Drift time mass spectrometric protein hydration experiments

Recent developments in electrospray ionization opened the field of mass spectrometry for macromolecules like proteins. The combination of ionization, drift time spectrometry, and mass spectrometry combines a large field of experimental techniques. In this new field it becomes possible to understand the interactions of isolated proteins with reaction partners like water. The combination of these techniques allows one to determine structural and thermodynamic properties. The experiments presented here give a first insight into the interaction of isolated protein ions with single solvent molecules. Results are presented for proteins like cytochrome C, bovine pancreatic trypsin inhibitor and lysozyme. MD-simulations on the same proteins and conditions as similar as possible to the experiments reflect the experimental results remarkable well.     

Optimized stationary phases for the high-performance liquid chromatography-electrospray ionization mass spectrometric analysis of basic pharmaceuticals

Stationary phases were investigated for HPLC coupled with electrospray ionization mass spectrometry (ESI-MS) for the analysis of basic drugs. Tricyclic antidepressants (TCAs) and beta-blockers were used as model solutes. The functional groups, pentafluorophenyl (PFP), OH, CN or CH3 were attached to the silica via a propyl chain. The effects of these stationary phases as well as C8 and C18 phases on retention and peak shape of the basic drugs were studied. The CN and PFP phases adequately retained (tR of 2 to 6 min) the basic drugs when the mobile phase was composed of 90% acetonitrile, whereas with the C4, C8 and C18 phases, less than 40% acetonitrile had to be used to provide adequate retention of the basic drugs. Because acetonitrile provides better desolvation in ESI than an aqueous solvent, it produces an increased MS signal. As an example of the HPLC-ESI-MS analysis of the beta-blocker, pindolol, on a CN phase, the use of 90% acetonitrile in the mobile phase increased the ESI-MS signal by 790% when compared to a C18 phase which could use only 5% acetonitrile in the mobile phase for retention of the solute. In addition, the CN and PFP phases provided better peak shape than the OH phase and the hydrophobic phases (C4, C8 and C18) and ion-pairing or ion-suppressing agents were not required. The retention behavior of the TCAs and beta-blockers on each of the phases is described.     

同位素质谱与无机质谱分析

本文是《分析试验室》定期评述中“无机质谱分析”课题的第二篇评述文章,它增加了同位素质谱分析的内容,故将题目改为现今题目,它综述了1985年～1990年间同位素质谱和无机质谱的发展概况。其中包括同位素示踪、同位素稀释、火花源质谱、二次离子质谱、等离子体质谱等。内容以国内为主,也收集了少量代表学科先进水平的外国文献。     

A new crosslinker for mass spectrometric analysis of the quaternary structure of protein complexes

Mass spectrometric structural analysis of crosslinked peptides is a powerful method to elucidate the spatial arrangement of polypeptides in protein complexes. Our aim is to develop bifunctional crosslinkers that, after crosslinking protein complexes followed by proteolytic digestion, give rise to crosslinked peptides that can be readily tracked down by mass spectrometry. To this end we synthesized the crosslinker N-benzyliminodiacetoyloxysuccinimid (BID), which yields stable benzyl cation marker ions upon low-energy collision-induced dissociation (CID) tandem mass spectrometry. Sensitive detection of the marker ion upon low-energy CID is demonstrated with different BID-crosslinked peptide preparations. With BID it becomes possible to retrieve crosslinked and crosslinker-adducted peptides, without the necessity of purifying crosslinked peptides prior to identification. The basic design of this crosslinker can be varied upon, in order to meet specific crosslinking needs.     

Normalization of relative peptide ratios derived from in-gel digests: applications to protein variant analysis at the peptide level

The ability to detect protein variants and post-translational modifications by mass spectrometry has become increasingly important. Unfortunately, the ability to detect variants in large intact proteins (>80,000 Da) is limited. Even in the analysis of smaller proteins, algorithms are required to determine the presence of a 2 Da mass shift in an intact 13 kDa protein because the isotopic distribution of the multiply charged ions of the variant overlaps the wild-type distribution. Fortunately, most modern instruments are capable of detecting variants in tryptic peptides derived from intact proteins. If a single common variant protein is known, the presence of a variant tryptic peptide can be easily demonstrated. A more difficult issue is the case where a multiplicity of peptides with multiple amino acid substitutions can be associated with pathology. In these cases a decrease in the relative amount of a variant peptide relative to other internal tryptic fragments would be diagnostic. However, the variability associated with the analysis of in-gel or solution digests of proteins, related to efficiencies in digestion, extraction and ionization, confounds variant analysis at the peptide level. A strategy was developed to normalize for this variability by utilizing multiple isotopically labeled internal standards for multiple peptides derived from the same protein. Erythrocyte spectrin from 36 normal and 25 abnormal osmotic fragility samples was analyzed as a test case. Three isotopically labeled target peptides comprising the alpha/beta-spectrin self-association sites were added to purified digested alpha-spectrin. The utilization of multiple internal standards demonstrates the capability to normalize for sample variability due to ionization efficiency, solvent effects, digestion and extraction efficiency.     

Micro-high-performance liquid chromatography/Fourier transform mass spectrometry with electron-capture dissociation for the analysis of protein enzymatic digests

Electron-capture dissociation (ECD) Fourier transform mass spectrometry (FTMS) employed to generate comprehensive sequence information for the chromatographic analysis of enzymatic protein digests is described. A pepsin digest of cytochrome c was separated by reversed-phase micro-high-performance liquid chromatography (microHPLC) and ionized 'on-line' by electrospray ionization (ESI). The ions thus formed were transferred to and trapped in the FTMS analyzer cell. Typically, no precursor ion isolation was performed. The trapped ions were subjected to a pulse of electrons to induce fragmentation. Mass spectra were acquired continuously to produce a three-dimensional LC/MS data set. The spectra were dominated by c and, to a lesser degree, z ions, which provided near complete sequence coverage. External calibration provided good mass accuracy and resolution, typical of FTMS. Thus microHPLC/ECD - FTMS is shown to be a highly informative method for the analysis of enzymatic protein digests.     

Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry of protein samples from two-dimensional (2-D) gels in conjunction with protein sequence database searches is frequently used to identify proteins. Moreover, the automatic analysis of complete 2-D gels with hundreds and even thousands of protein spots ("proteome analysis") is possible, without human intervention, with the availability of highly accurate mass spectrometry instruments, and high-throughput facilities for preparation and handling of protein samples from 2-D gels. However, the lack of software for precise automatic analysis and annotation of mass spectra, as well as software for in-batch sequence database queries, is increasingly becoming a significant bottleneck for the proteomics work flow. In the present paper we outline an algorithm for reliable, accurate, and automatic evaluation of mass spectrometric data and database searches. We show here that simply selecting from the sequence database the protein that has the most matching fragment masses often leads to false-positive results. Reliable protein identification is dependent on several parameters: the accuracy of fragment mass determination, the number of masses submitted for query, the mass distribution of query masses, the number of masses matching between sample and database protein, the size of the sequence database, and the kind and number of modifications considered. Using these parameters, we derive a simple statistical estimation that can be used to calculate the probability of true-positive protein identification.     

Solid-phase permethylation of glycans for mass spectrometric analysis

A miniaturized approach was developed for quantitative permethylation of oligosaccharides, which involves packing of sodium hydroxide powder in microspin columns or fused-silica capillaries (500 microm i.d.), permitting effective derivatization in less than a minute at microscale. Prior to mass spectrometry, analytes are mixed with methyl iodide in dimethyl sulfoxide solution containing traces of water before infusing through the microreactors. This procedure minimizes oxidative degradation and peeling reactions and avoids the need of excessive clean-up. Picomole amounts of linear and branched, sialylated and neutral glycan samples were rapidly and efficiently permethylated by this approach and analyzed by matrix-assisted laser desorption/ionization mass spectrometry.     

Diophantine mass spectrometric structure analysis

An efficient methodology has been designed to facilitate the elucidation of chemical structures of compounds synthesized by chemists engaged in silicone research—specifically as it pertains to the analyses of mixtures of organofunctionalized Si-containing compounds. By combining electrospray MS data, IR/NMR functional group data and Diophantine mathematical analysis, one can obtain a materials balance of a particular chemical reaction without requiring difficult/time-consuming separations. This approach has been applied successfully to the analysis of F-endblocked polydiphenylsiloxanes up to 3000 Da and can be readily tailored for the structural elucidation of any organic compound.     

Hydrophilic interaction chromatography coupled to electrospray mass spectrometry for the separation of peptides and protein digests

In this study, the analysis of a peptide set, chosen for their differences in hydrophilicity, and the tryptic digests of bovine cytochrome c and β-lactoglobulin by hydrophilic interaction chromatography–electrospray ionisation mass spectrometry (HILIC–ESI-MS) is demonstrated. Two different types of HILIC phases, i.e., an amide- and an amino-modified silica-based phase, packed into narrow bore or capillary columns, were investigated with separations conducted under either low pH or neutral pH conditions. The separation performance of the two HILIC columns with respect to peak efficiency and selectivity have been documented under these different mobile phase conditions, and the results compared with the performance of a conventional capillary reversed-phase C18 column of similar dimensions. It was found that very good separation of the peptide set could be achieved by using the amide-modified silica column over a broad pH range. Moreover, with the protein digest samples, excellent separation of the tryptic digests was obtained with the amide-modified HILIC column under neutral pH conditions. Compared to the conventional reversed-phase C18 separations, the use of these HILIC columns not only provided complementary separation selectivity, but also offered the capability to identify unique peptides using tandem HILIC–mass spectrometric techniques. These studies therefore highlight the potential of HILIC procedures for future proteomic applications.     

Potential of long capillary monolithic columns for the analysis of protein digests

The gain in separation efficiency for protein digests using long monolithic columns has been evaluated for a LC‐MS system with capillary monolithic columns of different lengths (150 and 750 mm). A mixture of BSA, α‐casein and β‐casein tryptic digests was used as a test sample. Peak capacity and productivity (peak capacity per unit time) were determined from base peak chromatograms and MS/MS data were used for protein identification by MASCOT database searching. Peak capacity and protein identification scores were higher for the long column. Analyses with similar gradient slope for the two columns produced ratios of the peak capacities that were slightly higher than the expected value of the square root of the column length ratio. Peak capacity ratios varied from 2.7 to 4.0 for four different gradient slopes, while protein identification scores were 2–4 times higher for the long column. Similar values were obtained for the productivity of both columns and the highest productivity was obtained at gradient times of 45 and 75 min for the short and long column, respectively. The use of long monolithic columns improves peptide separation and increases reliability of protein identification for complex digests, especially if longer gradients are chosen.     

An apparatus for simultaneous gas evolution analysis and mass spectrometric analysis

An apparatus is described which enables the gas evolution analysis(GEA) and mass spectrometric analysis(MSA) curves of a sample to be recorded simultaneously. The sample is pyrolyzed in a chamber in a dynamic helium atmosphere.The evolved products are detected in the helium gas by a thermal conductivity cell which results in the (GEA) curve. An inexpensive mass spectrometer is used to moniter the helium gas stream which gives the (MSA)curve. The advantages of the appparatus over other recent techniques are given.     

A rapid and efficient mass spectrometric method for the analysis of explosives

The high explosives trinitrotoluene, nitroglycerine, pentaerythritol tetranitrate and hexahydro-1,3,5-trinitro-1,3,5-triazine are efficiently ionised under negative ion atmospheric pressure chemical ionisation (APCI) conditions. The limit of detection is improved, in some cases by several orders of magnitude, by complexation with chlorine demonstrating this to be a highly suitable method for enhancing the detection capabilities for explosives. The spectra produced from introduction of the analytes in a liquid matrix, with and without chlorine present, contain a number of ions that arise through secondary processes including breakdown and adduct formation. Sample introduction into an APCI source in air, via a heated-plate inlet with a supplementary feed of dichloromethane, produces improved response for the chloride adducts of the analytes and minimises their decomposition during analysis. The tandem mass spectra produced from the chloride adducts are simple. Optimisation of the trapping parameters of the ion trap detector enhances selected transitions, yields highly reproducible spectra and improves the limits of detection for MS/MS analysis.     

Automated mass spectrometric sequence determination of cyclic peptide library members

Cyclic peptides have come under scrutiny as potential antimicrobial therapeutic agents. Combinatorial split-and-pool synthesis of cyclic peptides can afford single compound per well libraries for antimicrobial screening, new lead identification, and construction of quantitative structure-activity relationships (QSAR). Here, we report a new sequencing protocol for rapid identification of the members of a cyclic peptide library based on automated computer analysis of mass spectra, obviating the need for library encoding/decoding strategies. Furthermore, the software readily integrates with common spreadsheet and database packages to facilitate data visualization and archiving. The utility of the new MS-sequencing approach is demonstrated using sonic spray ionization ion trap MS and MS/MS spectrometry on a single compound per bead cyclic peptide library and validated with individually synthesized pure cyclic D,L-alpha-peptides.     

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.