Initial implementation of external accumulation liquid chromatography/electrospray ionization Fourier transform ion cyclotron resonance with automated gain control

HUMOS: How to Understand My Orbitrap Spectrum?-An Interactive Web-Based Tool to Teach the Basics of Mass-Spectrometry-Based Proteomics

The Orbitrap mass analyzer can provide high mass accuracy and throughput, which has significantly improved proteome research and made this type of instrumentation one of the most frequently applied in proteomics. The efficient use of Orbitrap mass spectrometers requires training. Students in the field of proteomics can benefit from a deeper understanding of the Orbitrap technology to comprehend mass spectral interpretation, troubleshooting, and judgment of experimental settings. Unfortunately, the cost of high-end mass spectrometers limits the implementation of this type of equipment in educational laboratories. Guided by these concerns, we developed an eLearning web application called HUMOS aimed to help teach Orbitrap mass spectrometry. Although a typical proteomics experiment includes the use of several different technologies, such as liquid chromatography, mass spectrometry, and bioinformatics, the learning objectives of HUMOS are focused on mass spectrometry. HUMOS models a mass spectrum of a peptide mixture, allowing us to investigate the influence of mass spectral acquisition parameters. By changing the parameters and observing the differences, students can learn more about the mass spectral resolution, duty cycle, throughput of the analysis, ion accumulation, and spectral dynamic range and get familiar with advanced spectral acquisition methods, such as BoxCar. HUMOS is an open-source software published under the Apache license; the live installation is available at http://humos.bmb.sdu.dk.

Mass recalibration of FT-ICR mass spectrometry imaging data using the average frequency shift of ambient ions

Achieving and maintaining high mass measurement accuracy (MMA) throughout a mass spectrometry imaging (MSI) experiment is vital to the identification of the observed ions. However, when using FTMS instruments, fluctuations in the total ion abundance at each pixel due to inherent biological variation in the tissue section can introduce space charge effects that systematically shift the observed mass. Herein we apply a recalibration based on the observed cyclotron frequency shift of ions found in the ambient laboratory environment, polydimethylcyclosiloxanes (PDMS). This calibration method is capable of achieving part per billion (ppb) mass accuracy with relatively high precision for an infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) MSI dataset. Comparisons with previously published mass calibration approaches are also presented.

The application of quantification techniques in proteomics for biomedical research

The systematic analysis of biological processes requires an understanding of the quantitative expression patterns of proteins, their interacting partners and their subcellular localization. This information was formerly difficult to accrue as the relative quantification of proteins relied on antibody-based methods and other approaches with low throughput. The advent of soft ionization techniques in mass spectrometry plus advances in separation technologies has aligned protein systems biology with messenger RNA, DNA, and microarray technologies to provide data on systems as opposed to singular protein entities. Another aspect of quantitative proteomics that increases its importance for the coming few years is the significant technical developments underway both for high pressure liquid chromatography and mass spectrum devices. Hence, robustness, reproducibility and mass accuracy are still improving with every new generation of instruments. Nonetheless, the methods employed require validation and comparison to design fit for purpose experiments in advanced protein analyses. This review considers the newly developed systematic protein investigation methods and their value from the standpoint that relative or absolute protein quantification is required de rigueur in biomedical research.

Current challenges in software solutions for mass spectrometry-based quantitative proteomics

Mass spectrometry-based proteomics has evolved as a high-throughput research field over the past decade. Significant advances in instrumentation, and the ability to produce huge volumes of data, have emphasized the need for adequate data analysis tools, which are nowadays often considered the main bottleneck for proteomics development. This review highlights important issues that directly impact the effectiveness of proteomic quantitation and educates software developers and end-users on available computational solutions to correct for the occurrence of these factors. Potential sources of errors specific for stable isotope-based methods or label-free approaches are explicitly outlined. The overall aim focuses on a generic proteomic workflow.

Current challenges in software solutions for mass spectrometry-based quantitative proteomics

Mass spectrometry-based proteomics has evolved as a high-throughput research field over the past decade. Significant advances in instrumentation, and the ability to produce huge volumes of data, have emphasized the need for adequate data analysis tools, which are nowadays often considered the main bottleneck for proteomics development. This review highlights important issues that directly impact the effectiveness of proteomic quantitation and educates software developers and end-users on available computational solutions to correct for the occurrence of these factors. Potential sources of errors specific for stable isotope-based methods or label-free approaches are explicitly outlined. The overall aim focuses on a generic proteomic workflow.

Expanding the data depth for the analysis of complex crude oil samples by Fourier transform ion cyclotron resonance mass spectrometry using the spectral stitching method

RATIONALE

Crude oil samples are very complex mixtures of compounds and only Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provides the ultra-high mass resolution necessary to resolve them. However, FT-ICR MS operates best when only a small amount of ions is present during each transient. This cannot be accomplished with crude oil samples without chromatography because more than 50,000 compounds can be present, with the result that species with low intensity may be suppressed and are detected either with low intensity or not at all.

METHODS

Spectral stitching was used to overcome the problems associated with suppression effects, where only short mass windows of 30 amu were scanned to reduce the amount of ions present in each individual scan. Afterwards, all the scans were co-added and the subsequent spectrum was used to calculate individual class distributions.

RESULTS

A heavy crude oil sample was analyzed using spectral stitching and this approach was compared with analysis using a broadband-method in order to illustrate the enhancement in depth of information. Although both methods took the same analysis time a seven-times increase in the number of detected species was observed when the spectral stitching method was used compared with the commonly applied broadband method in a 900 amu mass window.

CONCLUSIONS

Spectral stitching using smaller selected ion monitoring (SIM) windows for complex crude oil samples allows better class distribution to be obtained because less ion suppression is observed.

An external matrix-assisted laser desorption ionization source for flexible FT-ICR Mass spectrometry imaging with internal calibration on adjacent samples

We describe the construction and application of a new MALDI source for FT-ICR mass spectrometry imaging. The source includes a translational X-Y positioning stage with a 10×10 cm range of motion for analysis of large sample areas, a quadrupole for mass selection, and an external octopole ion trap with electrodes for the application of an axial potential gradient for controlled ion ejection. An off-line LC MALDI MS/MS run demonstrates the utility of the new source for data- and position-dependent experiments. A FT-ICR MS imaging experiment of a coronal rat brain section yields ∼200 unique peaks from m/z 400-1100 with corresponding mass-selected images. Mass spectra from every pixel are internally calibrated with respect to polymer calibrants collected from an adjacent slide.

Fibrin-mediated lentivirus gene transfer: implications for lentivirus microarrays

We employed fibrin hydrogel as a bioactive matrix for lentivirus mediated gene transfer. Fibrin-mediated gene transfer was highly efficient and exhibited strong dependence on fibrinogen concentration. Efficient gene transfer was achieved with fibrinogen concentration between 3.75 and 7.5mg/ml. Lower fibrinogen concentrations resulted in diffusion of virus out of the gel while higher concentrations led to ineffective fibrin degradation by target cells. Addition of fibrinolytic inhibitors decreased gene transfer in a dose-dependent manner suggesting that fibrin degradation by target cells may be necessary for successful gene delivery. Under these conditions transduction may be limited only to cells interacting with the matrix thereby providing a method for spatially-localized gene delivery. Indeed, when lentivirus-containing fibrin microgels were spotted in an array format gene transfer was confined to virus-containing fibrin spots with minimal cross-contamination between neighboring sites. Collectively, our data suggest that fibrin may provide an effective matrix for spatially-localized gene delivery with potential applications in high-throughput lentiviral microarrays and in regenerative medicine.

Sub-part-per-million precursor and product mass accuracy for high-throughput proteomics on an electron transfer dissociation-enabled orbitrap mass spectrometer

We demonstrate a new approach for internal mass calibration on an electron transfer dissociation-enabled linear ion trap-orbitrap hybrid mass spectrometer. Fluoranthene cations, a byproduct of the reaction used for generation of electron transfer dissociation reagent anions, are co-injected with the analyte cations in all orbitrap mass analysis events. The fluoranthene cations serve as a robust internal calibrant with minimal impact on scan time (<20 ms) or spectral quality. Following external mass calibration, 60 replicate LC-MS/MS runs of a complex peptide mixture were collected over the course of approximately 136 h (almost 6 days). Using only standard external mass calibration, the mass accuracy for a typical analysis was -3.31 +/- 0.93 ppm (sigma) for precursors and -2.32 +/- 0.89 ppm for products. After application of internal recalibration, mass accuracy improved to +0.77 +/- 0.71 ppm for precursors and +0.17 +/- 0.67 ppm for products. When all 60 replicate runs were analyzed together without internal mass recalibration, the mass accuracy was -1.23 +/- 1.54 ppm for precursors and -0.18 +/- 1.42 ppm for products, nearly a 2-fold drop in precision relative to an individual run. After internal mass recalibration, this improved to +0.80 +/- 0.70 ppm for precursors and +0.16 +/- 0.67 ppm for products, roughly equivalent to that obtained in a single run, demonstrating a near complete elimination of mass calibration drift.

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.

Data Self-Recalibration and Mixture Mass Fingerprint Searching (DASER-MMF) to enhance protein identification within complex mixtures

A novel algorithm based on Data Self-Recalibration and a subsequent Mixture Mass Fingerprint search (DASER-MMF) has been developed to improve the performance of protein identification from online 1D and 2D-LC-MS/MS experiments conducted on high-resolution mass spectrometers. Recalibration of 40% to 75% of the MS spectra in a human serum dataset is demonstrated with average errors of 0.3 +/- 0.3 ppm, regardless of the original calibration quality. With simple protein mixtures, the MMF search identifies new proteins not found in the MS/MS based search and increases the sequence coverage for identified proteins by six times. The high mass accuracy allows proteins to be identified with as little as three peptide mass hits. When applied to very complex samples, the MMF search shows less dramatic performance improvements. However, refinements such as additional discriminating factors utilized within the search space provide significant gains in protein identification ability and indicate that further enhancements are possible in this realm.

Quantitative mass spectrometry in proteomics: a critical review

The quantification of differences between two or more physiological states of a biological system is among the most important but also most challenging technical tasks in proteomics. In addition to the classical methods of differential protein gel or blot staining by dyes and fluorophores, mass-spectrometry-based quantification methods have gained increasing popularity over the past five years. Most of these methods employ differential stable isotope labeling to create a specific mass tag that can be recognized by a mass spectrometer and at the same time provide the basis for quantification. These mass tags can be introduced into proteins or peptides (i) metabolically, (ii) by chemical means, (iii) enzymatically, or (iv) provided by spiked synthetic peptide standards. In contrast, label-free quantification approaches aim to correlate the mass spectrometric signal of intact proteolytic peptides or the number of peptide sequencing events with the relative or absolute protein quantity directly. In this review, we critically examine the more commonly used quantitative mass spectrometry methods for their individual merits and discuss challenges in arriving at meaningful interpretations of quantitative proteomic data.

Advances in proteomics data analysis and display using an accurate mass and time tag approach

Proteomics has recently demonstrated utility for increasing the understanding of cellular processes on the molecular level as a component of systems biology approaches and for identifying potential biomarkers of various disease states. The large amount of data generated by utilizing high efficiency (e.g., chromatographic) separations coupled with high mass accuracy mass spectrometry for high-throughput proteomics analyses presents challenges related to data processing, analysis, and display. This review focuses on recent advances in nanoLC-FTICR-MS-based proteomics approaches and the accompanying data processing tools that have been developed to display and interpret the large volumes of data being produced.

Enhanced mixture analysis of poly(ethylene glycol) using high-field asymmetric waveform ion mobility spectrometry combined with fourier transform ion cyclotron resonance mass spectrometry

The combination of high-field asymmetric waveform ion mobility spectrometry (FAIMS) with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) makes possible lower detection limits, increased sensitivity, and increased dynamic range in the analysis of poly(ethylene glycol) (PEG) samples of low molecular weight. The signal gain obtained using FAIMS depends on ion identity, with a range between 1.8x and 14x obtained for various molecular ions of PEG 600. A 1.7-fold reduction in noise is obtained using FAIMS due to the elimination of chemical noise. The improved detection performance is predominantly due to a reduction in adverse Coulomb effects as a result of ions being selectively introduced into the mass spectrometer. The high ion transmission obtained using FAIMS combined with the high sensitivity of FTICR-MS detection make possible separation of multiple gas-phase conformers of PEG molecular cations that have low abundance (less than 0.2% relative abundance) and that have not been detected previously. Mixed dications of PEG that have the same nominal mass but differ by the number polymer subunits (m/Delta m up to 25,000) can be separately introduced into the mass spectrometer using FAIMS. Interactions of the carrier gas with the metal ions that are attached to the PEG molecules appear to be the most significant factor in these FAIMS separations.

Coaxial multi-electrode cell ('O-trap') for high-sensitivity detection at a multiple frequency in Fourier transform ion cyclotron resonance mass spectrometry: main design and modeling results

Separation of the functions of ion excitation and detection between different cell compartments allows for implementation of excitation and detection techniques unattainable in a single compartment of the conventional ion cyclotron resonance (ICR) cell. In particular, multi-electrode detection at a multiple of the main cyclotron frequency can be utilized without the loss of sensitivity and other negative effects. The new O-trap designed exclusively for ion detection adds an additional, internal coaxial cylinder around which ions with excited cyclotron orbits rotate. Comparison of simulated performance characteristics of the new O-trap with those of the same-size conventional cylindrical cell shows that the O-trap can provide higher sensitivity and ion capacity. Multiplexing of the O-traps can further increase the analysis speed. Future efforts will be aimed at building and testing experimentally the coaxial O-trap, including optimization of the method of ion transfer between the compartments of the cell.

A new hybrid electrospray Fourier transform mass spectrometer: design and performance characteristics

A new hybrid electrospray quadrupole Fourier transform mass spectrometry (FTMS) instrument design is shown and characterized. This instrument involves coupling an electrospray source and mass-resolving quadrupole, ion accumulation, and collision cell linear ion trap system developed by MDS Sciex with a home-built ion guide and ion cyclotron resonance (ICR) cell. The iterative progression of this design is shown. The final design involves a set of hexapole ion guides to transfer the ions from the accumulation/collision trap through the magnetic field gradient and into the cell. These hexapole ion guides are separated by a thin gate valve and two conduction limits to maintain the required <10(-9) mbar vacuum for FTICR. Low-attomole detection limits for a pure peptide are shown, 220 000 resolving power in broadband mode and 820 000 resolving power in narrow-band mode are demonstrated, and mass accuracy in the <2 ppm range is routinely available provided the signal is abundant, cleanly resolved, and internally calibrated. This instrument design provides high experimental flexibility, allowing Q2 CAD, SORI-CAD, IRMPD, and ECD experiments with selected ion accumulation as well as experiments such as nozzle skimmer dissociation. Initial top-down mass spectrometry experiments on a protein is shown using ECD.

Improved mass accuracy for tandem mass spectrometry

With the emergence of top-down proteomics, the ability to achieve high mass measurement accuracy on tandem MS/MS data will be beneficial for protein identification and characterization. (FT-ICR) Fourier transform ion cyclotron resonance mass spectrometers are the ideal instruments to perform these experiments with their ability to provide high resolution and mass accuracy. A major limitation to mass measurement accuracy in FT-ICR instruments arises from the occurrence of space charge effects. These space charge effects shift the cyclotron frequency of the ions, which compromises the mass measurement accuracy. While several methods have been developed that correct these space charge effects, they have limitations when applied to MS/MS experiments. It has already been shown that additional information inherent in electrospray spectra can be used for improved mass measurement accuracy with the use of a computer algorithm called DeCAL (deconvolution of Coulombic affected linearity). This paper highlights a new application of the strategy for improved mass accuracy in tandem mass analysis. The results show a significant improvement in mass measurement accuracy on complex electron capture dissociation spectra of proteins. We also demonstrate how the improvement in mass accuracy can increase the confidence in protein identification from the fragment masses of proteins acquired in MS/MS experiments.

Proteomics by FTICR mass spectrometry: top down and bottom up

This review provides a broad overview of recent Fourier transform ion cyclotron resonance (FTICR) applications and technological developments relevant to the field of proteomics. Both the "bottom up" (peptide level) and "top down" (intact protein level) approaches are discussed and illustrated with examples. "Bottom up" topics include peptide fragmentation, the accurate mass and time (AMT) tag approach and dynamic range extension technology, aspects of quantitative proteomics measurements, post-translational modifications, and developments in FTICR operation software focused on peptide and protein identification. Topics related to the "top down" approach include various aspects of high mass measurements, protein tandem mass spectrometry, methods for the study of protein conformations, and protein complexes as well as advanced technologies that may become of practical utility in the coming years. Finally, early examples of the integration of both FTICR approaches to biomedical proteomics applications are presented, along with an outlook for future directions.

Automatic Gain Control in Mass Spectrometry using a Jet Disrupter Electrode in an Electrodynamic Ion Funnel

We report on the use of a jet disrupter electrode in an electrodynamic ion funnel as an electronic valve to regulate the intensity of the ion beam transmitted through the interface of a mass spectrometer in order to perform automatic gain control (AGC). The ion flux is determined by either directly detecting the ion current on the conductance limiting orifice of the ion funnel or using a short mass spectrometry acquisition. Based upon the ion flux intensity, the voltage of the jet disrupter is adjusted to alter the transmission efficiency of the ion funnel to provide a desired ion population to the mass analyzer. Ion beam regulation by an ion funnel is shown to provide control to within a few percent of a targeted ion intensity or abundance. The utility of ion funnel AGC was evaluated using a protein tryptic digest analyzed with liquid chromatography Fourier transform ion cyclotron resonance (LC-FTICR) mass spectrometry. The ion population in the ICR cell was accurately controlled to selected levels, which improved data quality and provided better mass measurement accuracy.

Linear ion traps in mass spectrometry

Linear ion traps are finding new applications in many areas of mass spectrometry. In a linear ion trap, ions are confined radially by a two-dimensional (2D) radio frequency (RF) field, and axially by stopping potentials applied to end electrodes. This review focuses on linear ion trap instrumentation. Potentials and ion motion in linear multipole fields and methods of ion trapping, cooling, excitation, and isolation are described. This is followed by a description of various mass discrimination effects that have been reported with linear ion traps. Linear ion traps combined in various ways with three-dimensional (3D) traps, time-of-flight (TOF) mass analyzers, and Fourier transform ion cyclotron resonance mass spectrometers are then given. Linear ion traps can be used as stand alone mass analyzers, and their use for mass analysis by Fourier transforming image currents, by mass selective radial ejection, and by mass selective axial ejection are reviewed.

Effect of post-excitation radius on ion abundance, mass measurement accuracy, and isotopic distributions in Fourier transform ion cyclotron resonance mass spectrometry

We report an evaluation of a modern Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) instrument to determine the general trend of post-excitation radius on total ion abundance, mass measurement accuracy, and isotopic distributions for internally calibrated mass spectra. The optimum post-excitation radius was determined using total ion abundance, mass measurement accuracy (MMA), and isotope ratios. However, despite the utility of internal calibration for achieving ultimate MMA, the internal calibrant ions were insufficient for compensating for sub-optimum ICR cell conditions. The findings presented herein underscore the importance of determining the optimal post-excitation radius in FT-ICR-MS to achieve high ion abundance (low limits of detection), high MMA, and valid isotopic distributions.

Mass spectrometric methods for the determination of flavonoids in biological samples

There is an ever-increasing interest in the biological effects of the bioflavonoids, members of the large group of plant polyphenols. Because of the aromatic character of these compounds, they have been analyzed by several chromatographic methods. In the case of high-performance liquid chromatography, they are readily detected by their ultraviolet absorbance or electrochemical properties. More evidence that the bioflavonoids undergo extensive metabolism during uptake from the gut and distribution around the body and in specific tissues is accumulating. In addition, free radical products at sites of inflammatory processes react with bioflavonoids and their metabolites, generating important new compounds of as yet unknown properties. For these reasons, careful examination of the chemical nature of bioflavonoids and their products in biological systems is absolutely required. Combination of mass spectrometry with the various chromatographic methods has proved to be highly successful in this regard. This review of the literature on the bioflavonoids is focused on the methods that are currently available for their qualitative and quantitative analysis by mass spectrometry and covers the period 2001-2003. Emphasis is placed on the description and value of existing methods, followed by an examination of emerging technologies.

FTICR mass spectrometry for qualitative and quantitative bioanalyses

Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is playing an increasing role in the characterization of cellular systems owing to its capabilities for providing higher confidence of identification, increased dynamic range and sensitivity unmatched by other MS platforms. Particularly in proteomics, where global and quantitative approaches are essential, the attributes of FTICR-MS are poised to make significant contributions. Recent advances in the field that have particular importance for proteomic applications include the use of high-performance micro-capillary column separation techniques coupled to FTICR, as well as methods that improve protein identification, sensitivity, dynamic range and throughput.

Ultrasensitive and quantitative analyses from combined separations-mass spectrometry for the characterization of proteomes

This article describes developments in fundamental and applied aspects of separations, electrospray ionization phenomena, and mass spectrometric instrumentation that are interrelated and important for making more effective and quantitative measurements, particularly for proteomics applications. The basis for better quantitation and ultrahigh sensitivity is highlighted for high-resolution capillary liquid chromatography separations that provide low nanoliter per minute flow rates to an electrospray ionization interface. The increased dynamic range of measurements and low zeptomole regime detection limits obtainable open new avenues for biological research.

Automated Gain Control and Internal Calibration with External Ion Accumulation Capillary Liquid Chromatography-Electrospray Ionization-Fourier Transform Ion Cyclotron Resonance

When combined with capillary LC separations, electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) has demonstrated capabilities for advanced characterization of proteomes based upon analyses of proteolytic digests. Incorporation of external (to the ICR cell) multipole devices with FTICR for ion selection and ion accumulation has enhanced the dynamic range, sensitivity, and duty cycle of measurements. However, the highly variable ion production rate from an LC separation can result in "overfilling" of the external trap during the elution of major peaks and result in m/z discrimination and fragmentation of peptide ions. Excessive space charge trapped in the ICR cell also causes significant shifts in the detected ion cyclotron frequencies, reducing the achievable mass measurement accuracy (MMA) and making protein identification less effective. To eliminate m/z discrimination in the external ion trap, further increase duty cycle, and improve MMA, we have developed the capability for data-dependent adjustment of ion accumulation times in the course of an LC separation, referred to as automated gain control (AGC). This development has been implemented in combination with low kinetic energy gated ion trapping and internal calibration using a dual-channel electrodynamic ion funnel. The overall system was initially evaluated in the analysis of a tryptic digest of bovine serum albumin. In conjunction with internal calibration, the capillary LC-ESI-AGC-FTICR instrumentation provided a approximately 10-fold increase in the number of identified tryptic peptides compared to that obtained using a fixed ion accumulation time and external calibration methods.

Nano-high-performance liquid chromatography in combination with nano-electrospray ionization Fourier transform ion-cyclotron resonance mass spectrometry for proteome analysis

Fourier transform ion-cyclotron resonance (FTICR) mass spectrometry offers several advantages for the analysis of biological samples, including excellent mass resolution, ultra-high mass measurement accuracy, high sensitivity, and wide mass range. We report the application of a nano-HPLC system coupled to an FTICR mass spectrometer equipped with nanoelectrospray source (nano-HPLC/nano-ESI-FTICRMS) for proteome analysis. Protein identification in proteomics is usually conducted by accurately determining peptide masses resulting from enzymatic protein digests and comparing them with theoretically digested protein sequences from databases. A tryptic in-solution digest of bovine serum albumin was used to optimize experimental conditions and data processing. Spots from Coomassie Blue and silver-stained two-dimensional (2D) gels of human thyroid tissue were excised, in-gel digested with trypsin, and subsequently analyzed by nano-HPLC/nano-ESI-FTICRMS. Additionally, we analyzed 1D-gel bands of membrane preparations of COS-6 cells from African green monkey kidney as an example of more complex protein mixtures. Nano-HPLC was performed using 1-mm reverse-phase C-18 columns for pre-concentration of the samples and reverse-phase C-18 capillary columns for separation, applying water/acetonitrile gradient elution conditions at flow rates of 200 nL/min. Mass measurement accuracies smaller than 3 ppm were routinely obtained. Different methods for processing the raw data were compared in order to identify a maximum number of peptides with the highest possible degree of automation. Parallel identification of proteins from complex mixtures down to low-femtomole levels makes nano-HPLC/nano-ESI-FTICRMS an attractive approach for proteome analysis.