Fully automated determination of eserine N-oxide in human plasma using on-line solid-phase extraction with liquid chromatography coupled with electrospray ionization tandem mass spectrometry

Identifying bacterial species using CE–MS and SEQUEST with an empirical scoring function

CE-MS/MS analysis of proteolytic digests of bacterial cell extracts was combined with SEQUEST searching and a new scoring system to identify bacteria species in bacterial mixtures. Searches of MS/MS spectra against protein databases enabled the identification of bacterial species by the matching of the proteins associated with the corresponding species. An empirical scoring function was obtained by evaluating the SEQUEST search results of 38 samples that contained single bacterial species. The scoring by the empirical function helped move up the positive identification results from their original positions in the ranking based on Xcorr values alone. Therefore, the identification of bacteria in the samples that contained bacterial mixtures was improved. Bacterial species in 20 bacterial mixtures, including one real sample, were correctly identified by database searches and the new scoring function.

Improved method to quantify intracellular zidovudine mono- and triphosphate in peripheral blood mononuclear cells by liquid chromatography-tandem mass spectrometry

The determination of intracellular triphosphate metabolites of nucleoside analogs used in anti-HIV therapy is very challenging. Despite the well-known sensitivity and selectivity of LC-MS/MS, the measurement of the triphosphate metabolite of zidovudine (AZT-TP) remains difficult because of the interferences induced by endogenous nucleotides triphosphates. We describe a new approach that allows improved determination of AZT-TP simultaneously with AZT-monophosphate (MP). This was obtained, first, by monitoring a transition from the molecular ion of AZT-TP to a minor but very specific product ion. Then, the spiking of samples with a constant amount of AZT-TP allowed the signal to emerge from background, leading to increased sensitivity. Finally, the analytical run time was reduced to less than 10 min. The low limits of quantification were at 150 and 300 fmol per sample for AZT-TP and AZT-MP, respectively. Recoveries were higher than 85%. Inaccuracy and precision were lower than 10% and 15% (17% at the limit of quantification), respectively. The new method offers the possibility of determining simultaneously other nucleotide phosphates, as shown here for d4T-TP (the triphosphate metabolite of another nucleoside analog, stavudine or d4T) and 2'-deoxythymidine-5'-triphosphate or dTTP (the corresponding natural nucleotide triphosphate).

Identification of microbial mixtures by capillary electrophoresis/selective tandem mass spectrometry

In this paper, we propose a new strategy for identifying specific bacteria in bacterial mixtures by using CE-selective MS/MS of peptide marker ions associated with the bacteria of interest. We searched the CE-MS/MS spectra acquired from the proteolytic digests of pure bacterial cell extracts against protein databases. The identified peptides that match the protein associated with the corresponding species were selected as marker ions for bacterial identification. Specific peptide marker ions were obtained for each of the following three pathogens: Pseudomonas aeruginasa, Staphylococcus aureus, and Staphylococcus epidermidis. To identify a bacterial species in a sample, we performed CE-MS/MS analysis of the selected marker ions in the proteolytic digest of the cell extract and then performed protein database searches. The selected peptides that we identified correctly from Xcorr values ranking at the top of the search results allowed us to identify the corresponding bacterial species present in the sample. We have applied this method successfully to the identification of various mixtures of the three pathogens. Even minor bacterial species present at a concentration of 1% can be identified with great confidence. This method for CE-MS/MS analysis of bacteria-specific marker peptides provides excellent selectivity and high accuracy when identifying bacterial species in complex systems. In addition, we have used this approach to identify P. aeruginasa in a saliva sample spiked with E.coli and P. aeruginasa.

Identification of microbial mixtures by LC-selective proteotypic-peptide analysis (SPA)

This paper describes a method--using a combination of LC-MS/MS of selected bacteria-specific peptides and database search--for determining the species of bacteria present in a mixture. We identified the proteotypic peptides that were associated with specific bacteria by searching protein databases for the LC-MS/MS data. The retention time windows for specific peptide markers were used as an extra constraint so that the peptide markers of many bacterial species could be analyzed in a single LC-selective proteotypic-peptide analysis (SPA). We performed LC-MS/MS analyses on the proteolytic digest of cell extracts and monitored only the selected marker peptide ions at given elution time windows. The corresponding bacterial species could be characterized when the selected peptides that eluted at expected elution windows were identified correctly from the database. We managed to identify up to eight bacterial species simultaneously during a single LC-MS/MS analysis, as well as bacteria mixed in various abundances. Two marker ions having similar values of m/z, but obtained from two different bacterial samples, which would otherwise be selected as precursors within mass tolerance and would complicate the MS/MS data, were time-resolved using LC and then used to correctly identify their bacterial sources. The coupling of selective MS/MS monitoring with separation methods, such as LC, provides a highly selective and accurate analytical method for characterizing complex mixtures of bacterial species.

Using Capillary Electrophoresis−Selective Tandem Mass Spectrometry To Identify Pathogens in Clinical Samples

Analysis of microbial mixtures in complex systems, such as clinical samples, using mass spectrometry can be challenging because the specimens may contain mixtures of several pathogens or both pathogens and nonpathogens. We have successfully applied capillary electrophoresis-selective MS/MS of unique peptide marker ions to the identification of common pathogens in clinical diagnosis. We searched the CE-MS/MS spectra acquired from the proteolytic digests of pure bacterial cell extracts against protein databases. The identified peptides that matched a protein associated with a particular pathogen were selected as marker ions to identify that bacterium in clinical specimens. Thirty-four clinical specimens, obtained from pus, wound, sputum, and urine samples, were analyzed using both biochemical and selective MS/MS methods. The bacteria in these clinical samples were cultivated directly, without prior isolation of a pure colony, before performing the selective MS/MS analyses. The bacteria analyzed included both Gram-positive and -negative strains. The match with respect to the pathogens identified was good between the biochemical and the selective MS/MS methods; the matching rate was 91%. The rate was as high as 97% when not considering two specimens for which the bacteria were not grown successfully. Two of the specimens that we identified using the biochemical method as containing two bacterial species were confirmed also through selective tandem MS analysis.

Quantification of Small Therapeutic Proteins in Plasma by Liquid Chromatography−Tandem Mass Spectrometry: Application to an Elastase Inhibitor EPI-hNE4

LC/ESI-MS/MS is a promising alternative to immunoassays in improving the analysis of recombinant therapeutic proteins in biological fluids for toxicity and pharmacokinetics purposes. To assess the sensitivity and validation issues associated with this technique, we use here as a model EPI-hNE4, a 56-amino acid recombinant protein, and demonstrate that a method based on tandem mass spectrometry combined with liquid chromatography and electrospray interface can reach sensitivity similar to that of ELISA but without its potential cross-reactivity. For this purpose, a triple quadrupole mass spectrometer operating in positive ion and single reaction monitoring mode with transition, m/z 1040 --> 1224.5, was used for selective peak detection. Particular issues related to the internal standard, i.e., elution and ionization patterns similar to the protein without stable isotope labeling, and to analytical interference due to endogenous binding antibodies were addressed. A limit of quantification in human or monkey plasma of 5 ng/mL was reached with a sample volume of 100 microL, corresponding to 40 fmol injected into the HPLC column. Intra- and interassay precision and accuracy were below 15%. No matrix effect was detected.

Direct determination of phosphorylated intracellular anabolites of stavudine (d4T) by liquid chromatography/tandem mass spectrometry

The objective was to develop and validate a routine assay for active intracellular anabolites of stavudine (d4T), a nucleoside reverse transcriptase inhibitor in human PBMC, applicable to pharmacokinetic studies and treatment monitoring. This was achieved using liquid chromatography coupled to tandem mass spectrometry (LC/MS/MS), which theoretically allies optimum sensitivity, specificity and high sample throughput. After cellular lysis in a Tris/methanol buffer, the extract spiked with 2[H(8)]-ATP (internal standard) is directly injected into the LC/MS/MS system. Phosphorylated metabolites of d4T as well as deoxythymidine-triphosphate, the competitor on the reverse transcriptase, are separated from d4T on a reverse-phase microbore column with ion pairing. The detection is performed in the multiple reaction monitoring (MRM) mode after drug ionisation in negative mode electrospray. The limit of quantitation for d4T-TP was 138 fmol per 7 mL blood (9.8 fmol per 10(6) cells) and CV% for repeatability and intermediate precision were lower than 15%. Stability of compounds was checked before and during the process of isolation of PBMC. Cellular samples from several d4T-treated patients were successfully analysed using this method and d4T-triphosphate and deoxythymidine triphosphate were recovered. In conclusion, we have developed and validated a routine LC/MS/MS method that allows the simultaneous determination of mono-, di- and triphosphorylated anabolites of d4T in PBMC as well as the natural corresponding triphosphate in one analysis. For the first time, the chain terminator ratio (d4T-TP/dT-TP) could be directly measured. This method can be used simply and routinely on more than 35 samples per day. Extension to other nucleoside analogues is under development.