Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)

Infrared, surface-assisted laser desorption ionization mass spectrometry on frozen aqueous solutions of proteins and peptides using suspensions of organic solids

Surface-assisted, laser desorption ionization (SALDI) time-of-flight mass spectra of proteins and peptides have been obtained from bulk frozen aqueous solutions by adding solid organic powders to the solutions before freezing. Abundant analyte ions were obtained with a 3.28 microgram Nd:YAG/OPO laser. 20 compounds were evaluated as solid additives, and 16 yielded protein mass spectra. Successful solids included compounds like pyrene, aspartic acid, and polystyrene. The best results were obtained with nicotinic acid and indole-2-carboxylic acid, which yielded protein mass spectra anywhere on the sample and with every laser shot. Compared with ultraviolet-matrix-assisted laser desorption ionization on the same instrument, cryo-IR-SALDI had a comparable detection limit (approximately equal to 1 micro M), a lower mass resolution for peptides, and a higher mass resolution for large proteins. Approximately 2500 cryo-IR-SALDI mass spectra were obtained from a single spot on a 0.3-mm-thick frozen sample before the metal surface was reached. About 0.1 nL of frozen solution was desorbed per laser shot. The extent of protein charging varied between the SALDI solids used. With thymine, myoglobin charge states up to MH12(+12) were observed. It is tentatively concluded that observed ions are performed in the frozen sample.

Exploring infrared wavelength matrix-assisted laser desorption/ionization of proteins with delayed-extraction time-of-flight mass spectrometry

We report a study of the application of delayed extraction (DE) to infrared-wavelength matrix-assisted time-of-flight mass spectrometry (IR-MALDI-TOF-MS) of proteins. The shapes of the spectral peaks obtained with DE-IR-MALDI-MS are compared with those obtained from the same samples and matrix using continuous extraction (CE) IR-MALDI-MS. Application of DE results in significant improvements in the peak resolution, revealing spectral features (in proteins with molecular masses < 12 kDa) that were not resolved in the corresponding CE-IR-Maldi mass spectra. Particularly significant is a series of peaks on the high mass side of the protonated protein peaks that arise through replacement of protons by adventitious sodium ions in the sample. We deduced that these sodium replacement species are a significant contributor to the broad tails (and resulting peak asymmetries) that are a feature of the DE-IR-MALDI mass spectra of proteins with molecular masses > or = 17 kDa. The peak width reduction observed in IR-MALDI by DE suggests that, as in UV-MALDI, the initial velocity distribution for ions produced in the MALDI process contributes to the peak broadness in the CE mass spectra. In a systematic comparison between DE UV-MALDI and DE IR-MALDI, we determined that photochemical matrix adduction is present in UV-MALDI but absent in IR-MALDI. In addition, we find that protein ions produced by IR irradiation are less internally excited (i.e., cooler), exhibiting less fragmentation, more Na+ replacement and/or unspecified noncovalent adduction, and more heme adduction with apomyoglobin. Thus, IR-MALDI appears to be a softer means for producing gas-phase protein ions than is UV-MALDI. It will be of considerable practical interest to determine whether large protein ions produced by IR-MALDI are sufficiently cool to survive transport through reflecting TOF mass spectrometers (without loss of small neutral species such as H2O, NH3, and CO2) and the extended time periods required for detection by quadrupole ion trap and Fourier transform ion cyclotron resonance mass analyzers.

Methods to monitor process-induced changes in food proteins. An overview

Proteins in food systems may undergo various changes in their structural properties as a consequence of processing. Whether these changes are beneficial or detrimental in terms of the nutritional, biological or functional properties of the processed system, it is important to apply analytical methods which can monitor the course of protein structural changes, in order to elucidate the underlying mechanism behind the results of different processes. Proteins are usually found in high concentrations in foods; furthermore, these proteins frequently may either initially be part of a solid food or may become insoluble due to processing. As a result, many of the traditional biochemical methods for analysis of protein structural properties in dilute solution cannot be applied directly to study food proteins. This chapter gives an overview of some potential methods which may be used to monitor the changes in quaternary, tertiary, secondary and primary structure of proteins in food systems.

Combination of peptide profiling by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and immunodetection on single glands or cells

The combination of two sensitive and powerful analytical techniques on the same biological sample was examined: (i) matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), which gives informative peptide profiling on complex samples such as organs or cells; (ii) immunological tools such as enzyme-linked immunosorbent assay (ELISA) and immunocytochemistry to probe for specific peptides in biological extracts or cells. The cellular expression of the two precursors of the hyperglycemic hormone (cHH) was analyzed in neurosecretory cells (30-micron diameter) from the crayfish Orconectes limosus. Neurohemal organs were used to optimize the sample preparation and to demonstrate that, after peptide fingerprinting by MALDI-TOF MS, the sample can be recovered from the MALDI plate for further immunological analysis by ELISA. It was also established that, after immunocytochemistry following 4% paraformaldehyde fixation of the organ, the stained tissue could be recovered for further MALDI-TOF MS analysis. This dual characterization was successfully scaled down to the level of a single crayfish neurosecretory cell. Direct peptide profiling by MALDI-TOF MS on a single cHH-producing cell previously identified by immunocytochemistry demonstrated that both procHH isoforms were expressed in each cell analyzed.

Determination of diethylpyrocarbonate-modified amino acid residues in alpha 1-acid glycoprotein by high-performance liquid chromatography electrospray ionization-mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry

The chemical modification reagent diethylpyrocarbonate (DEPC) was used to modify alpha 1-acid glycoprotein (orosomucoid, OMD) under various conditions. The extents of DEPC modification of the histidine and tyrosine residues were followed by UV spectrophotometry. The resulting modified OMD was analyzed using enzyme digestion, reverse-phase HPLC, electrospray ionization-mass spectrometry (ESI/MS), and matrix-assisted laser desorption ionization time-of-flight-mass spectrometry (MALDI-TOF/MS). The inherent problem of instability of DEPC-modified histidine residues was overcome by adjusting the time scale of the postreaction processing of modified OMD. There were observed differences in reactivity of histidine 97 and histidine 100 that were consistent throughout the pH range 6-8. Furthermore, several lysine residues were modified and the amount of modification increased over the pH range 6-8. These experiments show that HPLC-ESI/MS and MALDI-TOF/MS analysis coupled with enzyme digestion provide the necessary information to describe the reaction of DEPC with OMD. In addition, the results provide the carbethoxy-histidine stability and histidine reactivity information of DEPC-modified OMD necessary for the design of experiments to characterize the drug binding properties of OMD.

Applications of mass spectrometry to the characterization of oligonucleotides and nucleic acids

Mass spectrometry-based techniques continue to undergo active development for applications to nucleic acids, fueled by methods based on electrospray and matrix-assisted laser desorption ionization. In the past two years, notable advances have occurred in multiple interrelated areas, including sequencing techniques for oligonucleotides, approaches to mixture analysis, microscale sample handling and targeted DNA assays, and improvements in instrumentation for greater sensitivity and mass resolution.

Direct comparison of infrared and ultraviolet wavelength matrix-assisted laser desorption/ionization mass spectrometry of proteins

In an effort to gain an understanding of the processes governing matrix-assisted laser desorption/ionization (MALDI), we made a direct comparison of ultraviolet (UV)- and infrared (IR)-MALDI linear time-of-flight mass spectra of proteins obtained from the same samples and matrices (on the same sample surface), using two different lasers, each having short duration (< 10-ns) pulses, i.e., a tunable wavelength Nd:yttrium aluminum garnet (YAG) pumped optical parametric oscillator laser operating at 2.94 microns and a Nd:YAG laser operating at 355 nm. We observed that (1) the IR-MALDI and UV-MALDI spectra of a given protein from the same matrix were strikingly similar; (2) protein ions produced by IR-MALDI experienced less fragmentation than those produced by UV-MALDI; and (3) photochemical adducts produced during UV-MALDI were absent in IR-MALDI. These results lead us to speculate on the mechanisms for the ionization process in UV- and IR-MALDI. Because photons with a wavelength of approximately 3 microns are unlikely to effect electronic excitation of the matrix at the irradiance used for MALDI we propose that ionization in IR-MALDI occurs as a natural consequence of the solid-to-gas phase transition induced by the IR irradiation, and involves proton transfer reactions in the intermediate phase between solid and gas. The strikingly similar UV- and IR-MALDI mass spectra leads us to the additional proposal that ionization in UV-MALDI may also be a natural consequence of the phase transition and that electronic excitation may not play a primary role in the ionization process.

Analysis of peptide synthesis products by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry is an easy, rapid method for the verification of proper peptide synthesis and for the identification of most synthetic by-products. A synthesis-purification scheme has been described that uses mass analysis to (1) confirm the presence of the proper product in the crude peptide mixture, (2) guide the purification process, and (3) confirm the mass and purity of the final product. Even though many of these steps could be performed just as well with other ionization techniques, the liquid-flow characteristics of electrospray source are clearly an advantage when LC-MS is required. In addition, the ease with which fragment ions can be generated to provide structural information, even with the least sophisticated instruments, is a further advantage of ESI-MS. Although much of the operation described here was done manually, many of the steps could be automated with little additional effort (e.g., use of an autosampler). Quadrupole and ion trap instruments are widely available at present and provide the chemist with a variety of instruments from which to choose. Electrospray time-of-flight instruments will be commercially have just become available and should also provide similar results. As electrospray instruments continue to evolve, the instruments display greater performance and enhanced user-friendly interfaces, yet are lower in price and smaller in size. These features should lead to even more widespread use for the characterization of synthetic peptides.

Sequencing branched peptides with CID/PSD MALDI-TOF in the low-picomole range: application to the structural study of the posttranslational polyglycylation of tubulin

Sequencing conditions for postsource decay and collision-induced dissociation/postsource decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry have been optimized to elucidate the structure of polyglycylation of tubulin. This posttranslational modification involves the linkage of multiple glycine residues through the gamma-carboxyl of glutamic acid residues in the carboxyl termini of the protein. Individual alpha- and beta-tubulin polypeptides contain respectively three and four potential glycylation sites. The sample preparation we used was the thin-layer preparation of the target specimen in the presence of alpha-cyano-4-hydroxycinnamic acid and nitrocellulose. The study of different synthetic polyglycylated peptides fragmentation (modified peptides with the linear sequence DATAEEEGEFEEEGEQ) shows that the peptides fragment regularly to form major fragments of b- and y-type ions with negligible side-chain fragmentation. The rules were applied to the structural elucidation of a Paramecium beta-tubulin hexaglycylated peptide available in the subpicomole range. Polyglycylation was identified on the last four glutamic acid residues.

C-terminal sequence determination of modified peptides by MALDI MS

Peptides, cleaved by a mixture of carboxypeptidases CPP and CPY, can be detected by MALDI MS and the amino acid sequence thereby determined by calculation of the differences between consecutive peaks. In the present study we have used derivatizations of Lys and Cys to facilitate identification of these residues. Since the mass values do not readily distinguish Lys from Gln, we have converted Lys to homoarginine by guanidination, allowing simple detection of Lys. To identify the Cys positions in peptides that contain cystine, cysteic acid, or carboxymethylcysteine is not possible using CPY and CPP because of the lack of proteolytic cleavage. Instead we find that identification of Cys residues within the sequence can be achieved after conversion to a basic derivative, 4-thialaminine (Thi), by trimethylaminoethylation.

Accurate mass measurements using MALDI-TOF with delayed extraction

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry is now an essential tool in biopolymer analysis. Sensitivity and mass range are unsurpassed, but mass measurement accuracy and resolution have been limited. With delayed extraction and a reflecting analyzer, mass measurements using MALDI-TOF can be made with an accuracy of a few parts per million (ppm). It is possible to distinguish Lys from Gln in peptides, and to determine the elemental composition of smaller molecules (mass 100-500). In database searching strategies, a smaller mass window, resulting from an increase in mass accuracy, greatly decreases the number of possible candidates. Mass measurement accuracy with errors less than 5 ppm is demonstrated on a mixture of 12 peptides ranging in mass from ca. 900 to 3700 Da. Mass measurements on 13 peaks in an unseparated tryptic digest of myoglobin gave results with an overall average error less than 3.5 ppm, with a maximum error of 7 ppm.

Efficient peptide ladder sequencing by MALDI-TOF mass spectrometry using allyl isothiocyanate

A new modification of the peptide ladder sequencing technique is described in which allyl isothiocyanate (AITC) replaces trifluoroethyl isothiocyanate as the volatile amine-modification reagent. AITC is commercially available, readily purified, stable up to 80 degrees C and reacts cleanly and rapidly with all amino groups of polypeptides. Several model peptides and two side chain-modified peptides were sequentially degraded using AITC and the cleavage reagent heptafluorobutyric acid (HFBA) up to seven amino acids from the N-terminus. Matrix-assisted laser-desorption and ionization coupled with time-of-flight (MALDI-TOF) mass spectroscopy of the peptide mixture provided a clear ladder-like mass profile with consecutive molecular ions corresponding to each shortened peptide at picomole range. The results indicate the general utility of this analytical protocol by the use of AITC as the amine-coupling reagent.

Purification and characterization of flavoproteins and cytochromes from the yellow bioluminescence marine bacterium Vibrio fischeri strain Y1

Several flavoproteins and cytochromes that occur as major components in extracts of the yellow bioluminescence Y1 strain of the marine bacterium Vibrio fischeri have been purified and characterized with respect to their mass (SDS/PAGE and matrix-assisted laser-desorption/ionization MS), chromatographic properties, N-terminal sequence, and spectroscopy (absorption, fluorescence emission and anisotropy decay). The investigated proteins were as follows: yellow fluorescence protein (YFP) with bound riboflavin, FMN or 6,7-dimethyl-8-ribityllumazine; a blue fluorescence protein (BFP) with bound 6,7-dimethyl-8-ribityllumazine, riboflavin, or 6-methyl-7-oxo-8-ribityllumazine; thioredoxin reductase with FAD as ligand; and two c-type diheme cytochromes, c551 and c554. We present evidence that the riboflavin-bound YFP has an N-terminal sequence corresponding to that published for the dimeric YFP. We show that an equilibrium replacement of the riboflavin can be made with excess lumazine derivative and that lumazine-bound YFP has different bioluminescence properties to those of the lumazine protein from Photobacterium leiognathi. BFP is a different protein again, and in the bacterial lysate it occurs in multiple forms, ligated to either riboflavin, lumazine, or the 7-oxolumazine derivative. The N-terminal sequence for BFP shows similarities to those of the YFP proteins and to lumazine protein and riboflavin synthase from Photobacterium. BFP in any form has no bioluminescence or riboflavin-synthase activity. A 70-kDa fluorescent flavoprotein with FAD as ligand has an N-terminal sequence highly similar to those of thioredoxin reductases from Haemophilus influenzae and Escherichia coli. Cytochrome contaminations in previous preparations of YFP have been removed and are identified as the two c-type cytochromes c551 and c554. Both inhibit the NADH-induced bioluminescence in the reductase/luciferase system with the luciferases from P. leiognathi and V. fischeri. The N-terminal amino acid sequence of the cytochrome (c551) corresponds to a diheme cytochrome c4. The spectral properties of c554 are similar to those of other c5 cytochromes, and both c554 and c551 have absorption spectra similar to those of the respective cytochromes from the gram-negative bacteria Pseudomonas and Azotobacter.

C-terminal sequence analysis of peptides and proteins using carboxypeptidases and mass spectrometry after derivatization of Lys and Cys residues

C-Terminal sequence analysis of peptides and proteins using carboxypeptidase digestion in combination with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is convenient for protein and peptide characterization. After a short digestion, a sequence up to 20 residues can be identified, but the total number depends on the individual sequence. Due to the accuracy limits of the MALDI time-of-flight arrangement, the assignment of several residues with close mass values, including Lys/Glx, may remain ambiguous. We have used derivatization of lysine residues by guanidination to overcome the problem of Lys identification. The reaction is rapid and specific and results in full derivatization. In the case of Cys-containing peptides, problems arise from the fact that carboxypeptidases Y and P do not cleave peptides that contain nonderivatized cystine, cysteic acid, or (carboxymethyl)cysteine. Successful identification of Cys residues within the sequence is instead achieved by conversion of Cys to 4-thialaminine by (trimethylamino)-ethylation. The two derivatizations of Lys and Cys side chains provide opportunities for proton attachment and therefore facilitate the analysis by MALDI-MS. This C-terminal sequence analysis method is also useful for large proteins after fragmentation with specific enzymes.

Metal complexation reactions of quinolone antibiotics in a quadrupole ion trap

We have undertaken a systematic study of the nature of quinolone metal complexes formed by electrospray ionization and laser desorption/ion-molecule reactions to evaluate the analytical utility of metal complexation as an alternative to conventional ionization via protonation. Metal ionization with laser-desorbed copper and nickel ions results in addition products of the form (L + Cu+) and (L + Ni+), respectively, where L is the quinolone, whereas addition-elimination products of the form (L + Co(+)-28) are observed when cobalt is used. The elimination of CO in order to form this unusual latter product seems to be favored by the formation of a cyclized structure that is stabilized by intramolecular hydrogen bonding. The CAD patterns of the Ni+ complexes prove to be the most structurally informative, more so than the fragmentation patterns of the protonated quinolones. Quinolone-metal complexes of the type [MII(L-H+)-(dipy)]+, where M is either Cu, Co, or Ni and dipy is 2,2'-dipyridine, are generated by electrospray ionization of a methanolic solution containing a quinolone antibiotic, a transition metal ion salt, and an auxiliary diimine ligand. Upon collisional activation, the ESI-generated complexes dissociate predominantly by loss of CO2, which is also the most common fragmentation pathway for the metal complexes formed through laser desorption/ion-molecule reactions. However, there are fewer structurally diagnostic fragment ions in the CAD spectra of the ESI complexes relative to those of the LD complexes.

Biochemical mass spectrometry: worth the weight?

The utility of mass spectrometry for the analysis of biological molecules has been enhanced by the development of two techniques that generate gas-phase ions via nondestructive vaporization and ionization. These techniques can be used not only to determine the primary structure of biological molecules with unprecedented accuracy, but also to map noncovalent biomolecular interactions.

Interpretation of oligonucleotide mass spectra for determination of sequence using electrospray ionization and tandem mass spectrometry

Procedures are described for interpretation of mass spectra from collision-induced dissociation of polycharged oligonucleotides produced by electrospray ionization. The method is intended for rapid sequencing of oligonucleotides of completely unknown structure at approximately the 15-mer level and below, from DNA or RNA. Identification of sequence-relevant ions that are produced from extensive fragmentation in the quadrupole collision cell are based primarily on (1) recognition of 3'- and 5'- terminal residues as initial steps in mass ladder propagation, (2) alignment of overlapping nucleotide chains that have been constructed independently from each terminus, and (3) use of experimentally measured molecular mass in rejection of incorrect sequence candidates. Algorithms for sequence derivation are embodied in a computer program that requires < 2s for execution. The interpretation procedures are demonstrated for sequence location of simple forms of modification in the base and sugar. The potential for direct sequencing of components of mixtures is shown using an unresolved fraction of unknown oligonucleotides from ribosomal RNA.