-MS/MS analysis. Accuracy was similar in the three systems, with recoveries always over 70 %. Precision was better for the QqLIT and QqQ systems (7-15%) than for the IT system (10-17%). The QqLIT (working in SRM mode) and QqQ systems offered a linear dynamic range of at least 3 orders of magnitude, whereas that of the IT system was 2 orders of magnitude. The QqLIT system achieved at least 20-fold higher sensitivity than the QqQ system, and this was at least tenfold higher sensitivity than for the IT system. In the IT system, identification was based on sensitive full mass range acquisition and MS( n ) fragmentation and in the QqLIT system, it was based on the use of an information-dependent-acquisition scan function, which allows the combination of an SRM or MS full scan acting as the survey scan and an enhanced product ion scan followed by MS(3) as the dependent scan in the same analysis. Three instruments were applied to monitor the content in fish and shellfish (anchovies, swordfish, tuna, mussels, and oysters) obtained from Valencia and Barcelona markets (Spain). The eight target PFCs were detected at mean concentrations in the range from 10 ng kg(-1) (perfluoro-7-methyloctanoic acid and perfluoro-1-decanesulfonate) to 4,200 ng kg(-1) (perfluoropentanoic acid). Furthermore, perfluoroheptanoic and perfluoroundecanoic acids (not covered as target analytes) were identified in some samples.

Investigations of the EPR parameters and local structures for the substitutional Cu2+centers in the tungstates

The high order perturbation formulas of the electron paramagnetic resonance (EPR) parameters (the g factors and the hyperfine structure constants) are established for a 3d(9) ion in orthorhombically compressed octahedra. These formulas are applied to the investigations of the EPR spectra and local structures for the substitutional Cu(2+) centers in the wolframite-type tungstates AWO(4) (where A = Cd, Zn, Mg). Based on the studies, the [CuO(6)](10-) clusters are found to experience the local planar bond length variations delta R' (approximate to 0.096, 0.021 and 0.028 angstrom for CdWO(4), ZnWO(4) and MgWO(4), respectively) along X and Y-axes. These values are quite different from the host planar bond length variations delta R (approximate to 0.013, 0.069 and 0.005 angstrom) for the A(2+) sites in the pure tungstates. The above local bond length variations in the impurity centers can be attributed to the Jahn-Teller effect and size mismatching substitution. The theoretical EPR parameters based on the above local structures agree well with the experimental data. By adopting the uniform theoretical formulas and fewer adjustable parameters in this work, the improvements are achieved for the EPR parameters as compared with the previous calculation results.

Neutron production from 7Li(d,xn) nuclear fusion reactions driven by high-intensity laser–target interactions

Numerical simulations of neutron production from deuterium–lithium nuclear fusion reactions have been performed. A set of differential cross sections for the 7Li(d,xn) reaction for incident deuteron energies of up to 50 MeV is assembled. The angular distribution of neutrons from a thick lithium target is simulated and benchmarked against experimental data. Two-stage neutron production from laser–target experiments has been studied as a function of laser intensity and energy. During the first stage a well collimated deuteron beam is generated using a high-intensity ultrashort pulse laser. During the second stage it is transported through a lithium target using a 3D Monte-Carlo ion beam–target deposition model. The neutron yield is estimated to be ∼108 neutrons J−1 laser energy. Some 1010 neutrons can be expected from a ∼100 J petawatt-class laser. For incident deuteron energies above 1 MeV the proposed scheme for neutron production from d–Li reactions is superior to that from d–d reactions, producing a collimated beam of neutrons with higher neutron yield.

K3 Fragment of Amyloidogenic β2-Microglobulin Forms Ion Channels: Implication for Dialysis Related Amyloidosis

Beta(2)-microglobulin (beta(2)m) amyloid deposits are linked to dialysis-related amyloidosis (DRA) in hemodialysis patients. The mechanism by which beta(2)m causes DRA is not understood. It is also unclear whether only the full-length beta(2)m induces pathophysiology or if proteolytic fragments are sufficient for inducing this effect. Ser20-Lys41 (K3) is a digestion fragment of full-length beta(2)m. Solid state NMR (ssNMR) combined with X-ray diffraction and atomic force microscopy (AFM) revealed the characteristic oligomeric amyloid conformation of the U-turn beta-strand-turn-beta-strand motif stacked in parallel and stabilized by intermolecular interactions also shown by Abeta(9-40)/Abeta(17-42) and the CA150 WW domain. Here we use the K3 U-turn atomic coordinates and molecular dynamic (MD) simulations to model K3 channels in the membrane. Consistent with previous AFM imaging of other amyloids that show channel-like structures in the membrane, in the simulations K3 also forms ion channels with 3-6 loosely attached mobile subunits. We carry out AFM, single channel electrical recording, and fluorescence imaging experiments. AFM images display 3D ion channel topography with shapes, morphologies, and dimensions consistent with the theoretical model. Electrical conductance measurements indicate multiple single channel conductances, suggesting that various K3 oligomer sizes can constitute the channel structure. Fluorescence measurements in kidney cells show channel-mediated cell calcium uptake. These results suggest that the beta(2)m-induced DRA can be mediated by ion channels formed by its K3 fragment. Because the beta-strand-turn-beta-strand motif appears to be a universal amyloid feature, its ability to form ion channels further suggests that the motif may play a generic role in toxicity.

Assigning glucose or galactose as the primary glycosidic sugar in 3‐O‐mono‐, di‐ and triglycosides of kaempferol using negative ion electrospray and serial mass spectrometry

Kaempferol 3-O-beta-glucopyranoside, kaempferol 3-O-beta-galactopyranoside and higher glycosides of these two flavonoids with alpha-rhamnose at C-2 and/or C-6 of the primary sugar were studied by negative ion electrospray ionisation and serial mass spectrometry in a three-dimensional (3D) ion trap mass spectrometer. Kaempferol 3-O-beta-glucopyranoside and kaempferol 3-O-alpha-rhamnopyranosyl(1-->6)-beta-glucopyranoside could be distinguished from their respective galactose analogues by differences in the ratio of the radical aglycone ion [Y(0) - H](*-) to the rearrangement aglycone ion Y(0) (-) following MS/MS of the deprotonated molecules. Kaempferol 3-O-rhamnopyranosyl(1-->2)-beta-glucopyranoside and kaempferol 3-O-alpha-rhamnopyranosyl(1-->2)[alpha-rhamnopyranosyl(1-->6)]-beta-glucopyranoside could be distinguished from their respective galactose analogues by differences in the product ion spectra of the [(M - H) - rhamnose](-) ion following serial mass spectrometry. In the triglycoside, it was deduced that this ion resulted from the loss of the rhamnose substituted at 2-OH of the primary sugar by observing that MS/MS of deprotonated kaempferol 3-O-beta-glucopyranosyl(1-->2)[alpha-rhamnopyranosyl(1-->6)]-beta-glucopyranoside showed the loss of glucose and not rhamnose. Thus the class of sugar (hexose, deoxyhexose, pentose) at C-2 and C-6 of the primary sugar can be determined. These observations aid the assignment of kaempferol 3-O-glycosides, having glucose or galactose as the primary glycosidic sugar, in LC/MS analyses of plant extracts, and this can be done with reference to only a few standards.

Three-dimensional velocity map imaging: Setup and resolution improvement compared to three-dimensional ion imaging

For many years the three-dimensional (3D) ion imaging technique has not benefited from the introduction of ion optics into the field of imaging in molecular dynamics. Thus, a lower resolution of kinetic energy as in comparable techniques making use of inhomogeneous electric fields was inevitable. This was basically due to the fact that a homogeneous electric field was needed in order to obtain the velocity component in the direction of the time of flight spectrometer axis. In our approach we superimpose an Einzel lens field with the homogeneous field. We use a simulation based technique to account for the distortion of the ion cloud caused by the inhomogeneous field. In order to demonstrate the gain in kinetic energy resolution compared to conventional 3D Ion Imaging, we use the spatial distribution of H(+) ions emerging from the photodissociation of HCl following the two photon excitation to the V (1)Sigma(+) state. So far a figure of merit of approximately four has been achieved, which means in absolute numbers Delta v/v = 0.022 compared to 0.086 at v approximately = 17,000 m/s. However, this is not a theoretical limit of the technique, but due to our rather short TOF spectrometer (15 cm). The photodissociation of HBr near 243 nm has been used to recognize and eliminate systematic deviations between the simulation and the experimentally observed distribution. The technique has also proven to be essential for the precise measurement of translationally cold distributions.

Studies of the g factors and the superhyperfine parameters for Ni3+ in the fluoroperovskites

The g factors and the ligand superhyperfine parameters A' and B' for Ni(3+) in KMgF(3), CsCaF(3) and RbCaF(3) are theoretically studied from the formulas of these parameters for a 3d(7) ion under octahedral environments in the weak field scheme. The unpaired spin densities for the fluorine 2s, 2p, and 2p, orbitals are quantitatively determined from the molecular orbital and configuration interaction coefficients based on the cluster approach. The calculated results show good agreement with the experimental data, based on only one adjustable parameter (i.e., the proportionality factor p related to the ligand s- and p-orbitals). The superhyperfine parameters for the axial and planar ligands in RbCaF(3):Ni(3+) are satisfactorily interpreted from the different impurity-ligand distances due to the elongation of the ligand octahedron during cubic-to-tetragonal phase transition.

An Ion Trap-Ion Mobility-Time of Flight Mass Spectrometer with Three Ion Sources for Ion/Ion Reactions

This instrument combines the capabilities of ion/ion reactions with ion mobility (IM) and time-of-flight (TOF) measurements for conformation studies and top-down analysis of large biomolecules. Ubiquitin ions from either of two electrospray ionization (ESI) sources are stored in a three dimensional (3D) ion trap (IT) and reacted with negative ions from atmospheric sampling glow discharge ionization (ASGDI). The proton transfer reaction products are then separated by IM and analyzed via a TOF mass analyzer. In this way, ubiquitin +7 ions are converted to lower charge states down to +1; the ions in lower charge states tend to be in compact conformations with cross sections down to approximately 880 A(2). The duration and magnitude of the ion ejection pulse on the IT exit and the entrance voltage on the IM drift tube can affect the measured distribution of conformers for ubiquitin +7 and +6. Alternatively, protein ions are fragmented by collision-induced dissociation (CID) in the IT, followed by ion/ion reactions to reduce the charge states of the CID product ions, thus simplifying assignment of charge states and fragments using the mobility-resolved tandem mass spectrum. Instrument characteristics and the use of a new ion trap controller and software modifications to control the entire instrument are described.

Studies of the spin-Hamiltonian parameters and the defect structure for Cu2+ at the rhombic Be2+ site of beryl crystal

The spin-Hamiltonian (SH) parameters (g factors g(i) and hyperfine structure constants A(i), where i = x, y, z) for Cu(2+) at the rhombic Be(2+) site of beryl (Be(3)Al(2)Si(6)O(18)) crystals are calculated from both the perturbation theory method (PTM) and the complete diagonalization (of energy matrix) method (CDM). The two methods are based on the cluster approach and so both the contribution to the SH parameters from the spin-orbit coupling parameters of central d(n) ion and that of ligand ion are included. The calculated results from the two theoretical methods are in reasonable agreement with the experimental values, suggesting that both methods are effective for the studies of SH parameters of 3d(9) ion in rhombic symmetry. The defect structural data (which are unlike the corresponding data in the host beryl crystal) of the rhombic Cu(2+) center in beryl are also acquired from the calculations. The results are discussed. (C) 2009 Elsevier B.V. All rights reserved.

Reconstruction of 3D ion beam micro-tomography data for applications in Cell Biology

The DISRA (Discrete Image Space Reconstruction Algorithm) reconstruction code, created by A. Sakellariou, was conceived for the ideal case of complete three-dimensional (3D) PIXET (Particle Induced X-ray Emission Tomography) data. This implies two major difficulties for biological samples: first, the long duration of such experiments and second, the subsequent damage that occurs on such fragile specimens. For this reason, the DISRA code was extended at CENBG in order to probe isolated PIXET slices, taking into account the sample structure and mass density provided by 3D STIMT (Scanning Transmission Ion Microscopy Tomography) in the volume of interest. This modified version was tested on a phantom sample and first results on human cancer cells are also presented.

Fragmentation Energy Index for Universalization of Fragmentation Energy in Ion Trap Mass Spectrometers for the Analysis of Chemical Weapon Convention Related Chemicals by Atmospheric Pressure Ionization-Tandem Mass Spectrometry Analysis

The use of mass spectra generated at 70 eV in electron ionization (EI) as a universal standard for EI has helped in the generation of searchable library databases and had a profound influence on the analytical applications of gas chromatography/mass spectrometry (GC/MS), similarly for liquid chromatography tandem mass spectrometry (LC-MS/MS), suggesting a novel method to normalize the collisional energy for the universalization of fragmentation energy for the analysis of Chemical Weapon Convention (CWC)-related chemicals by atmospheric pressure ionization-tandem mass spectrometry (API-MS(n)) using three-dimensional (3D) ion trap instruments. For normalizing fragmentation energy a "fragmentation energy index" (FEI) is proposed which is an arbitrary scale based on the fact of specific MS/MS fragmentation obtained at different collisional energies for the reference chemicals which are not CWC scheduled compounds. FEI 6 for the generation of an MS(n) library-searchable mass spectral database is recommended.

Negative hydrogen ion transport in RF-driven ion sources for ITER NBI

The injection of energetic neutral atoms is a major component of plasma heating in fusion experiments. In order to fulfill the requirements of the ITER neutral beam injection (NBI), a RF-driven ion source for negative ions has been developed at the MPI für Plasma Physik (IPP Garching). Negative hydrogen ions are generated on a converter surface by impinging neutral particles and positive ions under the influence of magnetic fields and the plasma sheath potential. A 3D negative ion trajectory calculation including a Monte Carlo description of reactions and collisions with plasma particles was used to calculate the total and spatially resolved extraction probabilities for realistic field topologies and geometries of the large scale extraction system LAG. The experimentally observed increase in extracted ion current by the use of chamfered aperture collars agrees with the results of the ion transport simulation. Profiles of the extraction probability on the converter show that most of the extracted negative ions are created in the vicinity of the plasma grid apertures. These areas of intensified extraction probability are influenced by the magnetic field configuration. The ion extraction probability is affected by the long ranging magnetic filter field. The short ranging electron deflection field, however, which is generated by magnets near the converter surface, does not significantly influence the extraction probability.

Electron capture dissociation in a linear radiofrequency‐free magnetic cell

Electron capture dissociation in a linear radiofrequency‐free magnetic cell

Computer Simulation of the Gap-Tripole Ion Trap with Linear Injection, 3D Ion Accumulation, and Versatile Packet Ejection

The behavior of a completely new ion trap is shown with SIMION 7.0 simulations. The simulated trap, which was a mix of a linear and a 3D trap, was made by axially setting two ion guides with a gap between them. Each guide consisted of three rods with three symmetrically delayed radio frequency (rf) voltages (tripole). The "injected" ions were linearly contained by pulsed potentials on the entrance and exit plates. Then the three-dimensional (3D) rf field in the gap, which was created by the tripole special rod arrangement, could trap the ions when the translational energy was dampened by collisions with low-pressure nitrogen. Because the injected ions were trapped in the small gap, the trapping cycle could be repeated many times before ion ejection, so a high concentrated ion cloud could be obtained. This trapping and accumulation methodology is not possible in most conventional multipole linear traps with even number of poles. Compared with quadrupole linear trap at the same rf amplitude, tripole lost more ions due to strong charge repulsion in the ion cloud. However, tripole could catch up the ions at higher voltage. Radial and axial mass-independent ejection of the ions localized in the tripole gap was very simple, compared with conventional linear ion traps that need extra and complicated electrodes for effective axial ejection.

A complex first-principles study of the L 2,3-edge XANES spectra and crystal field effects for divalent 3d ions in cubic ZnS

A detailed first-principles analysis of the L 2,3 X-ray absorption near edge structure (XANES) spectra, crystal field strength 10 Dq, covalent effects and molecular orbitals (MO) position for all divalent 3d ions from Sc 2+ to Cu 2+ in cubic ZnS is performed in the present paper. The calculations were done in the framework of the first-principles fully relativistic discrete variational multi-electron (DVME) based on numerical solution of the Dirac equation with the local density approximation. As a result of the performed calculations, the L 2,3 XANES spectra for all considered ions were calculated and assigned in terms of the electron configurations involved into the absorption transitions; fairly good agreement with available experimental data for Ti 2+, Mn 2+, Fe 2+, Co 2+ and Ni 2+ is demonstrated. Experimental XANES spectra for Sc 2+, V 2+, Cr 2+, Cu 2+ not reported previously were also calculated for the sake of completeness of the present study to enable a systematic analysis of all calculated results for the whole series considered. It was shown that the L 3 and L 2 bands shift to the higher energies on increasing a 3d ion atomic number. In addition, the separation between the L 3 and L 2 bands, the crystal field strength 10 Dq and mixture between the 3d ion and sulfur wave functions increase along the considered series, from Sc 2+ to Cu 2+. On the other hand, all orbitals of the 3d ions systematically lower down in the same direction. The above formulated trends were confirmed by the experimental data on the crystal field splittings and nephelauxetic effect.

Multiple ion/ion reactions in the 3D ion trap: Selective reagent anion production for ETD and PTR from a single compound

Electron transfer dissociation (ETD) is dedicated for the sequence analysis of larger peptides and proteins. It is particularly suited for the identification of post-translational modifications (PTMs), as weakly bonded PTMs like phosphorylation or glycosilation survive the electron-induced fragmentation of the backbone of the amino acid chain. A drawback however is that ETD MS/MS-data of proteins are typically highly complex because a large number of multiply charged fragment ions are obtained. This complexity of the ETD MS/MS-data is significantly reduced when the initial electron-induced fragmentation is followed by a subsequent proton transfer reaction (PTR) to reduce the charge states of the multiple charge fragments. Traditionally ETD and PTR are accomplished using different reagent ions generated from different neutral compounds. Here we show that the formation of reagent anions dedicated for either ETD or PTR can be accomplished from only one neutral compound. By altering the voltage of the negative chemical ionization source (nCI-source) either the odd electron anion (appropriate for ETD) or the even electron anion (appropriate for PTR) is extracted. The PTR-reagent as well as the ETD-reagent are exclusively generated at an appropriate ionization chamber voltage and no further mass selection of the reagent anion is needed. The voltage of the ionization chamber can be switched within milliseconds allowing applications for rapid sequential ion/ion reactions. One of the more interesting sequential ion/ion reactions is the combination of ETD followed by PTR, which make top–down sequencing of intact proteins possible for ion trap instruments.

Inductively coupled plasma mass spectrometry, coincidence laser spectroscopy (ICP-MS-CLS), simulation of the transmission efficiency of a 3D quadrupole ion trap for cooling energetic ions from the ICP prior to optical detection

A fundamental requirement of ICP-MS-CLS is a post mass separation ion beam with an energy spread of less than ∼0.2 eV to enable efficient pumping of fluorescent lines with a narrow band (Δν ∼ 100 kHz) laser for the optical detection step. The role of a 3D quadrupole ion trap for ion beam cooling, as an accessory for a new generation of ICP-MS-CLS (inductively coupled plasma mass spectrometry, coincidence laser spectroscopy) (B. L. Sharp, P. S. Goodall, L. M. Ignjatovic and H. Teng, J. Anal. At. Spectrom., 2007, 22, 1447) instrument, was investigated by means of numerical simulation. Whereas in-trap ion cooling is well established, it was found that extraction of cooled ions from the trap introduced additional broadening and a loss of transmission efficiency. Modelling was based on a beam of 20 eV mean energy with a spread of 3 eV which represents a worst case scenario for the ions derived from an ICP source. The efficiency of the cooling process (trapping + extraction), as well as the energy distributions of ions exiting the trap, were calculated and compared for several methods of extraction. Trapping efficiencies of ∼25% were obtained at buffer gas pressures up to 10 mTorr. The addition of virtual reflectrons to the trap resulted in an improvement in the energy distribution of the trapped ions by lowering the wings of the distribution, but did not significantly improve the efficiency. Zero field, rf field only, quadrupolar field and homogeneous field ion extraction were investigated to recover ions from the trap, and of these quadrupolar extraction was best. However, extraction efficiency and ion energy distribution were inversely related so that quadrupolar extraction at Uq = 10 V yielded an exit ion energy distribution of 0.5 eV half width, compared with a trapped width of 0.03 eV, but with only 10% transmission efficiency. Thus, it was demonstrated that a 3D trap can be used to cool energetic ions for post-trap mass or spectroscopic examination, but the low efficiency makes it unsuitable for use with ICP-MS-CLS.

The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools.

Tandem mass spectrometry (MS/MS) is frequently used in the identification of peptides and proteins. Typical proteomic experiments rely on algorithms such as SEQUEST and MASCOT to compare thousands of tandem mass spectra against the theoretical fragment ion spectra of peptides in a database. The probabilities that these spectrum-to-sequence assignments are correct can be determined by statistical software such as PeptideProphet or through estimations based on reverse or decoy databases. However, many of the software applications that assign probabilities for MS/MS spectra to sequence matches were developed using training data sets from 3D ion-trap mass spectrometers. Given the variety of types of mass spectrometers that have become commercially available over the last 5 years, we sought to generate a data set of reference data covering multiple instrumentation platforms to facilitate both the refinement of existing computational approaches and the development of novel software tools. We analyzed the proteolytic peptides in a mixture of tryptic digests of 18 proteins, named the "ISB standard protein mix", using 8 different mass spectrometers. These include linear and 3D ion traps, two quadrupole time-of-flight platforms (qq-TOF), and two MALDI-TOF-TOF platforms. The resulting data set, which has been named the Standard Protein Mix Database, consists of over 1.1 million spectra in 150+ replicate runs on the mass spectrometers. The data were inspected for quality of separation and searched using SEQUEST. All data, including the native raw instrument and mzXML formats and the PeptideProphet validated peptide assignments, are available at http://regis-web.systemsbiology.net/PublicDatasets/.