Comparison of 252californium plasma desorption and fast atom bombardment mass spectrometry for analysis of small peptides

Origins, Technological Development, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.

Characterization of braun's lipoprotein and determination of its attachment sites to peptidoglycan by (252)Cf-PD and MALDI time-of-flight mass spectrometry

A strategy for the characterization of bacterial lipoprotein-in this case Braun's lipoprotein (an outer membrane 7-ku lipoprotein) isolated from Escherichia coli-is described by time-of-flight mass spectrometric (TOF/MS) techniques [(252)Cf plasma desorption (PD) TOF/MS and matrix-assisted laser desorption-ionization (MALDI) TOF/MS]. Covalent linkage of lipid at the N-terminal cysteine (posttranslationally modified to a S-[2,3-bis(acyloxy)-propyl]-N-acylcysteine) and, therefore, strict insolubility in aqueous solution constitute common features for this class of proteins. Relative molecular mass determination of the major molecular species of Braun's lipoprotein was obtained by selection of an appropriate mixture of organic solvents compatible with matrix/support materials useful for the mass spectrometric techniques applied. Minor components of this lipoprotein that differ only in the fatty acid composition of the lipid anchor were detected by PD TOF/MS after enzymatic release of the extremely hydrophobic N-terminal amino acid followed by selective extraction with chloroform. Part of the primary sequence of this lipoprotein was confirmed based on peptide fragment ions observed in the positive ion PD mass spectra of cyanogen bromide-generated peptide fragments that had been isolated previously by reverse phase high-performance liquid chromatography (HPLC). Peptidoglycan fragments that represent the attachment sites of lipoprotein to peptidoglycan were enzymatically released, separated by reverse phase HPLC, and finally characterized by time-of-flight mass spectrometric techniques ((252)Cf-PD TOF/MS, MALDI TOF/MS). The results obtained with both techniques differed only in the better sensitivity obtained with MALDI TOF/MS, which consumed a factor of 100 to 1000 less material than with PD TOF/MS.

Fragmentations of dipeptides in plasma desorption mass spectrometry: new rules for the sequence elucidation of oligopeptides

252Cf plasma desorption mass spectrometry is well suited for determining both composition and sequence of unknown small oligopeptides. A systematic study of a large number of dipeptides first leads to establishing common rules of fragmentation from positive ion mass spectra. These rules are then applied to the sequence elucidation of larger peptides.

Performances and limits of plasma desorption mass spectrometry in the primary structure determination of proteins

The resolution, sensitivity, matrix effect, cationization and spectral suppression in plasma desorption mass spectrometry (PD-MS) were investigated in the context of peptide analysis. Excessive cationization may be avoided by the addition of citric acid on the target. The importance of the relative net charge of peptides in PD-MS spectra suppression was confirmed. Esterification of peptides is shown to be an easy way to overcome spectral suppression. Provided that cationization and spectral suppression of peptides are under control, PD-MS is an excellent tool for protein sequence analysis, affording the necessary complement to automated Edman degradation.

Collisionally induced fragmentation of protonated oligoalanines and oligoglycines

In a hybrid instrument under minimal multiple-collision conditions, the collision-induced fragmentation of the [M + H]+ ions of tetraalanine and tetraglycine are dominated by the gamma 2 fragment, in distinction to the fragmentation of the [M + H]+ ions of hexa- and octaalanine and -glycine; these latter fragmentations are instead a distribution of b and y ions, and to a lesser extent a ions. This difference may be rationalized on the basis of control of the fragmentation by the most basic site in the peptide, which may be identified by taking internal hydrogen bonding into account. On increasing the collision energy from 10 to 150 eV, a, b and y ions of lower mass appear; and in several cases a peak due to a smaller b ion becomes the base peak. The ion distribution in the spectra of these protonated peptides serves as a baseline from which the effects of conformation on side-group rearrangements and other fragmentations may be explored.

Sequence determination of N-acetylated-N,O-permethylated peptides by plasma desorption mass spectrometry

The plasma desorption mass spectra of N-acetylated-N,O-permethylated peptides contain sufficient fragment ions to allow partial or complete sequence determination. By optimization of the derivatization procedure and an inclusion of a purification step by high-performance liquid chromatrography (HPLC) overall sensitivities on the high picomole level are obtained. By using limiting derivatization conditions the fully derivatized peptide is easily selected from the HPLC separation. Mainly N-terminal sequence ions are observed, facilitating sequence determination of naturally N-blocked peptides. Complete sequence determination of naturally formylated gramicidin A containing 15 amino acid residues and the naturally N-acetylated N-terminal heptapeptide from an acyl-CoA binding protein is demonstrated. The sequence of the first six N-terminal residues was obtained by derivatization of the A-chain of insulin.

Hydrophobic surfactant-associated polypeptides: SP-C is a lipopeptide with two palmitoylated cysteine residues, whereas SP-B lacks covalently linked fatty acyl groups

Pulmonary surfactant contains two hydrophobic polypeptides, SP-B and SP-C, with known amino acid sequences and with truncated subforms lacking the N-terminal residues. Treatment of SP-C with KOH releases fatty acids (palmitic acid to more than 85%) in molar ratios of 1.8-2.0 relative to the polypeptide. Furthermore, plasma-desorption mass spectrometry shows native SP-C of both the intact and truncated types to be monomers with masses about 500 units higher than those expected for the polypeptide chains. After treatment with KOH, trimethylamine, or dithioerythritol, the polypeptide masses are obtained. These results prove that native SP-C is a lipopeptide with two palmitoyl groups covalently linked to the polypeptide chain. The deacylation conditions, the presence of two cysteine residues in the polypeptide, and the absence of other possible attachment sites establish that the palmitoyl groups are thioester-linked to the two adjacent cysteine residues. In contrast, the major form of porcine SP-B is a dimer without fatty acid components. That SP-C is a true lipopeptide with covalently bound palmitoyl groups suggests possibilities for functional interactions. It gives a direct physical link between SP-C and surfactant phospholipid components. Long-chain acylation may constitute a means for association of proteins with membranes and could conceivably modulate the stability and biological activity of surfactant films.

New results of hemoglobin variant structure determinations by fast atom bombardment mass spectrometry

Fast atom bombardment mass spectrometry has already been used for the identification of mutations in abnormal human hemoglobin chains. This paper presents new results obtained with this technique. The methodology used here is compared with more conventional biochemical techniques and automated microsequencing. In every case, a well-chosen combination of peptide-high performance liquid chromatography, mass spectrometry, amino acid analysis, and sequence analysis led rapidly to the identification of the mutant. The high sensitivity of these techniques holds great promise for the analysis of molecular abnormalities in various genetic disorders presently detectable only by the application of a molecular biological approach.

Rapid identification of calbindin-D28k cyanogen bromide peptide fragments by plasma desorption mass spectrometry

Chicken intestinal calbindin-D28k is an intracellular protein which is believed to have a fundamental role in vitamin D-mediated transport of calcium. A mapping approach based on 252Cf plasma desorption mass spectrometry (PD mapping) was used to screen the DNA-deduced sequence of calbindin-D28k for sequence changes and post-translational modifications. In the PD mapping experiment, purified calbindin-D28k was cleaved with cyanogen bromide and the resulting peptides were subjected to PD mass spectrometric analysis either as a mixture or as high-performance liquid chromatography isolated fractions. The DNA-derived primary structure of calbindin-D28k was confirmed by rapid PD mass spectral identification of the CNBr peptide fragments, and the nature of the N-terminal blocking group was readily determined to be an acetyl group. The relatively non-destructive nature of the PD mass spectrometric analysis allowed the mapping of the N-terminal peptide through an additional in situ V8 protease enzymatic reaction.

Comparison of 252Cf plasma desorption mass spectrometry and fast atom bombardment mass spectrometry in identification of simple monoglucosyl conjugates

The fast atom bombardment (glycerol) and 252Cf plasma desorption mass spectra of 16 simple monoglucosyl conjugates have been compared. Plasma desorption mass spectrometry, in general, has been found to be the superior technique for characterizing these low molecular weight conjugates because of the relative absence of interfering matrix peaks.

Peptide and protein mapping by 252Cf-plasma desorption mass spectrometry

The mapping of peptide digests by using fast atom bombardment mass spectrometry for evaluating the correctness of known or expected protein sequences is a well-established strategy. A similar approach ("PD mapping") is described which utilizes 252Cf-plasma desorption mass spectrometry (PDMS). This PD mapping approach is demonstrated and evaluated by screening the DNA-deduced sequences of recombinant interleukin-2 and human growth hormone. In the PD mapping experiment, the protein is cleaved either chemically or enzymatically and the molecular weights of the peptides predicted from the proposed amino acid sequence are compared with those determined mass spectrometrically. The relatively nondestructive nature of the PD mass spectrometric analysis allows further confirmation of the sequence assignments of individual peptides through additional steps of enzymatic or chemical modification on the nitrocellulose-bound peptides. The PD mapping method is both fast and sensitive, requiring only low nanomole amounts per map.

A study of the positive and negative ion fast atom bombardment mass spectra of alpha-amino acids

The fast atom bombardment mass spectra of 24 alpha-amino acids have been studied. These include the mass spectra as well as the metastable ion MI and collisional activation CA spectra of [M + H]+ and [M - H]- ions. The extent of the common neutral losses as NH3, H2O and CO2H2 in the positive ion spectra is governed by the nature of the side chain. The relationship between the fragmentation behaviour of the negative ions and the presence of particular functional groups is less obvious. Mixtures of amino acids in glycerol show pronounced surface effects.