Gas-phase separations of complex tryptic peptide mixtures

High-resolution ion mobility and time-of-flight mass spectrometry techniques have been used to analyze complex mixtures of peptides generated from tryptic digestion of fourteen common proteins (albumin, bovine, dog, horse, pig, and sheep; aldolase, rabbit; β-casein, bovine; cytochrome c, horse; β–lactoglobulin, bovine; myoglobin, horse; hemoglobin, human, pig, rabbit, and sheep). In this approach, ions are separated based on differences in mobilities in helium in a drift tube and on differences in their mass-to-charge ratios in a mass spectrometer. From data recorded for fourteen individual proteins (over a m/z range of 405 to 1000), we observe 428 peaks, of which 205 are assigned to fragments that are expected from tryptic digestion. In a separate analysis, the fourteen mixtures have been combined and analyzed as one system. In the single dataset, we resolve 260 features and are able to assign 168 peaks to unique peptide sequences. Many other unresolved features are observed. Methods for assigning peptides based on the use of m/z information and existing mobilities or mobilities that are predicted by use of intrinsic size parameters are described. Received: 26 August 2000 / Revised: 15 November 2000 / Accepted: 16 November 2000     

Gas-phase separations of protease digests

A mixture of peptides from a complete tryptic digest of ubiquitin has been analyzed by ion mobility/time-of-flight mass spectrometry techniques. All components of the mixture were electrosprayed and ions were separated in the gas phase based on differences in their mobilities through helium before being dispersed into a time-of-flight mass spectrometer for mass-to-charge analysis. The data show that ions separate into families primarily according to differences in their charge states and, to a lesser extent, differences in conformation. This approach reduces spectral congestion typically associated with electrosprayed mixtures and provides charge assignments for mass-to-charge ratio data. Gas-phase separations of ions appear to provide a new physical basis for characterizing components of biological mixtures.     

Gradient separations of complex mixtures by micro high-performance liquid chromatography

High-performance micro packed fused-silica and open-tubular glass capillary columns were prepared and applied to separations of complex mixtures. Solvent-gradient elution proved quite useful for the separation of solutes with wide polarity. Instruments and some applications are described.     

Using HPTLC/DESI-MS for peptide identification in 1D separations of tryptic protein digests

Desorption electrospray ionization mass spectrometry (DESI-MS) was investigated as a method to detect and identify peptides from tryptic digests of cytochrome c and myoglobin separated on ProteoChrom HPTLC Silica gel 60 F(254s) plates and ProteoChrom HPTLC Cellulose sheets. Full-scan mass spectra and data-dependent tandem mass spectra were acquired in separate plate scans and used to identify peptide ions. Peptide distributions along the development lane were mapped for each separated protein digest. Signal levels ranged over several orders of magnitude. In general, highest signal levels were obtained for the peptides with the highest R (f) values on a plate, while peptides with very low R (f) values were often not detected. Sequence coverages for cytochrome c were 58% for the digest separated on the silica gel plate and 72% for the separation on the cellulose sheet; myoglobin sequence coverages were 62% and 68% on silica gel and cellulose, respectively. Weak correlations between peptide hydrophilicity and R (f) values on the silica gel and cellulose plates were found, with the more hydrophilic peptides having lower R (f) values.     

Gas-phase fragmentation characteristics of benzyl-aminated lysyl-containing tryptic peptides

The fragmentation characteristics of peptides derivatized at the side-chain ε-amino group of lysyl residues via reductive amination with benzaldehyde have been examined using collision-induced dissociation (CID) tandem mass spectrometry. The resulting MS/MS spectra exhibit peaks representing product ions formed from two independent fragmentation pathways. One pathway results in backbone fragmentation and commonly observed sequence ion peaks. The other pathway corresponds to the unsymmetrical, heterolytic cleavage of the C_ζ-N_ε bond that links the benzyl derivative to the side-chain lysyl residue. This results in the elimination of the derivative as a benzylic or tropylium carbocation and a (n − l)⁺-charged peptide product (where n is the precursor ion charge state). The frequency of occurrence of the elimination pathway increases with increasing charge of the precursor ion. For the benzylmodified tryptic peptides analyzed in this study, peaks representing products from both of these pathways are observed in the MS/MS spectra of doubly-charged precursor ions, but the carbocation elimination pathway occurs almost exclusively for triply-charged precursor ions. The experimental evidence presented herein, combined with molecular orbital calculations, suggests that the elimination pathway is a charge-directed reaction contingent upon protonation of the secondary ε-amino group of the benzyl-derivatized lysyl side chain. If the secondary ε-amine is protonated, the elimination of the carbocation is observed. If the precursor is not protonated at the secondary ε-amine, backbone fragmentation persists. The application of appropriately substituted benzyl analogs may allow for selective control over the relative abundance of product ions generated from the two pathways.     

Comprehensive two-dimensional separations of complex mixtures using reversed-phase reversed-phase liquid chromatography

A comprehensive two-dimensional reversed-phase reversed-phase liquid chromatographic system for the separation of a complex mixture of oligostyrenes was developed using results from a previous theoretical assessment of the informational similarity, percent synentropy, orthogonality and peak capacity of hypothetically coupled systems. The degree of sample attribute order in the first separation dimension was also used in the development of the experimental two-dimensional system. A C18(methanol)/CCZ(acetonitrile) two-dimensional system was chosen for the comprehensive analysis of the oligostyrene mixtures because this system had the lowest solute crowding, highest orthogonality and was observed to have order with respect to a sample attribute in the first separation dimension. The separations achieved were in full agreement with the results from information theory and (a geometric approach to) factor analysis assessments. High sampling rates in the first liquid chromatographic dimension were shown to be impossible or inefficient when the peak capacity and separation time of the second dimension was high or when the aim of the exercise was to isolate individual sample constituents in high yield.     

Mass spectrometric detection for capillary isoelectric focusing separations of complex protein mixtures

Capillary isoelectric focusing (CIEF) can provide high-resolution separations of complex protein mixtures, but until recently it has primarily been used with conventional UV detection. This technique would be greatly enhanced by much more information-rich detection methods that can aid in protein characterization. We describe progress in the development of the combination of CIEF with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry and its application to proteome characterization. Studies have revealed 400-1000 putative proteins in the mass range of 2-100 kDa from total injections of approximately 300 ng protein in single CIEF-FTICR analyses of cell lysates for both Escherichia coli (E. coli) and Deinococcus radiodurans (D. radiodurans). We also demonstrate the use of isotope labeling of the cell growth media to improve mass measurement accuracy and provide a means for quantitative proteome-wide measurements of protein expression. The ability to make such comprehensive and precise measurements of differences in protein expression in response to cellular perturbations should provide new insights into complex cellular processes.     

Gas-phase concentration,purification, and identification of whole proteins from complex mixtures

Five proteins present in a relatively complex mixture derived from a whole cell lysate fraction of E. coli have been concentrated, purified, and dissociated in the gas phase, using a quadrupole ion trap mass spectrometer. Concentration of intact protein ions was effected using gas-phase ion/ion proton-transfer reactions in conjunction with mass-to-charge dependent ion "parking" to accumulate protein ions initially dispersed over a range of charge states into a single lower charge state. Sequential ion isolation events interspersed with additional ion parking ion/ion reaction periods were used to "charge-state purify" the protein ion of interest. Five of the most abundant protein components present in the mixture were subjected to this concentration/purification procedure and then dissociated by collisional activation of their intact multiply charged precursor ions. Four of the five proteins were subsequently identified by matching the uninterpreted product ion spectra against a partially annotated protein sequence database, coupled with a novel scoring scheme weighted for the relative abundances of the experimentally observed product ions and the frequency of fragmentations occurring at preferential cleavage sites. The identification of these proteins illustrates the potential of this "top-down" protein identification approach to reduce the reliance on condensed-phase chemistries and extensive separations for complex protein mixture analysis.     

Gas-phase uranyl-nitrile complex ions

Electrospray ionization was used to generate doubly charged complex ions composed of the uranyl ion and nitrile ligands. The complexes, with general formula [UO2(RCN)n]2+, n = 0-5 (where R=CH3-, CH3CH2-, or C6H5-), were isolated in an ion-trap mass spectrometer to probe intrinsic reactions with H2O. For these complexes, two general reaction pathways were observed: (a) the direct addition of one or more H2O ligands to the doubly charged complexes and (b) charge-reduction reactions. For the latter, the reactions produced uranyl hydroxide, [UO2OH], complexes via collisions with gas-phase H2O molecules and the elimination of protonated nitrile ligands.     

Phase separations in liquid crystal-colloid mixtures

We present a mean-field theory to describe phase separations in mixtures of a nematic liquid crystal and a colloidal particle. The theory takes into account an orientational ordering of liquid crystals and a crystalline ordering of colloidal particles. We calculate phase diagrams on the temperature-concentration plane, depending on interactions between a liquid crystal and a colloidal surface and a coupling between nematic and crystalline ordering. We find various phase separation processes, such as a nematic-crystal phase separation and nematic-isotropic-crystal triple point. Inside binodal curves, we find new unstable and metastable regions which are important in phase ordering dynamics. We also find a stable nematic-crystalline (NC) phase, where colloidal particles dispersed in a nematic phase can form a crystalline structure. The coexistence between two NC phases with different concentrations can be appear though the coupling between nematic and crystalline ordering.     

Gas-phase conformation-specific photofragmentation of proline-containing peptide ions

Singly-protonated proline-containing peptides with N-terminal arginine are photodissociated with vacuum ultraviolet (VUV) light in an ESI linear ion trap/orthogonal-TOF (LIT/o-TOF). When proline is the n^th residue from the N-terminus, unusual b _n + 2 and a _n + 2 ions are observed. Their formation is explained by homolytic cleavage of the C_α− C bond in conjunction with a rearrangement of electrons and an amide hydrogen. The latter is facilitated by a proline-stabilized gas-phase peptide conformation.     

Preparative-scale isoelectric trapping separations in methanol-water mixtures

The typically low aqueous solubilities of small, hydrophobic organic ampholytic molecules limit the production rates that can be achieved in their isoelectric trapping (IET) separations and call for the use of hydro-organic mixtures as solvents. The compatibility of methanol-water mixtures and poly(ethylene terephthalate) substrate-supported isoelectric polyacrylamide hydrogels, developed for binary IET separations in a Gradiflow BF200IET unit, was investigated. The isoelectric polyacrylamide-based hydrogels retained their functional and mechanical integrities when the methanol concentration in the hydro-organic solvent mixture was kept at or below 25% (v/v). The utility of the hydro-organic media was demonstrated in the purification of a hydrophobic ampholytic compound, technical grade 4-hydroxy-3-(morpholinomethyl) benzoic acid. Production rates as high as 7 mg/h were achieved using small, 15 cm2 active surface area isoelectric membranes.     

Gas-phase ion chemistry in germane-propane and germane-propene mixtures

Germane-propane and germane-propene gaseous mixtures were studied by ion trap mass spectrometry. Variations of ion abundances observed under different partial pressure ratios and mechanisms of ion-molecule reactions elucidated by multiple isolation steps are reported. In addition, the rate constants for the main reactions were experimentally determined and compared with the collisional rate constants to obtain the reaction efficiencies. The yield of ions containing both Ge and C atoms is higher in the germane-propene than in the germane-propane system. In the former mixture, chain propagation takes place starting from germane ions reacting with propene and proceeds with the formation of clusters such as Ge(2)C(4)H(n) (+) and Ge(3)CH(n) (+).     

Gas-phase dissociation pathways of multiply charged peptide clusters

Numerous studies of cluster formation and dissociation have been conducted to determine properties of matter in the transition from the condensed phase to the gas phase using materials as diverse as atomic nuclei, noble gasses, metal clusters, and amino acids. Here, electrospray ionization is used to extend the study of cluster dissociation to peptides including leucine enkephalin with 7–19 monomer units and 2–5 protons, and somatostatin with 5 monomer units and 4 protons under conditions where its intramolecular disulfide bond is either oxidized or reduced. Evaporation of neutral monomers and charge separation by cluster fission are the competing dissociation pathways of both peptides. The dominant fission product for all leucine enkephalin clusters studied is a proton-bound dimer, presumably due to the high gas-phase stability of this species. The branching ratio of the fission and evaporation processes for leucine enkephalin clusters appears to be determined by the value of z²/n for the cluster where z is the charge and n the number of monomer units in the cluster. Clusters with low and high values of z²/n dissociate primarily by evaporation and cluster fission respectively, with a sharp transition between dissociation primarily by evaporation and primarily by fission measured at a z²/n value of 0.5. The dependence of the dissociation pathway of a cluster on z²/n is similar to the dissociation of atomic nuclei and multiply charged metal clusters indicating that leucine enkephalin peptide clusters exist in a state that is more disordered, and possibly fluid, rather than highly structured in the dissociative transition state. The branching ratio, but not the dissociation pathway of [somatostatin₅ + 4H]⁴⁺ is altered by the reduction of its internal disulfide bond indicating that monomer conformational flexibility plays a role in peptide cluster dissociation.     

Quantitative analysis of complex peptide mixtures using FTMS and differential mass spectrometry

Label-free LC-MS profiling is a powerful quantitative proteomic method to study relative peptide abundances between two or more biological samples. Here we demonstrate the use of a previously described comparative LC-MS method, differential mass spectrometry (dMS), to analyze high-resolution Fourier transform mass spectrometry (FTMS) data for detection and quantification of known peptide differences between two sets of complex mixtures. Six standard peptides were spiked into a processed plasma background at fixed ratios from 1.25:1 to 4:1 to make two sets of samples. The resulting mixtures were analyzed by microcapillary LC-FTMS and dMS. dMS successfully identified five out of the six peptides as statistically significant differences (p 相似文献   

Micellar electrokinetic chromatography separations of dynorphin peptide analogs

Prodynorphin is a precursor that has multiple cleavage sites to release various dynorphin opioid peptides. The dynorphin analogs used in this study have 18 amino acid residues. A series of dynorphin-like peptides, differing by a single residue (alanine substitution) were assembled by Fmoc solid-phase procedures and purified by preparative high performance liquid chromatography (HPLC). Separation of the Ala-scan dynorphin analogs was investigated by micellar electrokinetic chromatography (MEKC) employing anionic, cationic and zwitterionic surfactants. The role of electrostatic and hydrophobic forces in analyte-surfactant interactions is discussed with respect to the observed elution patterns. Separation of all dynorphin analogs by MEKC using a zwitterionic surfactant shows this technique to be powerful for separating closely related peptide species. It also demonstrates the potential for using MEKC for the prescreening of peptide libraries to determine their biological activity toward specific receptors. Results from the separation of dynorphin analogs by free solution and ion-pairing capillary electrophoresis are also presented.     

Gas-phase dissociation pathways of a tetrameric protein complex

The gas-phase dissociation of the tetrameric complex transthyretin (TTR) has been investigated with tandem-mass spectrometry (tandem-MS) using a nanoflow-electrospray interface and a quadrupole time-of-flight (Q-TOF) mass spectrometer. The results show that highly charged monomeric product ions dissociate from the macromolecular complex to form trimeric products. Manipulating the pressure conditions within the mass spectrometer facilitates the formation of metastable ions. These were observed for the transitions from tetrameric to monomeric and trimeric product ions and additionally for losses of small molecules associated with the protein complex in the gas phase. These results are interpreted in the light of recent mechanisms for the electrospray process and provide insight into the composition and factors governing the stability of macromolecular ions in the gas phase.     

Methacrylate monolithic capillary columns for gradient peptide separations

For the separation of peptides with gradient-elution liquid chromatography a poly(butyl methacrylate-co-ethylene dimethacrylate) (BMA) monolithic capillary column was prepared and tested. The conditional peak capacity was used as a metric for the performance of this column, which was compared with a capillary column packed with C18-modified silica particles. The retention of the peptides was found to be smaller on the BMA column than on the particulate C18 column. To obtain the same retention in isocratic elution an approximately 15% (v/v) lower acetonitrile concentration had to be used in the mobile phase. The retention window in gradient elution was correspondingly smaller with the BMA column. The relation between peak width and retention under gradient conditions was studied in detail. It was found that in shallow gradients, with gradient times of 30min and more, the peak widths of the least retained compounds are strongly increased with the BMA column. This was attributed to the fact that these compounds migrate and elute with an unfavorable high retention factor. More retained compounds are eluted later in the gradient, but with a lower effective retention factor. With shallow gradients the peak capacity of the BMA column ( approximately 90) was clearly lower than that of a conventional packed column ( approximately 150). On the other hand, with steep gradients, when components elute with a low effective retention factor, the performance of the BMA column is relatively good. With a gradient time of 15min similar peak widths and thus similar peak capacities ( approximately 75) were found for the packed and the monolithic column. Two strategies were investigated to obtain higher peak capacities with methacrylate monolithic columns. The use of lauryl methacrylate (LMA) instead of butyl methacrylate (BMA) gave an increase in retention and narrower peaks for early eluting peptides. The peak capacity of the LMA column was approximately 125 in a 60min gradient. Another approach was to use a longer BMA column which resulted in a peak capacity of approximately 135 could be obtained in 60min.     

Biocompatible polymeric monoliths for protein and peptide separations

The concept of biocompatibility with reference to chromatographic stationary phases for separation of biomolecules (including proteins and peptides) is introduced. Biocompatible is a characteristic that indicates resistance to nonspecific adsorption of biomolecules and preservation of their structures and biochemical functions. Two types of biocompatible polymeric monoliths [i. e., polyacrylamide‐ and poly(meth)acrylate‐based monoliths] used for protein and peptide separations are reviewed in detail, with emphasis on size exclusion, ion exchange, and hydrophobic interaction chromatographic modes. Biocompatible monoliths for enzyme reactors are also included. The two main synthetic approaches to produce biocompatible monoliths are summarized, i. e., surface modification of a monolith that is not inherently biocompatible and direct copolymerization of hydrophilic monomers to form a biocompatible monolith directly. Integration of polyethylene glycol into the poly(meth)acrylate monolith network is becoming popular for reduction of non‐specific protein interactions.     

Simplification of complex peptide mixtures for proteomic analysis: reversible biotinylation of cysteinyl peptides

A rapid means of identifying many components in an enriched mixture of proteins is enzymatic digestion of the entire protein fraction. This complex peptide mixture is then subjected to reversed-phase high performance liquid chromatography (HPLC) coupled on-line with a mass spectrometer capable of data-dependent ion selection for fragmentation (LC-tandem mass spectrometry; MS/MS). Thus, as many peptides as possible in the sample are fragmented to produce MS/MS spectra, which can then be searched against sequence databases. Ideally, one peptide from each protein in the mixture would be fragmented and identified. To this end, we employed an affinity selection method to capture cysteinyl peptides and thereby simplify the mixture. Both the captured cysteinyl and the noncysteinyl peptides are analyzed by LC-MS/MS, to increase the number of proteins identified. The method was tested on a limited set of standard proteins and applied to the analysis of a protein fraction obtained from isolated mitochondria treated with atractyloside. To further increase the number of different precursor ions selected for fragmentation, dynamic exclusion and ion selection from multiple narrow mass ranges of consecutive runs were employed.