Protein conformational changes determined by matrix-assisted laser desorption mass spectrometry

Caldesmon is an actin/calmodulin/tropomyosin protein located in the thin filaments of smooth muscle cells and microfilaments of nonmuscle cells. Two isoforms of caldesmon, h- and l-types, shown to exist in vertebrate smooth and nonmuscle cells respectively, are produced by alternative splicing of the caldesmon mRNA encoded by a single gene. To study the expression of smooth muscle specific h-caldesmon during the differentiation of mesenchymal cells into smooth muscle cells, soluble protein and total RNA from the gizzard primordium in the gut region of 5-day and gizzards of 7-, 9-, 13-, 17- and 21-day embryos and 2-days post-hatch chicks were extracted and analyzed for caldesmon expression at both protein and mRNA levels. Western blot analysis of proteins and immunofluorescence microscopy of tissue section were carried out using an antibody specific for h-caldesmon. Total RNA was analyzed by Northern blotting using a caldesmon cDNA probe, and h- and l-caldesmon cDNAs were identified due to the difference in their molecular sizes (4.8 and 4.1 kb respectively). The mRNA was also analyzed by reverse transcribed-polymerase chain reaction (RT-PCR) and Southern blot analysis. Our results show that the I-caldesmon mRNA was expressed at higher levels in the gizzard primordium during the early stages of development, and decreased gradually during growth. The h-caldesmon protein and mRNA, not expressed at day 5, is minimally expressed at day 7 and is fully turned on by day 9. Additionally, sequence analyses of the RT-PCR products of I-caldesmon showed that it lacked the spacer region, as predicted. RT-PCR analysis of total RNA gave two h-caldesmon fragments. These two fragments were identified as two different isoforms of h-caldesmon since they both contained the spacer region. They also showed homology in the region of exon 4 had differences in the region of exon 3b.     

Genotyping of apolipoprotein E by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The genotyping of the various isoforms of Apolipoprotein E (apo E) has been performed using matrix-assisted laser desorption/ionization (MALDI-MS). The polymerase chain reaction was used to amplify the specific apo E gene sequence followed by digestion with Cfo I (Clostridium formicoaceticum), for generating restriction fragments for rapid and accurate mass analysis. An exonuclease I digestion step was introduced to remove the unused primers after PCR, which can otherwise interfere in the mass spectral analysis. By replacing the gel electrophoresis detection step with MALDI-MS, restriction isotyping of the apo E gene was achieved. Genotyping of an unknown sample and obtained from an independent diagnostic laboratory demonstrated the validity of the MALDI-MS method for the routine analysis of apo E.     

Evaluation of IgG glycation levels by matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry has been employed for the evaluation of the glycation level of IgG from healthy subjects and also from well- and badly-controlled diabetic patients. The measurements have been performed on untreated plasma protein fractions. The data obtained have shown that a clear mass increase, originating from non-enzymatic glycation processes, is observed in the case of diabetic patients: for well-controlled ones it is in the range 512-1565 Da, while it becomes 827-4270 Da for badly-controlled diabetic patients. This approach indicates that MALDI mass spectrometry is a highly specific tool that can be employed in the metabolic control of diabetic patients and in studies relating the IgG glycation level to possible immunological impairment.     

Characterization of enzymatic pectin digests by matrix-assisted laser desorption/ionization mass spectrometry

The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the characterization of partially methyl-esterified enzymatic pectin digests is described. The sensitivities of several matrices, positive and negative ion modes and desalting techniques for these acidic oligosaccharides were compared. The most favorable results were obtained with a thin-layer preparation of a mixture of 2,4,6-trihydroxyacetophenone and nitrocellulose in the negative ion mode. Results are presented demonstrating the sensitive characterization of separated and unseparated high-ester pectin digests obtained after complete digestion using Aspergillus niger pectin lyase and the analysis of digests after chemical modification. In the case of unseparated digests, the analysis of methylation patterns is demonstrated. Oligomers with a degree of polymerization up to 40 were detected after enrichment of large oligomers by propan-2-ol precipitation.     

Unknown peptide sequencing using matrix-assisted laser desorption/ionization and in-source decay

The results of a study to determine the utility of in-source decay fragmentation of matrix-assisted laser-desorbed ions for obtaining useful sequence information on unknown peptides are presented. Six peptides were purified by high-performance liquid chromatography and submitted as single blind unknowns. The in-source decay fragment ion data were collected on a linear time-of-flight mass spectrometer equipped with delayed extraction. These fragment ion data were manually interpreted on the basis of known fragmentation pathways to determine a proposed sequence. The proposed sequences for three of the unknowns were essentially correct, with a few minor errors. A fourth unknown had significant errors associated with its proposed sequence due to misinterpretation of the fragmentation data. Two unknowns were found to have undergone significant sample degradation prior to analysis, which compromised the results for these samples. An example of the use of protein database searching of a partial peptide sequence to aid in a sequence determination is also presented.     

Accurate peptide sequencing by post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Partial 18O-labeling of peptides has been applied to post-source decay experiments in a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. The ions which originate from the carboxyl terminus of a peptide partially retain 18O atoms which have readily been incorporated into the C-terminal carboxyl groups during enzymatic hydrolysis in a buffer containing 40 atom percent H218O. The isotopic resolution of singly charged precursor ions and their product ions obtained for peptides up to ca. 2800 Da has been achieved using the delayed extraction method, which permits the rapid identification and assignment of the 18O-labeled and non-labeled ion species in the PSD spectra. The results obtained from several 18O-labeled peptides, derived from an enzymatic digest, demonstrate the accuracy and reproducibility of the present method, which will be in widespread use for protein identification via database searching or for investigations of totally unknown proteins.     

Anion dopant for oligosaccharides in matrix-assisted laser desorption/ionization mass spectrometry

Visible light (>470 nm) irradiation of an oxygen-saturated solution of C-phycocyanin (C-PC) in the presence of the spin trap 5, 5-dimethyl-1-pyrroline-N-oxide (DMPO) gave an ESR spectrum characteristic of the DMPO-hydroxyl radical spin adduct DMPO-OH. The signal intensities of DMPO-OH adduct were enhanced by superoxide dismutase (SOD) and partly inhibited by catalase. It was partly responsible for the production of DMPO-OH that superoxide anion radical (O.-2) dismutated to generate hydrogen peroxide (H2O2) which decomposed ultimately to generate the highly reactive .OH. In addition, it can be concluded that singlet oxygen (1O2) was an important intermediate according to the strong inhibitory action of 1,4-diazabicyclo[2.2.2]octane (DABCO) and histidine on DMPO-OH formation. The experimental results suggest that photodynamic action of C-PC proceed via both type I and type II mechanisms. Furthermore, the decay kinetics of DMPO-OH adduct, the effects of DMPO and C-PC concentrations as well as irradiation time on DMPO-OH adduct formation were also discussed. Concentration of C-PC should be an important factor to influence the ESR signal intensities of DMPO-OH. Therefore, it may be concluded that reasonably lower concentration of C-PC might prolong the duration of photosensitized formation of .OH and might strengthen the photodynamic action.     

Structure analysis of trivalent glycoclusters by post-source decay matrix-assisted laser desorption/ionization mass spectrometry

Post-source decay (PSD) matrix-assisted laser desorption/ionization time-of-flight mass spectra were found to be useful for the structural elucidation of a series of tris [2-(glycosylthiourylene)ethyl]amines. The reported fragmentation behaviours of [M + H]+, [M + Na]+ and [M - H]- ions differ from each other significantly; however, they can be compared to tree pruning in every case. Whereas detailed structural information on unprotected glycoclusters is obtained from all PSD experiments, only the positive-ion mode can be used to gain relevant information about the acetylated glycoclusters.     

Identification of urinary oligosaccharides by matrix-assisted laser desorption ionization time-of-flight mass spectrometry

A new method of urinary oligosaccharides identification by matrix-assisted laser desorption time-of-flight mass spectrometry is presented. The method involves three steps: coupling of the urinary oligosaccharides with 8-aminonaphthalene-1,3,6-trisulfonic acid; fast purification over a porous graphite carbon extraction column; and mass spectrometric analysis. Identification of urinary oligosaccharides is based on the patterns and values of the pseudomolecular ions observed. We report here the patterns in urines from patients with Pompe disease, alpha and beta mannosidoses, galacto-sialidosis, and GM1 gangliosidosis. The protocols described here allowed facile and sensitive identification of the pathognomonic oligosacchariduria present in lysosomal diseases and can be extended to any pathological oligosacchariduria.     

Optimization of a hydrophobic solid-phase extraction interface for matrix-assisted laser desorption/ionization

Matrix-assisted laser desorption/ionization (MALDI) probe surfaces derivatized with octadecanethiol (C18) can be used as hydrophobic solid-phase extraction devices to isolate and desalt biopolymers directly on the probe surface. Using quantitative MALDI, it was possible to determine the approximate amount of peptide that bound to C18 surfaces and thus to calculate a surface density. It was determined that the amount of peptide bound at the probe surface was independent of the analyte concentration in the immersion solution (from high- to sub-ng ml-1 concentrations), but rather was dependent on the immersion time of the surface as it was exposed to the analyte. The capacity of C18-derivatized probes to bind biopolymers in fixed amounts frees the analyst from the necessity for adjusting analyte concentration through multiple step procedures such as serial dilution or vacuum drying. This time savings result in an overall increase in the efficiency of the MALDI technique.     

Off-line coupling of capillary electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

An automated fraction collection interface is used in conjunction with matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry to analyze material isolated by capillary electrophoresis (CE). CE fractions are deposited directly on the MALDI probes so that individual peaks from the electropherogram are associated with a single sample spot on the probe. MALDI matrices with high acid concentrations afford enhanced tolerance of electrophoresis buffers. The utility of this hybrid instrument is demonstrated by separation and mass analysis of a tryptic digest of cytochrome c and synthetic mixtures of four proteins. Mass assignments corresponding to the protonated molecular ions are in good agreement with those predicted from molecular structure. Miniaturization of the interface affords enhanced sensitivity, with good-quality spectra from separations of as little as 25 fmol of protein.     

Lipid analysis by matrix-assisted laser desorption and ionization mass spectrometry: A methodological approach

It has been hypothesized that protein factors may protect CpG islands from methyltransferase during development and that demethylation may involve protein-DNA interactions at demethylated sites. However, direct evidence has been lacking. In this study, demethylation at the EBNA-1 binding sites of the Epstein-Barr virus latent replication origin, oriP, was investigated by using human cells. Several novel findings are discussed. First, there are specific preferential demethylation sites within the oriP region. Second, the DNA sequence of oriP alone is not the target of an active demethylation process. Third, EBNA-1 binding is required for the site-specific demethylation in oriP. Interestingly, CpG sites adjacent to and between the EBNA-1 sites do not become demethylated. Fourth, demethylation of the first DNA strand in oriP at the EBNA-1 binding sites involves a passive (replication-dependent) mechanism. The second-strand demethylation appears to occur through an active mechanism. That is, EBNA-1 protein binding prevents the EBNA-1 binding sites from being remethylated after one round of DNA replication, and it appears that an active demethylase then demethylates these hemimethylated sites. This study provides clear evidence that protein binding specifies sites of DNA demethylation and provides insights into the sequence of steps and the mechanism of demethylation.     

Analysis of phospho- and glycopolypeptides with infrared matrix-assisted laser desorption and ionization

The analytical characteristics of infrared (IR) matrix-assisted laser desorption and ionization (MALDI) were investigated for the analysis of phosphopeptides, a phosphopolypeptide, and glycopeptides. Two commercially available instruments, a high-resolution delayed extraction (DE) reflectron time-of-flight (RETOF) mass spectrometer and a high-power pulsed Er:YAG laser, were interfaced to produce a high-resolution MALDI-DE-RETOF instrument that is easy to use and can be switched between UV- and IR-MALDI mode within seconds. In the interface design, particular attention was paid to maintaining the same professional operating environment for the new IR-MALDI mode as exists for the commercial UV-MALDI mode. This instrument configuration facilitates comparative observation and investigation of the relative analytical merits of IR- and UV-MALDI. The results of studies of the tryptic alpha-casein phosphopeptides, RP1 (a Thr45-monophosphorylated congener of the recombinant protein hirudin variant 1), and fetuin Asn81 tryptic glycopeptides are presented. The elimination of labile substituents such as phosphoric acid and sialic acid is suppressed in IR-MALDI-RETOF mass spectrometry, with concomitant higher analyte ion yields. These results reflect the advantages that accrue from deposition of significantly less internal energy in the case of IR-MALDI.     

Identifying the glycosylation sites and site-specific carbohydrate heterogeneity of glycoproteins by matrix-assisted laser desorption/ ionization mass spectrometry

A sensitive and facile method is described to identify the glycosylation sites and site-specific heterogeneity in the carbohydrate attached to glycoproteins. In this procedure, the peptide backbone of the glycoprotein is cleaved enzymatically. The resulting peptide/glycopeptide mixture is divided into three fractions. The first is analyzed directly by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), while the other two aliquots are analyzed by MALDI-MS after enzymatic release of the N-linked chains and the N- and O-linked chains. Comparison of these MALDI mass spectra provides the molecular weight of each carbohydrate side chain and of the peptide to which it was attached. This information combined with the amino acid sequence of the protein identifies the glycosylation sites, and provides information concerning site-specific oligosaccharide heterogeneity. This approach does not require time-consuming liquid chromatographic separations and can be performed on as little as 10 pmol of glycoprotein. Thus, our approach is faster and simpler than procedures currently used for glycosylation site mapping, and may offer a slight sensitivity advantage.     

Enhanced detection of phosphopeptides in matrix-assisted laser desorption/ionization mass spectrometry using ammonium salts

The hydrolytic degradation of poly(DL-lactide) (PLA50) material was investigated in order to elucidate the effects of temperature and acidity of the external medium on the degradation characteristics. It was observed that at 60 degrees C and at pH = 7.4, degradation was extremely rapid as compared with degradation at 37 degrees C. After only 2 days, heterogeneous degradation was observed due to larger internal autocatalysis. On the other hand, in the case of degradation at 37 degrees C in an acidic medium with pH = 3.7, the heterogeneous degradation was preceded by a much longer lag time. Water absorption was found to be pH dependent. At pH = 7.4, water absorption was increased due to the osmotic pressure driving the buffer solution into the polymer matrix to neutralize acidic endgroups, which was not the case for degradation at pH = 3.7. In both cases, the oligomeric stereocomplex was obtained as degradation residue at the end of the degradation period.     

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.     

Characterization of transthyretin mutants from serum using immunoprecipitation, HPLC/electrospray ionization and matrix-assisted laser desorption/ionization mass spectrometry

A mass spectrometry approach for the detection and identification of variants of the plasma protein transthyretin (TTR) is presented. The single amino acid substitutions found in TTR are closely associated with familial transthyretin amyloidosis (ATTR), a hereditary degenerative disease. A definitive diagnosis of ATTR relies on the detection and identification of TTR variants. The approach presented here is based on isolation of serum TTR using immunoprecipitation. The detection of the variant is achieved by mass measurement of the intact protein with electrospray ionization mass spectrometry (ESIMS). The liquid chromatography/ESIMS analysis of the tryptic digest of the protein followed by subsequent matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry and MALDI postsource decay of the relevant recovered chromatographic fraction containing the variant peptide allows the identification of unknown variants. The method was successfully tested using serum from ATTR patients with known variants (Val30-->Met and Val122-->Ile). A new TTR variant, Ser23-->Asn, was detected and identified using the above method where isoelectric focusing and restriction enzyme analysis failed to identify the nature of the variant.