Platform for identification of Salmonella serovar differentiating bacterial proteins by top-down mass spectrometry: S. Typhimurium vs S. Heidelberg.

Intact protein expression profiling has proven to be a powerful tool for bacterial subspecies differentiation. To facilitate typing, epidemiology, and trace-back of Salmonella contamination in the food supply, a minimum of serovar level differentiation is required. Subsequent identification and validation of marker proteins is integral to rapid screening development and to determining which proteins are subject to environmental pressure. Bacterial sequencing efforts have expanded the number of sequenced genomes available for single-nucleotide polymorphism (SNP) analyses, but annotation is often missing, start site errors are not uncommon, and the likelihood of expression is not known. In this work we show that the combination of intact protein expression profiles and top-down liquid chromatography-mass spectrometry (LC-MS/MS) facilitates the identification of proteins that result from expressed serovar specific nonsynonymous SNPs. Combinations of these marker proteins can be used in assays for rapid differentiation of bacteria. LC-MS generated intact protein expression profiles establish which bacterial protein masses differ across samples and can be determined without prior knowledge of the sample. Subsequent top-down LC-MS/MS is used to identify expressed proteins and their post-translational modifications (PTM), identify serovar specific markers, and validate genomic predicted orthologues as expressed biomarkers.

Draft Genome Sequences of Two O104:H21 Escherichia coli Isolates Causing Hemorrhagic Colitis during a 1994 Montana Outbreak Provide Insight into Their Pathogenicity.

We sequenced the genomes of two strains of O104:H21 enterohemorrhagic Escherichia coli (EHEC) isolated during an outbreak of hemorrhagic colitis in Montana in 1994. These strains carried a plasmid that contains several virulence genes not present in pO157. The genome sequences will improve phylogenetic analysis of other non-O157 E. coli strains in the future.

A discriminant based charge deconvolution analysis pipeline for protein profiling of whole cell extracts using liquid chromatography-electrospray ionization-quadrupole time-of-flight mass spectrometry.

A discriminant based charge deconvolution analysis pipeline is proposed. The molecular weight determination (MoWeD) charge deconvolution method was applied directly to the discrimination rules obtained by the fuzzy rule-building expert system (FuRES) pattern classifier. This approach was demonstrated with synthetic electrospray ionization-mass spectra. Identification of the tentative protein biomarkers by bacterial cell extracts of Salmonella enterica serovar typhimurium strains A1 and A19 by liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) was also demonstrated. The data analysis time was reduced by applying this approach. In addition, this method was less affected by noise and baseline drift.

Identification of the decarboxylated analog of tetrabromotetrachloro-fluorescein and its quantification in the color additives D&C Red Nos. 27 and 28 (phloxine B) using high-performance liquid chromatography.

The present work describes (a) the identification and characterization of an impurity, 2,4,5,7-tetrabromo-6-hydroxy-9-(2,3,4,5-tetrachlorophenyl)-3H-xanthen-3-one (BCPX), in the color additives D&C Red Nos. 27 and 28 (phloxine B) and (b) the determination of the extent and level of BCPX contamination in certified lots of these colors. For these purposes, BCPX (a compound not previously reported in the literature) was synthetically prepared. Test portions from 42 certified lots of D&C Red Nos. 27, 28 and 27 lakes were analyzed for BCPX using an HPLC method that included gradient elution and UV-vis photodiode array detection. Those lots were submitted for certification by both domestic (six) and foreign (six) manufacturers during the past 4 years. Of the test portions analyzed, 32 (76.2%) contained BCPX in amounts ranging from 0.01 to 3.21%. The remaining 10 test portions (23.8%) contained no detectable BCPX or less than 0.008%, which is the limit of quantification for the present method. The analyses revealed substantial differences in the level of BCPX across different manufacturers. The wide range of BCPX levels found in the analyzed lots suggests that the presence of BCPX in D&C Red Nos. 27 and 28 may be avoided or significantly reduced during the manufacturing process.

Determination of 2,4,6-tribromoaniline in the color additives D&C Red Nos. 21 and 22 (Eosin Y) using solid-phase microextraction and gas chromatography-mass spectrometry.

The present work demonstrates the presence of an impurity, 2,4,6-tribromoaniline (TBA), in the color additives D&C Red Nos. 21 and 21 lake (21L) and describes the determination of TBA in certified lots of D&C Red Nos. 21, 21L and 22 (Eosin Y). A method was developed using solid-phase microextraction with [13C6]TBA as an internal standard followed by gas chromatography-mass spectrometry analysis. Test portions from 23 lots of US-certified color additives D&C Red Nos. 21, 21L and 22 were analyzed for TBA using the new method. These lots represent domestic (four) and foreign (four) manufacturers that requested certification for the color additives during the past 2 years. Of the test portions analyzed, 12 (52.2%) contained TBA in amounts ranging from 19.9 to 638.9 ppm with an average value of approximately 278.7 ppm. The remaining 11 (47.2%) test portions contained no detectable TBA or less than 0.01 ppm, which is the limit of quantification of the present method. The wide range of TBA levels found in lots submitted for certification suggest that the contamination with TBA may be avoided or significantly decreased through appropriate changes in the color-manufacturing process.

Analysis of coffee for the presence of acrylamide by LC-MS/MS.

A variety of popular instant, ground, and brewed coffees were analyzed using a modified liquid chromatography-tandem mass spectrometry (LC-MS/MS) method specifically developed for the determination of acrylamide in foods. Coffee test portions were spiked with 13C3-labeled acrylamide as an internal standard prior to their extraction and cleanup. Ground coffees (1 g) and instant coffees (0.5 g) were extracted by shaking with 9 mL of water for 20 min. Brewed coffee test portions (9 mL) were taken through the cleanup procedure without further dilution with extraction solvent. Coffee test portions were cleaned up by passing 1.5 mL first through an Oasis HLB (hydrophilic/lipophilic copolymer sorbent) solid phase extraction (SPE) cartridge and then a Bond Elut-Accucat (cation and anion exchange sorbent) SPE cartridge. The cleaned up extracts were analyzed by positive ion electrospray LC-MS/MS. The MS/MS data was used to detect, confirm, and quantitate acrylamide. The limit of quantitation of the method was 10 ng/g for ground and instant coffees and 1.0 ng/mL for brewed coffee. The levels of acrylamide ranged from 45 to 374 ng/g in unbrewed coffee grounds, from 172 to 539 ng/g in instant coffee crystals, and from 6 to 16 ng/mL in brewed coffee.

Rugged LC-MS/MS survey analysis for acrylamide in foods.

The described liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the detection of acrylamide in food entails aqueous room temperature extraction, SPE cleanup, and analysis by LC-MS/MS. The method is applicable to a wide variety of foods. [(13)C(3)]acrylamide is the internal standard. The limit of quantitation is 10 ppb (microg/kg). Data were obtained in duplicate from >450 products representing >35 different food types. The variability in analyte levels in certain food types suggests that it may be possible to reduce acrylamide levels in those foods.

Identification of 2-bromo-3,4,5,6-tetrachloroaniline and its quantification in the color additives D&C Red Nos. 27 and 28 (phloxine B) using solid-phase microextraction and gas chromatography-mass spectrometry.

The present work describes (a) the identification and characterization of a contaminant, 2-bromo-3,4,5,6-tetrachloroaniline (2BTCA), in the color additives D&C Red Nos. 27 and 28 (phloxine B) and (b) the determination of the extent and level of 2BTCA contamination in certified lots of these colors. For these purposes, 2BTCA (a compound not previously reported in the literature) and its positional isomer 4-bromo-2,3,5,6-tetrachloroaniline (4BTCA) were synthetically prepared. 4BTCA was used as the internal standard for the quantification of 2BTCA in the colors. Test portions from 35 certified lots of D&C Red Nos. 27 and 28 were analyzed for 2BTCA using a solid-phase microextraction-GC-MS method. Those lots were submitted for certification by both domestic (seven) and foreign (four) manufacturers during the past 4 years. Of the test portions analyzed, 22 (62.9%) contained 2BTCA in amounts ranging from 0.15 to 435.7 ppm with an average value of approximately 131.7 ppm. The remaining 13 (37.1%) test portions contained no detectable 2BTCA or less than 0.01 ppm, which is the limit of quantification of the present method. The analyses revealed substantial differences in the level of 2BTCA across lots from the same manufacturer as well as among different manufacturers. The wide range of 2BTCA levels found in the analyzed lots suggests that the presence of 2BTCA in D&C Red Nos. 27 and 28 may be avoided or significantly reduced during the manufacturing process. A direct correlation was observed between the presence of 2BTCA and that of 3,4,5,6-tetrachlorophthalic acid in analyzed batches of D&C Red Nos. 27 and 28. A chemical pathway that could explain the presence of 2BTCA in these color additives, and ways to avoid its formation, are also proposed.

Experimental factors affecting the quality and reproducibility of MALDI TOF mass spectra obtained from whole bacteria cells.

Numerous experimental factors are shown to significantly influence the spectra obtained when bacteria are analyzed by MALDI TOF/MS. Detailed investigation of the instrument parameters and sample preparation are all shown to influence the spectra. Of these, the preanalysis sample preparation steps incorporate the most important elements influencing the quality and reproducibility of the spectra. Some of the most important sample preparation factors include the method employed for sterilization, the type of matrix, the matrix solvent and concentration of cells in the matrix, as well as the type and concentration of acid added to the matrix. The effects of these parameters, as well as other aspects of sample preparation and the effects of several instrumental parameters on spectra are presented. Optimization and control of all experimental variables leads to a stable protocol for analysis of bacteria. The protocol employs a Nd:Yag laser and describes both sample handling and instrument conditions which consistently yield reproducible MALDI TOF mass spectra with greater than 25 peaks from both gram-positive and gram-negative bacteria.

Attachment of neutrals during tandem mass spectrometry of sulfonic acid dyes and intermediates in an ion trap.

Several positional isomers of 2-(2-quinolinyl)-1H-indene-1,3(2H)-dione mono- and disulfonic acids prepared as reference materials for development of analytical methods involved in FDA certification of D&C Yellow No. 10 (Quinoline Yellow) were found consistently to show [MH + 14](+) ions when their electrospray- or atmospheric pressure chemical ionization-prepared MH(+) ions were subjected to collisional activation. The source of these ions was found to be the methanol used as solvent in these procedures which combined with their [MH - H(2)O](+) ions under chemical ionization conditions. The reaction was found to be sensitive to their isomeric and chemical structures and other examples of this process are reviewed.