Deamidation as a Consequence of β-Elimination of Phosphopeptides

Beta-elimination procedures often precede mass spectrometric analyses of phosphorylated peptides. Unfortunately, the commonly employed reaction conditions facilitate the deamidation of amide-containing residues. In addition to being 1 Da heavier than their amide counterparts, the newly created acidic residues greatly influence peptide tandem mass spectra. The effects of deamidation are investigated for five different amide-containing synthetic peptides exposed to beta-elimination conditions. MALDI-generated ions are analyzed with a tandem TOF mass analyzer. Methodologies for estimating the degree of deamidation from peptide mass spectra are presented, the influence that adjacent residues exert on the rate of deamidation is catalogued, and the impact that deamidation can have on peptide tandem mass spectra is demonstrated. The complications this side reaction can cause for automated data interpretation are also noted.

Peptide photodissociation at 157 nm in a linear ion trap mass spectrometer

The photodissociation by 157 nm light of singly- and doubly-charged peptide ions containing C- or N-terminal arginine residues was studied in a linear ion trap mass spectrometer. Singly-charged peptides yielded primarily x- and a-type ions, depending on the location of the arginine residue, along with some related side-chain fragments. These results are consistent with our previous work using a tandem time-of-flight (TOF) instrument with a vacuum matrix-assisted laser desorption/ionization (MALDI) source. Thus, the different internal energies of precursor ions in the two experiments seem to have little effect on their photofragmentation. For doubly-charged peptides, the dominant fragments observed in both photodissociation and collisionally induced dissociation (CID) experiments are b- and y-type ions. Preliminary experiments demonstrating fragmentation of multiply-charged ubiquitin ions by 157 nm photodissociation are also presented.

Fragmentation of oligosaccharide ions with 157 nm vacuum ultraviolet light

The 157 nm photofragmentation of native and derivatized oligosaccharides was studied in a linear ion trap and in a home-built matrix-assisted laser desorption/ionization (MALDI) tandem time-of-flight (TOF/TOF) mass spectrometer, and the results were compared with collision-induced dissociation (CID) experiments. Photodissociation produces product ions corresponding to high-energy fragmentation pathways; for cation-derivatized oligosaccharides, it yields strong cross-ring fragment ions and provides better sequence coverage than low- and high-energy CID experiments. On the other hand, for native oligosaccharides, CID yielded somewhat better sequence coverage than photodissociation. The ion trap enables CID hybrid MS3 experiments on the high-energy fragment ions obtained from photodissociation.

Denaturation of metalloproteins with EDTA to facilitate enzymatic digestion and mass fingerprinting

Metal ions bound to a protein often stabilize tertiary and/or quaternary structure. Consequently, the digestion of metalloproteins that precedes analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is frequently incomplete. It is demonstrated that ethylenediaminetetraacetic acid (EDTA) successfully destabilizes metalloprotein structure and thereby facilitates tryptic digestion and protein identification.

Microdeposition Device Interfacing Capillary Electrochromatography and Microcolumn Liquid Chromatography with Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

A sample deposition device has been constructed and optimized for interfacing CEC and capillary LC columns to MALDI mass spectrometry. For CEC analysis, the device is composed of an inlet buffer reservoir and an outlet buffer reservoir connected to a matrix reservoir through a connection sleeve. The matrix reservoir is connected to a deposition capillary via another connection sleeve. CEC eluent is transported to the matrix reservoir via a capillary that is connected to the deposition capillary by the connection sleeve inside the matrix reservoir. This connection sleeve also acts as a mixing chamber, allowing the CEC eluent to be mixed with matrix prior to deposition. Complex glycan mixtures can be separated by CEC using hydrophilic-phase monolithic columns, with capillary eluent being deposited on a standard MALDI plate along with a suitable matrix solution. Thousands of discrete, highly homogeneous dots can be generated for a subsequent mass spectrometric analysis. With minor modifications, this device is also applicable to capillary LC of peptides using gradient elution. In this configuration, the outlet of the LC column is connected to a deposition capillary inside a matrix reservoir through a connection sleeve that allows mixing of the LC effluent with an appropriate matrix. The device has been evaluated with the tryptic digests of 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.

Fragmentation of amidinated peptide ions

The collision-induced dissociation characteristics of amidinated and unmodified tryptic peptides are compared using an ion trap mass spectrometer with both electrospray ionization and matrix-assisted laser/desorption ionization (MALDI). Several fragmentation pathways in a number of tryptic peptides of various precursor charge states are found to be enhanced. The additional information conveyed by the observed fragment ions should facilitate protein identifications.

Lesions in phycoerythrin chromophore biosynthesis in Fremyella diplosiphon reveal coordinated light regulation of apoprotein and pigment biosynthetic enzyme gene expression

We have characterized the regulation of the expression of the pebAB operon, which encodes the enzymes required for phycoerythrobilin synthesis in the filamentous cyanobacterium Fremyella diplosiphon. The expression of the pebAB operon was found to be regulated during complementary chromatic adaptation, the system that controls the light responsiveness of genes that encode several light-harvesting proteins in F. diplosiphon. Our analyses of pebA mutants demonstrated that although the levels of phycoerythrin and its associated linker proteins decreased in the absence of phycoerythrobilin, there was no significant modulation of the expression of pebAB and the genes that encode phycoerythrin. Instead, regulation of the expression of these genes is coordinated at the level of RNA accumulation by the recently discovered activator CpeR.

Quantitation using enhanced signal tags: a technique for comparative proteomics

Differential amidination of N-termini and lysine residues provides the basis for a novel approach to protein quantitation using MALDI mass spectrometry. Because the amidination of lysines increases their basicity and therefore MALDI ionization yields, the method is called quantitation using enhanced signal tags (QUEST). Amidine labels differ by methylene groups, leading to 14 Da mass differentials. The utility of QUEST is demonstrated while analyzing the digests of two model proteins using MALDI-TOF mass spectrometry.

Artifacts and unassigned masses encountered in peptide mass mapping

In peptide mass mapping of isolated proteins, a significant number of the observed mass spectral peaks are often uninterpreted. These peaks derive from a number of sources: errors in the genome that give rise to incorrect peptide mass predictions, undocumented post-translational modifications, sample handling-induced modifications, contaminants in the sample, non-standard protein cleavage sites, and non-protein components of the sample. In a study of the stalk organelle of Caulobacter crescentus, roughly one-third (782/2215) of all observed masses could not be assigned to the proteins identified in the gel spots (Karty et al., J. Proteome Res., 1 (2002) 325). By interpreting these masses, this work illuminates a number of phenomena that may arise in the course of peptide mass mapping of electrophoretically separated proteins and presents results from a number of related studies.

On-probe digestion of bacterial proteins for MALDI-MS

On-probe digestion combined with MALDI mass spectrometry is studied as a rapid method for the analysis and identification of bacterial proteins. The use of trypsin adsorbed to the probe surface reduces the digestion time from hours to minutes. A high amount of trypsin must be applied to the probe for the successful digestion of bacterial proteins. Mass spectra of the digest contain a number of low-mass digest fragments. Several components of a B. subtilis bacterial digest can be identified through postsource decay and database searching.

Proteomic analysis of the Caulobacter crescentus stalk indicates competence for nutrient uptake

Caulobacter crescentus, a Gram-negative alpha-purple proteobacterium, is an oligotroph that lives in aquatic environments dilute in nutrients. This bacterium divides asymmetrically. Part of this asymmetric cell division involves the formation of a prosthecum at one pole, referred to as the stalk, which replaces the flagellum of the motile swarmer cell. Little is known about the synthesis or function of the stalk. The stalk is an extension of the cell membranes and peptidoglycan layer, and stalk elongation is stimulated by phosphate starvation. In this study, we have taken advantage of two-dimensional gel (2D gel) electro-phoresis as well as the fully sequenced genome of Caulobacter to study the proteome of the stalk. We modified a stalk-shedding mutant strain of Caulobacter crescentus to increase the yield of stalk material shed and performed 2D gel electrophoresis of purified stalks and cellular fractions. Comparison of the stalk 2D gel with the 2D gels of cell membrane and soluble fractions showed that the stalk is mostly free of cytoplasmic proteins and has a profile very similar to that of the cell membrane. Of the 172 proteins on a stalk 2D gel, we report the identification of 64 spots, corresponding to 39 different proteins present in the stalk of Caulobacter. The identifications include several TonB-dependent receptors, two OmpA family proteins, a dipeptidase, GlpQ, two alkaline phosphatases, 3-phytase, a putative TolC protein and 11 proteins of unknown function. These identifications are consistent with the hypothesis that the stalk plays a role in nutrient uptake.

Defining absolute confidence limits in the identification of Caulobacter proteins by peptide mass mapping

A derivatization reaction, guanidination, was recently reported that increases MALDI-TOF MS sensitivity toward lysine-terminated peptides. Its application conveys sequence information that can be used as a parameter in peptide mass mapping database searches. This paper presents a systematic study of the impact of guanidination on proteomic analysis of an entire bacterial organelle. Sixty-two 2-D gel isolated proteins from Caulobacter crescentus stalks were studied. A novel computer algorithm, Prodigies, was developed to analyze the data. Absolute confidence limits associated with protein assignments were established using Monte Carlo simulations of database searches. The advantages of guanidination are illustrated using both experimental and theoretical data.