Attomole biomolecule mass analysis by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance

Multicomponent molecular memory

Multicomponent reactions enable the synthesis of large molecular libraries from relatively few inputs. This scalability has led to the broad adoption of these reactions by the pharmaceutical industry. Here, we employ the four-component Ugi reaction to demonstrate that multicomponent reactions can provide a basis for large-scale molecular data storage. Using this combinatorial chemistry we encode more than 1.8 million bits of art historical images, including a Cubist drawing by Picasso. Digital data is written using robotically synthesized libraries of Ugi products, and the files are read back using mass spectrometry. We combine sparse mixture mapping with supervised learning to achieve bit error rates as low as 0.11% for single reads, without library purification. In addition to improved scaling of non-biological molecular data storage, these demonstrations offer an information-centric perspective on the high-throughput synthesis and screening of small-molecule libraries.

Small non-polymeric molecules have tremendous structural diversity that can be used to represent information. Here the authors encode data in synthesized libraries of Ugi products.

Comparative evaluation of the extraction and analysis of urinary phospholipids and lysophospholipids using MALDI-TOF/MS

Lipids, particularly phospholipids (PLs) and lysophospholipids (LPLs), are attracting increasing scientific interest for their biological functions in cells and their potential as disease biomarkers for Alzheimer's disease and several types of cancer. Urinary PLs and LPLs could be ideal clinical biomarkers, because urine can be collected easily and noninvasively. However, due to their very low concentrations in urine compared with the relatively large quantity of contaminants in this matrix, efficient extraction and sensitive detection are required for analyzing urinary PLs and LPLs. In this study, various methods for analyzing PLs and LPLs in urine were compared and optimized from a clinical perspective. An optimized lipid extraction method and a matrix for matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) were established using two external ionization standards and an internal standard mix containing 13 human urinary lipids. 9-Aminoacridine (9-AA) was a useful and effective matrix for the MALDI-TOF/MS analysis of all the internal standard lipids in both positive and negative ion modes. However, it was necessary to determine the proportional lipid concentrations from the balance between the extracted lipid and the matrix. The extraction efficiency and reproducibility of the acidified Bligh and Dyer method were excellent for both positively and negatively charged lipids. Analysis of small volumes of urine was the most efficient with the 9-AA MALDI matrix at concentrations of or below 5 mM. The combined analytical procedures allowed rapid and comprehensive screening of low concentrations of PLs and LPLs in clinical samples.

Sustainable Nanosystem Development for Mass Spectrometry

Nowadays, considerable efforts are invested into development of sustainable nanosystems as front end technology for either Electrospray Ionization (ESI) or Matrix-Assisted Laser Desorption/Ionization (MALDI) mass spectrometry (MS). Since their first introduction in MS, nanofluidics demonstrated a high potential to discover novel biopolymer species. These systems confirmed the unique ability to offer structural elucidation of molecular species, which often represent valuable biomarkers of severe diseases. In view of these major advantages of nanofluidics-MS, this chapter reviews the strategies, which allowed a successful development of nanotechnology for MS and the applications in biological and clinical research. The first part will be dedicated to the principles and technical developments of advanced nanosystems for electrospray and MALDI MS. The second part will highlight the most important applications in clinical proteomics and glycomics. Finally, this chapter will emphasize that advanced nanosystems-MS has real perspectives to become a routine method for early diagnosis of severe pathologies.

Porous silicon mass spectrometry as an alternative confirmatory assay for compliance testing of methadone

Porous silicon based surface-assisted laser desorption ionization mass spectrometry (pSi SALDI-MS) is an analytical technique well suited for high throughput analysis of low molecular weight compounds from biological samples. A potential application of this technology is the compliance monitoring of opioid addiction programmes, where methadone is used as a pharmacological treatment for drugs such as heroin. Here, we present the detection and quantification of methadone and 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP) from water and clinical samples (saliva, urine, and plasma) from opioid dependent participants using pSi SALDI-MS. A one-step solvent phase extraction using chloroform was developed for the detection of methadone from clinical samples for analysis by pSi SALDI-MS. Liquid chromatography-mass spectrometry (LC-MS) was used as a comparative technique for the quantification of methadone from clinical saliva and plasma samples. In all cases, we obtained a good correlation of pSi SALDI-MS and LC-MS results, suggesting that pSi SALDI-MS may be an alternative procedure for high-throughput screening and quantification for application in opioid compliance testing. Copyright © 2016 John Wiley & Sons, Ltd.

Direct detection of illicit drugs from biological fluids by desorption/ionization mass spectrometry with nanoporous silicon microparticles

Surface assisted laser desorption/ionization mass spectrometry (SALDI-MS) with porous silicon microparticles was used for the all-in-one extraction and detection of illicit drugs from saliva, urine and plasma.

Multistage accurate mass spectrometry: a "basket in a basket" approach for structure elucidation and its application to a compound from combinatorial synthesis

A "basket in a basket" method based on a multistage accurate mass spectrometric (MAMS) technique was developed and demonstrated by obtaining a unique elemental composition of a compound (with a molecular weight of 517) from combinatorial synthesis. The accurate masses for the parent and the fragment ions were obtained with up to five stages of MAMS using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). This approach requires only input of elements used in the synthetic processes and some constraints about unusual light elements, such as fluorine, while the compositions of the parent ions and their fragments are obtained for structure elucidation. Conversely, accuracy of better than 0.02 ppm (assuming elements C, H, N, O, S, and F are involved) would be required in order to define a unique composition for the same mass using a direct accurate mass measurement because the number of possible elemental compositions increases sharply as the mass increases. Similarly, due to the uncertainty in determining elemental compositions of fragments and complexity of possible internal fragmentation, tandem mass spectrometry may not provide enough information for structure elucidation of unknown compounds, especially of the organic molecules in the mass range of 300-1000 Da, typically encountered in combinatorial lead generation. The application of MAMS to combinatorial drug discovery is particularly advantageous since the built-in chemical information from the synthesis can be used as constraints. The implementation of a nanoelectrospray ionization technique makes this approach practical for characterization of small quantities of compounds typically available from lead generation processes.

Development of nanomaterials for SALDI-MS analysis in forensics

Within the last decade, the escalation of research output in the field of nanotechnology has spurred the development of new nanomaterials for use as assisting agents in surface assisted laser desorption ionization mass spectrometry (SALDI-MS). Specifically modified nanomaterials, coupled with mass spectrometry, have improved the detection sensitivity, specificity, flexibility and reproducibility of SALDI-MS analysis. The technological advancement of LDI-MS has in turn, propelled the use of the analytical technique in the field of forensics. In this report, the various roles and applications of metal-, silicon- and carbon-based nanostructured materials as SALDI matrices in the analysis of forensic samples are described. The advantages of SALDI-MS as an analytical tool for forensic sample analysis are also discussed.

Miniaturizing sample spots for matrix-assisted laser desorption/ionization mass spectrometry

The trend of miniaturization in bioanalytical chemistry is shifting from technical development to practical application. In matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), progress in miniaturizing sample spots has been driven by the needs to increase sensitivity and speed, to interface with other analytical microtechnologies, and to develop miniaturized instrumentation.We review recent developments in miniaturizing sample spots for MALDI-MS. We cover both target modification and microdispensing technologies, and we emphasize the benefits with respect to sensitivity, throughput and automation.We hope that this review will encourage further method development and application of miniaturized sample spots for MALDI-MS, so as to expand applications in analytical chemistry, protein science and molecular biology.

Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra

For automated production of tandem mass spectrometric data for proteins and peptides >3 kDa at >50 000 resolution, a dual online-offline approach is presented here that improves upon standard liquid chromatography-tandem mass spectrometry (LC-MS/MS) strategies. An integrated hardware and software infrastructure analyzes online LC-MS data and intelligently determines which targets to interrogate offline using a posteriori knowledge such as prior observation, identification, and degree of characterization. This platform represents a way to implement accurate mass inclusion and exclusion lists in the context of a proteome project, automating collection of high-resolution MS/MS data that cannot currently be acquired on a chromatographic time scale at equivalent spectral quality. For intact proteins from an acid extract of human nuclei fractionated by reversed-phase liquid chromatography (RPLC), the automated offline system generated 57 successful identifications of protein forms arising from 30 distinct genes, a substantial improvement over online LC-MS/MS using the same 12 T LTQ FT Ultra instrument. Analysis of human nuclei subjected to a shotgun Lys-C digest using the same RPLC/automated offline sampling identified 147 unique peptides containing 29 co- and post-translational modifications. Expectation values ranged from 10 (-5) to 10 (-99), allowing routine multiplexed identifications.

Improving the signal intensity and sensitivity of MALDI mass spectrometry by using nanoliter spots deposited by induction-based fluidics

A new contact-free, small droplet deposition method using an induction-based fluidics (IBF) technique to dispense nanoliter drops is described and evaluated for sample preparation in matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The signal intensities available when using nanoliter spots are greater than those obtained with normal, microliter spots when the same amount of analyte is used. When using an ionic-liquid matrix, the improvement in sensitivity is equal to the concentration enhancement that was achieved by using smaller quantities of matrix. When using a conventional solid matrix, however, the increase in signal intensity shows a more complicated relationship to concentration. The approach of nanoliter deposition also supports multiple spotting to increase sample concentration and, thus, sample signal intensity. Nanoliter spotting not only improves the signal intensity and sensitivity achieved by MALDI-MS but also allows a major fraction of trace samples to be saved for other experiments, thus expanding the application of MALDI-MS to biological studies where sample quantity is limited.

Achieving high detection sensitivity (14 zmol) of biomolecular ions in bioaerosol mass spectrometry

Bioaerosol mass spectrometry (BAMS) performs single-cell analysis in real time. However, the specificity of BAMS mass signatures has been limited by low sensitivity at high masses. To increase the mass range and sensitivity of BAMS, a novel design was developed that utilizes a linear flight tube with delayed extraction and an electrostatic ion guide. This study quantifies the sensitivity limits of the novel BAMS design and evaluates the feasibility of BAMS to detect higher mass biomarkers from single cells. All experiments were carried out using MALDI aerosol particles that were nebulized from solution. Sensitivity was assessed by generating particles with decreasing amounts of analyte via serial dilutions. The amount of analyte contained within each particle was calculated based on particle size, density, and molarity of the analyte within solution. A variety of biomolecular ions were studied and signals obtained from particles containing 300 zmol of maltopentaose, 132 zmol of alpha-cyclodextrin, and 14 zmol (approximately 8400 molecules) of gramicidin S are reported. The detection of 14 zmol of gramicidin S is to the best of our knowledge a record in sensitivity for MALDI TOF-MS.

In vivo protein sampling using capillary ultrafiltration semi-permeable hollow fiber and protein identification via mass spectrometry-based proteomics

Here, we advanced a novel technique using capillary ultrafiltration (CUF) probes to collect in vivo secreted proteins in the subcutaneous tissue of mouse ear. We fabricated two kinds of CUF probe, one with and one without a semi-permeable membrane hollow fiber. Proteins collected by CUF probes were profiled and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MADLI-TOF-MS) and quadrupole time-of-flight tandem mass spectrometry (Q-TOF-MS/MS) without using two-dimensional gel electrophoresis (2-DE) separation. Five proteins including cofilin-1, futuin-A, complement C3, gelsolin, and apolipoprotein C-1 were identified from the sample collected by the CUF probe with a semi-permeable membrane hollow fiber. The presence of well documented secretory proteins supports the efficiency of CUF probes in sampling in vivo secreted proteins. We also found that hemoglobin collected by the CUF probe without a semi-permeable membrane hollow fiber completely masked protein identification by mass spectrometry. The presence of relatively large amounts of hemoglobin in this condition illustrates the necessity of the semi-permeable membrane hollow fiber to the technique of CUF probe in conjunction with mass spectrometry. Also, the technique represents a powerful method for the identification of in vivo secreted proteins and has potential application for in the detection of biomarkers for human diseases.

Combining low and high mass ion accumulation for enhancing shotgun proteome analysis by accurate mass measurement

A simple procedure is described that increases sensitivity and dynamic range for the analysis of a proteome batch digest by FT-ICR mass spectrometry. Ions at the low and high mass ranges are preferentially collected using two different sets of tuning conditions. By combing data collected using tuning conditions that favor low mass (m/z < 2000) and high mass (m/z > 2000) ions, 277 proteins are identified for a whole cell lysate of Methanococcus maripaludis in a single HPLC-MALDI FT-ICR mass spectrometry experiment, a 70% improvement compared with previous analyses using a wide mass range acquisition. This procedure improves the detection of low abundance ions and thereby increases the range of proteins that are observed. Because the observed mass range is effectively narrower for each spectrum, mass calibration is more accurate than for the standard method that provides a wide range of masses. The trap plate potential on the analyzer cell may be set to a higher value than used for wide mass range measurements, increasing the ion capacity of the analyzer cell and extending the dynamic range, while still maintaining mass accuracy.

Matrix-Assisted Laser Desorption/Ionization Fourier Transform Mass Spectrometry for the Identification of Orcokinin Neuropeptides in Crustaceans Using Metastable Decay and Sustained Off-Resonance Irradiation

Vacuum UV matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance mass spectrometry (FTMS) has been applied to the direct analysis of crustacean neuronal tissues using in-cell accumulation techniques to improve sensitivity. In an extension of previous work by Li and co-workers (Kutz, K. K.; Schmidt, J. J.; Li, L. Anal. Chem. 2004, 76, 5630-5640), and with a focus on the Maine lobster, Homarus americanus, we report that many peaks appearing in direct tissue spectra from crustaceans result from the metastable decay of aspartate-containing neuropeptides with localized protonation sites. We report on mass spectral characteristics of crustacean neuropeptides under MALDI-FTMS conditions and show how fragments formed by Asp-Xxx cleavages can be used to advantage for the identification of orcokinin peptides, a ubiquitous family of crustacean neuropeptides with a highly conserved N-terminus sequence. We show that predicted fragment ion fingerprints (FIFs) can be used to screen internally calibrated direct tissue spectra to provide high-confidence identification of previously identified orcokinin peptides. We use FIFs, identified based upon characteristic neutral losses, to screen for new members of the orcokinin family. Sustained off-resonance irradiation of y-series fragment ions is used to sequence the variable C-terminus. We apply these techniques to the analysis of CoG tissues from Cancer borealis and Panulirus interruptus and show that orcokinins in P. interruptus were misidentified in a previous MALDI-TOF study.

Attomole peptide analysis by high-pressure matrix-assisted laser desorption/ionization Fourier transform mass spectrometry

A new high-pressure matrix-assisted laser desorption/ionization (HP-MALDI) source for FTMS has recently been described (O'Connor et al. J. Am. Soc. Mass Spectrom., in press). Improvements to the source design, including the incorporation of a new high-pressure gas channel plate, resulted in ions devoid of metastable fragmentation and also in increased sensitivity compared to the HP-MALDI prototype source design. The focus of this contribution is the evaluation of the current HP-MALDI FTMS configuration. The use of nonconductive sample surfaces, such as Parafilm and Teflon, was explored, and spectra from 30 amol of peptide applied to these surfaces were routinely obtained. In addition, the current limit of detection for this configuration is demonstrated to be 300 zmol for the phosphopeptide RRREEE(pS)EEEAA using multishot accumulation of the ions from 15 laser shots in the hexapole and 1 scan. In addition, the performance of the new HP-MALDI FTMS configuration and its potential application for high-throughput proteomics analyses are discussed.

Protein sequencing by mass analysis of polypeptide ladders after controlled protein hydrolysis

The characterization of protein modifications is essential for the study of protein function using functional genomic and proteomic approaches. However, current techniques are not efficient in determining protein modifications. We report an approach for sequencing proteins and determining modifications with high speed, sensitivity and specificity. We discovered that a protein could be readily acid-hydrolyzed within 1 min by exposure to microwave irradiation to form, predominantly, two series of polypeptide ladders containing either the N- or C-terminal amino acid of the protein, respectively. Mass spectrometric analysis of the hydrolysate produced a simple mass spectrum consisting of peaks exclusively from these polypeptide ladders, allowing direct reading of amino acid sequence and modifications of the protein. As examples, we applied this technique to determine protein phosphorylation sites as well as the sequences and several previously unknown modifications of 28 small proteins isolated from Escherichia coli K12 cells. This technique can potentially be automated for large-scale protein annotation.

Development of new methodologies for the mass spectrometry study of bioorganic macromolecules

In recent years, mass spectrometry has been increasingly used for the analysis of various macromolecules of biological, biomedical, and biochemical interest. This increase has been made possible by two key developments: the advent of electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) sources. The two new techniques produce a significant increase in mass range and in sensitivity that led to the development of new applications and of new analyzer designs, software, and robotics. This review, apart from the description of the status of mass spectrometry in the analysis of bioorganic macromolecules, is mainly devoted to the illustration of the more recent promising techniques and on their possible future evolution.

Sample depletion of the matrix-assisted laser desorption process monitored using radionuclide detection

To investigate analyte consumption during the laser desorption process, matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is combined with radionuclide detection. Radionuclide detection provides highly sensitive and quantitative information on the amount of radiolabeled analytes in a MALDI MS sample spot. 14C-Labeled cytochrome c is deposited with 2,5-dihydroxybenzoic acid in 10-nL volume spots. By comparing radioactivity levels of the labeled cytochrome c both before and after spectral acquisition, the reduction in labeled analyte molecules on the target allows monitoring of the moles of desorbed sample. Through a depletion study on this sample, the amount of analyte consumed for MALDI time-of-flight spectral acquisition and the average number of molecules desorbed per laser ablation are determined. When [14C]-cytochrome c is no longer detected by MALDI MS, approximately 70% of the original analyte remains in the sample spots. Redissolving the spots produced further desorption, indicating that the analyte before dissolution was in a physical environment that did not facilitate the desorption process. As a technique with a response that does not depend on the environment of the analyte, radionuclide detection allows characterization of mass-limited sampling methods to better understand the MALDI process.

Analysis of the saliva from patients with oral cancer by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), this study analyzed the saliva obtained from patients with oral cancer and compared these mass spectra with those obtained from healthy controls. Saliva without pre-treatment was mixed directly with a sinapinic acid matrix. Alpha-amylase (57 kDa) dominated the high mass range in the MALDI mass spectra of the saliva from healthy subjects, but the peak was suppressed for patients with oral cancer and was replaced by a peak at m/z 66 k in the spectra of patients' samples (15 out of 20). Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) with in-gel tryptic digestion combined with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) was employed to characterize this 66-kDa protein, which was thus shown to be albumin. However, based on SDS-PAGE results, concentrations of both alpha-amylase and albumin in patients' saliva were significantly higher than those in healthy subjects. This discrepancy was shown to be due to MALDI suppression effects due to the albumin. MALDI-MS thus has potential as a possible rapid diagnostic screening tool for oral cancer.

Gas phase hydrogen deuterium exchange reactions of a model peptide: FT-ICR and computational analyses of metal induced conformational mutations

We utilized gas phase hydrogen/deuterium (H/D) exchange reactions and ab initio calculations to investigate the complexation between a model peptide (Arg-Gly-Asp[triple bond]RGD) with various alkali metal ions. The peptide conformation is drastically altered upon alkali metal ion complexation. The associated conformational changes depend on both the number and type of complexing alkali metal ions. Sodium has a smaller ionic diameter and prefers a multidentate interaction that involves all three amino acids of the peptide. Conversely, potassium and cesium form different types of complexes with the RGD. The [RGD + 2Cs - H]+ species exhibit the slowest H/D exchange reactivity (reaction rate constant of approximately 6 x 10(-13) cm3molecule(-1)s(-1) for the fastest exchanging labile hydrogen with ND3). The reaction rate constant of the protonated RGD is two orders of magnitude faster than that of the [RGD + 2Cs - H]+. Addition of the first cesium to the RGD reduces the H/D exchange reaction rate constant (i.e., D0) by a factor of seven whereas sodium reduces this value by a factor of thirty. Conversely, addition of the second alkali metal ions has the opposite effect; the rate of D0 disappearance for all [RGD + 2Met - H]+ species (Met[triple bond]Na, K, and Cs) decreases with the alkali metal ion size.

Mass analysis at the advent of the 21st century

There have been many new and exciting developments in mass spectrometer systems in recent years. Many of these developments are being driven by challenges presented by molecular biology. The activity is fueled by resources being devoted to drug development, for example, and other medically and biologically related activities. Progress in these applications will be accelerated by improved sensitivity, specificity, and speed. In mass spectrometry, this translates to greater mass resolving power, mass accuracy, mass-to-charge range, efficiency, and speed. It is safe to say that the demands resulting from current analytical needs are likely to be met to varying degrees but probably not by a single analyzer technology or hybrid instrument. On-line and/or off-line separations and manipulations combined with mass spectrometry will also play increasingly important roles. For any analyzer, or combination of analyzers, to become widely used it must have an important application for which its figures of merit are best suited, relative to competing approaches. The relative cost of competing technologies is also an important factor. The mass filter has seen so much use in the past 30 years because its characteristics best fit a wide range of applications. As an example, biological applications, which are currently driving many instrument development activities in mass spectrometry, demand more information, of higher quality, from less material, faster, and at lower cost. Which technologies will dominate biological applications in the coming years is open to speculation. However, in considering the relative merits of today's dominant mass analyzers, areas of opportunity for improvement are apparent. Furthermore, new and more demanding measurement needs are constantly being recognized that will continue to exercise the creativity of the mass spectrometry community.

Analysis of fatty acids by graphite plate laser desorption/ionization time-of-flight mass spectrometry

Fatty acids obtained from triglycerides (trioelin, tripalmitin), foods (milk, corn oil), and phospholipids (phosphotidylcholine, phosphotidylserine, phosphatidic acid) upon alkaline hydrolysis were observed directly without derivatization by graphite plate laser desorption/ionization time-of-flight mass spectrometry (GPLDI-TOFMS). Mass-to-charge ratios predicted for sodium adducts of expected fatty acids (e.g. palmitic, oleic, linoleic and arachidonic acids) were observed without interference. Although at present no quantitation is possible, the graphite plate method enables a simple and rapid qualitative analysis of fatty acids.

Protein identification methods in proteomics

A combination of high-resolution two-dimensional (2-D) polyacrylamide gel electrophoresis, highly sensitive biological mass spectrometry, and the rapidly growing protein and DNA databases has paved the way for high-throughput proteomics. This review concentrates on protein identification. We first discuss the use of protein electroblotting and Edman sequencing as tools for de novo sequencing and protein identification. In the second part, we highlight matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) as one of the main contemporary analytical methods for linking gel-separated proteins to entries in sequence databases. In this context we describe the two main MALDI-MS-based identification methods: (i) peptide mass fingerprinting, and (ii) post-source decay (PSD) analysis. In the last part, we briefly emphasize the importance of sample preparation for obtaining highly sensitive and high-quality MALDI-MS spectra.

Measuring the peptides in individual organelles with mass spectrometry

New sampling protocols combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) allow the assay of single dense core vesicles. Understanding the packaging of vesicles is important as vesicles are the quanta of information for intercellular communication. Using vesicles from the exocrine atrial gland of Aplysia californica as the model, a wide range of bioactive peptides are detected within each vesicle. Although the expression of the egg-laying hormone gene family of type 1 atrial gland cells has been previously examined, chemical characterization of individual 1-2 microm diameter vesicles demonstrates that products from several genes are colocalized. The mass sensitivity of MALDI MS can be further improved to enable the analysis of even smaller subcellular organelles.

Benefits of 2.94 micron infrared matrix-assisted laser desorption/ionization for analysis of labile molecules by Fourier transform mass spectrometry

A 2.94 microm Er:YAG laser was used together with a commercial Fourier transform mass spectrometer to study labile biomolecules. The combination has shown superior performance over conventional 337 nm ultraviolet matrix-assisted laser desorption/ionization (UV-MALDI) Fourier transform mass spectrometry (FTMS), especially for the analysis of peptides with post-translational modifications. With succinic acid as a matrix, the sensitivity of the single-shot analysis was increased by an order of magnitude to the low femtomole level, with significantly less fragmentation observed. Intact molecular ions of a range of O-glycosylated and sulfated peptides were detected. Urea was found to induce even less fragmentation, although at the expense of the total ion yield. Molecular ions of a noncovalent complex (vancomycin + diacetyl-L-Lys-D-Ala-D-Ala) have been observed for the first time in MALDI-FTMS. 2.94 microm infrared (IR) MALDI also produced abundant molecular ions of a range of nonbiological samples, including C60 and C70 fullerenes as well as dimetal coordination complexes.

Applications of mass spectrometry to signal transduction

Advances in mass spectrometry instrumentation, protocols for sample handling, and computational methods provide powerful new approaches to solving problems in analytical biochemistry. This review summarizes recent work illustrating ways in which mass spectrometry has been used to address questions relevant to signal transduction. Rather than encompass all of the instruments or methodologies that might be brought to bear on these problems, we present an overview of commonly used techniques, promising new methodologies, and some applications.

Nanoliter chemistry combined with mass spectrometry for peptide mapping of proteins from single mammalian cell lysates

A nanoliter-chemistry station combined with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry was developed to characterize proteins at the attomole level. Chemical reactions including protein digestion were carried out in nanoliter or subnanoliter volumes, followed by microspot sample deposition of the digest to a MALDI-TOF mass spectrometer. Accurate mass determination of the peptides from the enzyme digest, in conjunction with protein database searching, allowed the identification of the proteins in the protein database. This method is particularly useful for handling small-volume samples such as in single-cell analysis. The high sensitivity and specificity of this method were demonstrated by peptide mapping and identifying hemoglobin variants of sickle cell disease from a single red blood cell. The approach of combining nanoliter chemistry with highly sensitive mass spectrometric analysis should find general use in characterizing proteins from biological systems where only a limited amount of material is available for interrogation.

Monitoring protein expression in whole bacterial cells with MALDI time-of-flight mass spectrometry

We report the application of matrix-assisted laser desorption ionization (MALDI) to monitor recombinant protein expression in whole bacteria. This technique is characterized by rapid sample preparation that provides analysis of samples extracted directly from the growth media in less than 10 min. The mass spectrometric method holds several advantages over gel electrophoresis, the conventional method for examining the protein content of cells. Comparisons between the two methods of analysis are presented in terms of increased speed, efficiency, resolution, and mass accuracy. Delayed extraction time-of-flight mass spectrometry identifies posttranslational modifications and other changes in the expected structure which are not recognized by gel electrophoresis. The utility of this method is demonstrated for proteins with molecular masses ranging from 5 to 50 kDa. Low molecular mass proteins (< 10 kDa) can be efficiently analyzed without any treatment of the bacterial broth prior to MALDI sample preparation. The MALDI analysis of higher molecular weight proteins shows enhanced sensitivity when the bacterial solutions are first sonicated.

Electrospray ionization and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry of permethylated oligosaccharides

Mass spectra of fragments of permethylated oligosaccharides are analyzed by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. Sustained off-resonance irradiation (SORI) collision-induced dissociation (CID), quadrupolar axialization, multiple stages of isolation and dissociation (MSn), and ion remeasurement are exploited for carbohydrate structural analyses. That SORI CID internal energies are adequate for linkage analysis of a permethylated glucose oligomer is demonstrated by identifying ring-opened fragment ions from MALDI-generated mass-isolated and collisionally activated ions. Ion remeasurement and axialization techniques enhance the sensitivity of ion fragmentation analysis. Multiple stages of isolation and dissociation of ion fragments (MSn) provide for structural analysis of an electrospray-ionized permethylated lacto-N-fucopentaose isomer (LNFP II). Compared to MS2 spectra taken with a triple quadrupole, FT-ICR MSn (n > 2) provides more extensive characterization of the parent molecular structure than is available from a single stage of ion isolation and dissociation (MS2).

Mass spectrometry of peptides in neuroscience

This review focuses on the contributions of modern mass spectrometry to neuropeptide research. An introduction to newer mass spectrometric techniques is provided. Also, the use of mass spectrometry in combination with high-resolution separation techniques for neuropeptide identification in biological samples is illustrated. The amino acid sequence information that is important for the identification and analysis of known, novel, or chemically modified neuropeptides may be obtained using mass spectrometric techniques. Because mass spectrometry techniques can be used to reflect the dynamic properties associated with neuropeptide processing in biological systems, they may be used in the future to monitor peptide profiles within organisms in response to environmental challenges such as disease and stress.

Fourier transform ion cyclotron resonance mass spectrometry: a primer

This review offers an introduction to the principles and generic applications of FT-ICR mass spectrometry, directed to readers with no prior experience with the technique. We are able to explain the fundamental FT-ICR phenomena from a simplified theoretical treatment of ion behavior in idealized magnetic and electric fields. The effects of trapping voltage, trap size and shape, and other nonidealities are manifested mainly as perturbations that preserve the idealized ion behavior modified by appropriate numerical correction factors. Topics include: effect of ion mass, charge, magnetic field, and trapping voltage on ion cyclotron frequency; excitation and detection of ICR signals; mass calibration; mass resolving power and mass accuracy; upper mass limit(s); dynamic range; detection limit, strategies for mass and energy selection for MSn; ion axialization, cooling, and remeasurement; and means for guiding externally formed ions into the ion trap. The relation of FT-ICR MS to other types of Fourier transform spectroscopy and to the Paul (quadrupole) ion trap is described. The article concludes with selected applications, an appendix listing accurate fundamental constants needed for ultrahigh-precision analysis, and an annotated list of selected reviews and primary source publications that describe in further detail various FT-ICR MS techniques and applications.

Mass spectrometry at low and high mass

The introduction of novel methods as well as expanding applications to diverse areas highlight truly impressive progress in mass spectrometry. These developments are illustrated here by two seemingly different areas of research: new methods designed for the determination of isotopic enrichment and novel ionization methods; and mass analyzers which have enabled the precise determination of the molecular weight of proteins and large oligonucleotides.

Protein stability and conformational rearrangements in lipid bilayers: linear gramicidin, a model system

The replacement of four tryptophans in gramicidin A by four phenylalanines (gramicidin M) causes no change in the molecular fold of this dimeric peptide in a low dielectric isotropic organic solvent, but the molecular folds are dramatically different in a lipid bilayer environment. The indoles of gramicidin A interact with the anisotropic bilayer environment to induce a change in the molecular fold. The double-helical fold of gramicidin M, as opposed to the single-stranded structure of gramicidin A, is not compatible with ion conductance. Gramicidin A/gramicidin M hybrid structures have also been prepared, and like gramicidin M homodimers, these dimeric hybrids appear to have a double-helical fold, suggesting that a couple of indoles are being buried in the bilayer interstices. To achieve this equilibrium structure (i.e., minimum energy conformation), incubation at 68 degrees C for 2 days is required. Kinetically trapped metastable structures may be more common in lipid bilayers than in an aqueous isotropic environment. Structural characterizations in the bilayers were achieved with solid-state NMR-derived orientational constraints from uniformly aligned lipid bilayer samples, and characterizations in organic solvents were accomplished by solution NMR.

Detection, number, and sequence location of sulfur-containing amino acids and disulfide bridges in peptides by ultrahigh-resolution MALDI FTICR mass spectrometry

Here, we present several strategies for determining the number of sulfur atoms and disulfide bridges in selected biologically active peptides, based on MALDI FTICR mass spectrometry at femtomole sample consumption level. First, based on the 2-Da mass increase per disulfide bridge reduction, we show that repeated laser shots on the same sample spot can reduce (and therefore reveal the presence of) the disulfide bridge in oxytocin. Second, we show that the primary sequence positions of the disulfide-bridged cystines can be inferred from the presence/absence of MALDI-induced reduction in cystine-containing fragment ions. Third, we show that the presence and number of sulfur atoms as well as the degree of reduction in a peptide can all be determined directly from isotopic relative abundances of mass-resolved 34S, 13C2, and reduced all-12C species in a single ultrahigh-resolution MALDI FTICR mass spectrum. Methods for achieving such ultrahigh mass resolution of peptide ions of closely spaced m/z (m/delta m50% approximately 950,000 at m/z approximately 650) at modest magnetic field (3 T) are discussed.

Two-way conversation with a mass spectrometer: nondestructive interactive mass spectrometry

Most mass spectrometers employ destructive detection, so that it is necessary to repeat an experiment in order to vary even one parameter. In contrast, Fourier transform ion cyclotron resonance mass spectrometry offers nondestructive detection, so that ions remain available for further manipulation and redetection. Here, we show for the first time how to perform mass spectrometry interactively. Following each elementary experimental stage, such as ion generation, isolation, dissociation, or detection, the operator is free to choose and tailor the next stage without creating a fresh supply of ions. For example, we can test the effect of varying one parameter over several values without having to repeat the entire experimental event sequence each time, much like varying one letter or word in a sentence without having to rewrite the whole sentence. Such interactive control promises to speed development of complex experimental event sequences, as for optimizing the sequencing and structural analysis of tiny amounts (e.g., femtomoles or less) of biomacromolecules (peptides, nucleic acids, oligosaccharides).