Profiling of hydrophilic proteins from Olea europaea olive pollen by MALDI TOF mass spectrometry

The antigenic profile of Olea europaea pollen from different Mediterranean cultivars was obtained by MALDI mass spectrometry. A simple procedure of chemical fractionation of the whole antigen extract was developed, whereby less complex, or pure, fractions of antigen candidate were obtained prior to mass spectrometric analysis. Some of the features of protein structure and distribution probably depend on cultivar adaptation to the environment. The profilings of pollen proteins thus obtained allow the distinction of the analyzed cultivars into three distinct groups: (i) those characterized by a low Ole e 1 content; (ii) those over-enriched in Ole e 1 and (iii) that containing Ole e 3 and Ole e 7 only. The latter consists of at least four isoforms differing by the degree of glycosilation. These results demonstrate that the proposed experimental procedure, can supply valuable information on the antigens' micro heterogeneity.     

Fragmentation characteristics of collision-induced dissociation in MALDI TOF/TOF mass spectrometry

The identification of proteins by tandem mass spectrometry relies on knowledge of the products produced by collision-induced dissociation of peptide ions. Most previous work has focused on fragmentation statistics for ion trap systems. We analyzed fragmentation in MALDI TOF/TOF mass spectrometry, collecting statistics using a curated set of 2459 MS/MS spectra and applying bootstrap resampling to assess confidence intervals. We calculated the frequency of 18 product ion types, the correlation between both mass and intensity with ion type, the dependence of amide bond breakage on the residues surrounding the cleavage site, and the dependence of product ion detection on residues not adjacent to the cleavage site. The most frequently observed were internal ions, followed by y ions. A strong correlation between ion type and the mass and intensity of its peak was observed, with b and y ions producing the most intense and highest mass peaks. The amino acids P, W, D, and R had a strong effect on amide bond cleavage when situated next to the breakage site, whereas residues including I, K, and H had a strong effect on product ion observation when located in the peptide but not adjacent to the cleavage site, a novel observation.     

Characterization of the protein subset desorbed by MALDI from whole bacterial cells

This study characterizes various features of the proteins that are detected in MALDI mass spectra when whole bacteria cells are analyzed, in an effort to understand why some proteins are successfully detected and many others are not. Forty peaks observed in the mass range 4,000-20,000 Da in the spectra of Escherichia coli K-12 and 11775 are tentatively assigned to proteins in a protein database, and these proteins are characterized by cell location, copy number, pI, and hydropathicity. Those detected originate in the cytosol and generally share the traits of high abundance within the cell, strong bacisity, and medium hydrophilicity.     

Increased identification of peptides by enhanced data processing of high-resolution MALDI TOF/TOF mass spectra prior to database searching

This paper presents application of sequential enhanced data processing procedures to high-resolution tandem mass spectra for identification of peptides using the Mascot database search algorithm. A strategy for (1) selection of fragment ion peaks from MS/MS spectra, (2) utilization of improved mass accuracy of the precursor ions, and (3) wavelet denoising of the mass spectra prior to fragment ion selection have been developed. The number of peptide identifications obtained using the enhanced processing was then compared with that obtained using software provided by the instrument manufacturer. Approximately 9000 MS/MS spectra acquired by the Applied Biosystems 4700 TOF/TOF MS instrument were used as a model data set. After application of the new processing, an increase of 33% unique peptides and 22% protein identifications with at least two unique peptides were found. The influence of the processing on the percentage of false positives, estimated by searching against a randomized database, was estimated to increase false positive identifications from 2.7 to 3.9%, which was still below the 5% error rate specified in the Mascot search. These data processing approaches increase the amount of information that can be extracted from LC-MS analysis without the necessity of additional experiments.     

Enhanced ionization of phosphorylated peptides during MALDI TOF mass spectrometry

Although alpha-cyano-4-hydroxycinnamic acid functions as an excellent matrix for the analysis of most peptides using matrix-assisted laser desorption/ionization time-of-flight (MALDI TOF) mass spectrometry, the ionization of phosphorylated peptides is usually suppressed by nonphosphorylated peptides. As an alternative matrix, 2',4',6'-trihydroxyacetophenone (THAP) with diammonium citrate was found to overcome this problem for the MALDI TOF mass spectrometric analysis of proteolytic digests of phosphorylated proteins. Specifically, the abundances of phosphorylated peptides in tryptic digests of bovine beta-casein and protein kinase C (PKC)-treated mouse cardiac troponin I were enhanced more than 10-fold using THAP during positive ion MALDI TOF mass spectrometry. The protonated molecules of phosphorylated peptides were sufficiently abundant that postsource decay TOF mass spectrometry was used to confirm the number of phosphate groups in each peptide. Finally, tryptic digestion followed by analysis using MALDI TOF mass spectrometry with THAP as the matrix facilitated the identification of a unique phosphorylation site in PKC-treated troponin I.     

MALDI TOF mass spectrometry for the characterization of phosphorus-containing dendrimers. Scope and limitations

Neutral phosphorus-containing dendrimers with aldehyde groups at the periphery have been analyzed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) up to generation four. Although the expected quasi-molecular ion is generally observed, the mass spectral pattern, presence of fragments and adducts related to the original skeleton, is highly relevant to the sample preparation (nature of the matrix: 2-5-dihydroxybenzoic acid (2.5-DHB), 1,8-dihydroxy-9[10H]-anthracenone (dithranol), 6-azathiothymine, 2,4,6-trihydroxyacetophenon, 7-hydroxycoumarin or 2-anthramine, and addition of alkali metal salts). The dithranol matrix with addition of LiI offers milder conditions; however, abundant fragments are still observed for the higher generation dendrimers. Investigation of these effects in connection with SEC, NMR, and MALDI-TOFMS studies of UV preirradiated dendrimers allows the assumption to be made that fragmentation occurs in MALDI due to the relatively strong absorption of the dendrimers at 337 nm. Fragmentations and formation of adducts involve nitrogen-nitrogen bond cleavage, imine metathesis, and reaction of aldehyde groups with internal imino groups.     

Characterization of protein biomarkers desorbed by MALDI from whole fungal cells.

In this publication, the use of ultraviolet (UV) matrix-assisted laser desorption/ionization (MALDI) time-of-fight (TOF) mass spectrometry (MS) for rapid identification and characterization of Saccharomyces cerevisiae, a fungus, is reported. S. cerevisiae is a unicellular eukaroyte that can serve as a model to study more complex organisms. We have determined that the best technique for cell wall lyses for MALDI involves the use of high concentrations of formic acid solutions. We also have shown that different fungal species exhibit different mass spectra, which can be used to distinguish them readily. Protein peaks from S. cerevisiae spectra have been tentatively identified using bioinformatics and are mainly assigned to ribosomal and mitochondrion-related proteins.     

Photoimmobilization of proteins for affinity capture combined with MALDI TOF MS analysis

Affinity capture surfaces can be prepared in a number of ways. A method of obtaining such surfaces through UV-activated immobilization of binding proteins using a benzophenone derivative is reported. Photoimmobilized protein G was used to selectively capture and preconcentrate bovine IgG from a mixture with BSA, and the affinity of photoattached concanavalin A toward ovalbumin was compared with that of commercially available concanavalin A on agarose beads. The results of the capture after tryptic digestion were analyzed by MALDI TOF MS. Immobilized trypsin was also prepared through photoimmobilization and later used to digest hemoglobin. Immobilized enzyme digestion resulted in more partial cleavages than solution-phase digestion. More methionine and tryptophan oxidation was also observed. Photoimmobilization was shown to be a quick and easy way of immobilizing ligands on surfaces.     

An automated interpretation of MALDI/TOF postsource decay spectra of oligosaccharides. 1. Automated peak assignment.

A computer program has been developed that helps the interpretation of MALDI/TOF postsource decay (PSD) spectra of N-linked oligosaccharides of a protein. The program includes routines for automated peak assignment and generation of a simulated PSD spectrum. From a raw spectrum, peaks are assigned automatically; i.e., numbers of saccharide residues removed from the parent ion are calculated. If the structure of the oligosaccharide is known, a simulated PSD spectrum of the oligosaccharide will be generated. The simulated PSD spectrum helps interpretation of the observed spectrum. While, in a case where several candidate structures are given, one can narrow the field of plausible structures for the unknown oligosaccharide by comparing the observed spectrum with the simulated PSD spectra. Using a Pentium 233-MHz microprocessor, it takes only a few seconds to interpret a spectrum.     

Nanoliter solvent extraction combined with microspot MALDI TOF mass spectrometry for the analysis of hydrophobic biomolecules

A nanoliter solvent extraction technique combined with microspot matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is presented. This method involves the use of a nanoliter droplet containing organic solvents at the tip of a small capillary for extraction. The droplet is formed inside a microliter aqueous sample containing the analyte of interest. After extraction, the droplet is deposited onto a MALDI target precoated with a thin matrix layer. Since the nanoliter droplet never touches the sample container wall, any possible extraction of contaminants adsorbed on the plastic or glassware is avoided. In addition, there is no need to concentrate the organic phase after the extraction, thus avoiding any possible loss during the concentration step. The nanoliter volume can be readily deposited onto a MALDI target, producing a high analyte concentration within a microspot. Combined with microspot MALDI, this technique allows for very sensitive analysis of the extracted analyte. The performance of this technique is illustrated in several applications involving the detection of hydrophobic peptides or phospholipids. It is shown that very hydrophobic analytes can be extracted from small-volume samples containing a large amount of salts and/or more hydrophilic analytes, which tend to give dominant signals in conventional MALDI experiments. Nanoliter extraction of analyte from samples containing less than 100 nM hydrophobic analyte and over 1 microM easily ionized hydrophilic species is demonstrated. Finally, using the analysis of the ionophore valinomycin as an example, it is demonstrated that the technique is a more reliable tool for probing metal-peptide complexes than regular MALDI sample preparations.     

Direct profiling of proteins in biological tissue sections by MALDI mass spectrometry

The direct profiling of proteins present in tissue sections for several organs of the mouse has been accomplished using matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS). Fresh tissue was sectioned and blotted on a conductive polyethylene membrane. The dried membrane blot was coated with matrix, typically sinapinic acid, and directly analyzed in the mass spectrometer. Generally, well over 100 peptide/protein signals in the 2000-30,000 Da range were observed, with 30-50 having relatively high signal intensities. Analysis of different areas of the same tissue gave remarkably similar mass spectra with greater than 90% homology. However, different parts of a segmented tissue, such as the proximal, intermediate, and distal colon, gave some unique protein signals. After treatment of the tissue blot with protease and subsequent MALDI MS analysis using postsource decay methods for peptide sequencing, some of the proteins were identified. The unique protein profiles measured from these tissue blots also showed differences from strain to strain of the mouse, with genetically similar strains having very similar patterns.     

SearchXLinks. A program for the identification of disulfide bonds in proteins from mass spectra

We present the computer program SearchXLinks that analyzes mass spectra with the aim of identifying disulfide bonds and other modifications in proteins of known amino acid sequence. Disulfide bonds can be intra- or intermolecular. To decrease the number of false positives, the analysis of in-source decay and tandem mass spectra are coupled into the program. The steps taken during a SearchXLinks run are outlined, and the computational costs are discussed. The application of the program is illustrated by the analysis of data from recent studies on bovine ribonuclease A and bovine serum albumin. The software can be used free of charge on the Internet at http://www.searchxlinks.de.     

Identification of unusual bacterial glycosylation by tandem mass spectrometry analyses of intact proteins

The characterization of protein glycosylation can be a complex and time-consuming procedure, especially for prokaryote O-linked glycoproteins, which often comprise unusual oligosaccharide structures with no known glycosylation motif. In this report, we describe a "top-down" approach that provides information on the extent of glycosylation, the molecular masses, and the structure of oligosaccharide residues on bacterial flagella, important structural proteins involved in the motility of pathogenic bacteria. Flagella from four bacterial pathogens, namely, Campylobacter jejuni, Helicobacter pylori, Aeromonas caviae, and Listeria monocytogenes, were analyzed by this top-down mass spectrometry approach. The approach needs minimal sample preparation and can be performed within a few minutes compared to the tedious and often time-consuming "bottom-up" approach involving proteolytic digestion and LC-MS-MS analyses of the suspected glycopeptides. Multiply protonated protein precursor ions subjected to low-energy collisional activation in a quadrupole time-of-flight instrument showed extensive and specific gas-phase deglycosylation resulting in the formation of abundant oxonium ions with very few fragment ions from peptidic bond cleavages. Structural information on individual carbohydrate residues is obtained using a second-generation product ion scan of oxonium ions formed by collisional activation of the intact protein ions in the source region. The four bacterial flagella examined differed not only by the extent of glycosylation but also by the nature of carbohydrate substituents. For example, the flagellin from the Gram-positive bacterium, L. monocytogenes showed O-linked GlcNAc residues at up to 6 sites/protein monomer. In contrast, the three Gram-negative bacterial pathogens C. jejuni, H. pylori and A. caviae displayed up to 19 Ser/Thr O-linked sites modified with residues structurally related to N-acetylpseudaminic acid (Pse5Ac7Ac) and in the case of Campylobacter include a novel N-acetylglutamine substituent on Pse5Am7Ac.     

High-throughput method for N-terminal sequencing of proteins by MALDI mass spectrometry

A high-throughput method for sequencing of N termini of proteins by using postsource decay (PSD) of matrix-assisted laser desorption/ionization mass spectrometry has been developed. After a protein blotted on the PVDF membrane was successively reduced, S-alkylated, and guanidinated, its N-amino group was coupled to biotinylcysteic acid. The protein was then extracted from the membrane and digested with trypsin. The derivatized N-terminal fragment was then specifically isolated from the tryptic digest with avidin resins, and its de novo sequencing was successfully performed by PSD utilizing a sulfonic acid group introduced to the N terminus.     

Submicrosecond surface-induced dissociation of peptide ions in a MALDI TOF MS

Surface-induced dissociation (SID) has been implemented in a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI TOF MS), allowing production of tandem mass spectrometric information for peptide ions (MALDI TOF SID TOF). The instrument retains the standard operational modes such as the reflectron monitoring of the MALDI-generated intact ions and postsource decay. We show through ion trajectory simulations and experimental results that implementing SID in a commercial MALDI TOF spectrometer is feasible and that the SID products in this instrument fall in an observation time frame that allows the specific detection of fast-fragmentation channels. The instrument design, pulse timing sequence, and high-voltage electronics together with SID spectra of MALDI-generated peptide ions are presented. Standard peptides such as YGGFLR, angiotensin III, fibrinopeptide A, and des-Arg1-bradykinin were dissociated by means of hyperthermal collisions with a gold surface coated with a self-assembled monolayer of 2-(perfluorodecyl)ethanethiol. With the extraction fields and the short observation times used, the spectra obtained show intense low-mass ion signals such as immonium, b2, b3, and y2 ions. TOF data analysis involved matching simulated and experimental flight times and indicates that the observed fragments are produced at approximately 250 ns after the precursor ion collides with the surface. This submicrosecond gas-phase fragmentation time frame is complementary to the observation time frame of existing SID spectrometers, which are on the order of 10 micros for tandem quadrupoles and are larger than a few milliseconds for SID implemented in Fourier transform ion cyclotron resonance spectrometers.     

Identification of trichloroethanol visualized proteins from two-dimensional polyacrylamide gels by mass spectrometry

Proteins visualized by 2,2,2-trichloroethanol (TCE) on two-dimensional electrophoresis gels are efficiently identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and MS/MS. In a previous study, a method was developed that placed TCE in the polyacrylamide gel so that protein bands can be visualized without staining in less than 5 min. A visible fluorophore is generated by reaction of TCE with tryptophan that allows for protein visualization. In this study, MALDI-TOF MS and LC-MS/MS are used to identify randomly selected Escherichia coli proteins. The identification of TCE visualized proteins is compared to the identification of Coomassie brilliant blue (CBB) stained proteins from two-dimensional gel electrophoresis of E. coli proteins. This study demonstrated that TCE visualized proteins are compatible with protein identification by MALDI-TOF peptide mass fingerprinting. For 10 randomly selected spots, TCE visualization lead to statistically significant identification of 5 proteins and CBB visualization lead to identification of 6 proteins. TCE visualized proteins are also shown to be well suited for protein identification using LC-MS/MS. In 16 spots selected for MS/MS analysis, TCE samples lead to the identification of 79 peptides; while CBB samples lead to the identification of 65 peptides. TCE samples also supported the identification of more proteins. The low stoichiometry of labeling of tryptophan residues does not require inclusion of this modification for database searches. In addition to being a rapid visualization technique compatible with MS, TCE visualization utilizes rapid washing conditions for sample preparation of proteins spots excised from polyacrylamide gels.     

Intensities of E. coli nucleic acid Raman spectra excited selectively from whole cells with 251-nm light

Escherichia coli bacteria in the logarithmic growth phase have been investigated by UV resonance Raman spectroscopy. Bacterial whole-cell Raman spectra excited at 251 nm reflect nearly exclusively the nucleic acid composition even though a very large fraction of the bacterial mass is composed of protein. It has been demonstrated that if bacteria are grown under controlled (logarithmic growth) conditions, which give rise to organisms of known average biochemical composition, the intensities of E. coli Raman spectra can be explained quantitatively from the knowledge of component nucleic acid base resonance Raman cross sections.     

On the difference between surface-enhanced raman scattering (SERS) spectra of cell growth media and whole bacterial cells

It has been recently suggested [N. E. Marotta and L. A. Bottomley, Appl. Spectrosc. 64, 601-606 (2010)] that previously reported surface-enhanced Raman scattering (SERS) spectra of vegetative bacterial cells are due to residual cell growth media that were not properly removed from samples of the lab-cultured microorganism suspensions. SERS spectra of several commonly used cell growth media are similar to those of bacterial cells, as shown here and reported elsewhere. However, a multivariate data analysis approach shows that SERS spectra of different bacterial species grown in the same growth media exhibit different characteristic vibrational spectra, SERS spectra of the same organism grown in different media display the same SERS spectrum, and SERS spectra of growth media do not cluster near the SERS spectra of washed bacteria. Furthermore, a bacterial SERS spectrum grown in a minimal medium, which uses inorganics for a nitrogen source and displays virtually no SERS features, exhibits a characteristic bacterial SERS spectrum. We use multivariate analysis to show how successive water washing and centrifugation cycles remove cell growth media and result in a robust bacterial SERS spectrum in contrast to the previous study attributing bacterial SERS signals to growth media.     

Enhancement of the quality of MALDI mass spectra of highly acidic oligosaccharides by using a nafion-coated probe

Spectra of highly acidic oligosaccharides obtained by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) can be greatly enhanced in quality by coating the MALDI probe surface with a film consisting of a perfluorosulfonated ionomer (Nafion) prior to the addition of the sample-matrix mixture. For comparison, three mixtures containing highly acidic oligo- and polysaccharides derived from partial acidic hydrolysis of alginate, pectin, or carboxymethyl cellulose (CMC) were analyzed by employing probes with an uncoated gold surface or a surface coated with a Nafion or nitrocellulose film. The negative ion-mode MALDI spectra of the oligouronates (oligomers containing mannuronic/guluronic and galacturonic acid residues) obtained using uncoated or nitrocellulose-coated probes consisted of a series of broad, multiple peaks. These multiple peaks were assigned to the molecular ions of the nondissociated [M - H]- and partially sodiated [MnNa - H]-, where n = 1, 2, or 3, oligomers. In contrast, the corresponding spectra obtained with Nafion-coated probes contained only a single series of sharp peaks originating from the molecular ions ([M - H]-) of nondissociated oligomers exhibiting chain lengths of as many as approximately 15 uronic acid residues. The Nafion coating was apparently capable of removing the sodium counterions remaining in the deposit of the sample-matrix mixture on the probe, thereby greatly enhancing the signal-to-noise ratios of the peaks in the spectra. In a similar manner, higher quality spectra could also be obtained by using Nafion-coated probes for analysis of the oligouronates and CMC oligomers by positive ion-mode MALDI-MS.     

Effect of reducing disulfide-containing proteins on electrospray ionization mass spectra

Electrospray ionization produces multiply charged molecular ions for biomolecules with molecular weights in excess of 100,000. This allows mass spectrometers with limited mass-to-charge range to extend their molecular weight range by a factor equal to the number of charges. The maximum number of observed charges for peptides and smaller proteins correlates well with the number of basic amino acid residues (Arg, Lys, His), except for disulfide-containing molecules, such as lysozyme and bovine albumin. However, reduction of disulfide linkages with 1,4-dithiothreitol (Cleland's reagent) may allow the protein to be in an extended conformation and make "buried" basic residues available for protonation to yield higher charged molecular ions by the electrospray ionization process. For larger proteins reduction of disulfide bridges greatly increases the maximum charge state, but charging of basic amino acid residues remains less efficient than for smaller proteins.