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Appendix J: White Paper 5: State of the Art for Autonomous Detection Systems Using Mass Spectrometry
Pages 215-244

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From page 215...
... Mass spectrometry (MS) is being considered as a candidate for the Tier 1, Tier 2, and Tier 3 autonomous detection systems.
From page 216...
... A mass spectrometer can measure the mass of a molecule only after it converts the neutral molecule to a gas-phase ion. To do so, it imparts an electrical charge to molecules and converts the resultant flux of electrically charged ions into a proportional electrical current that a data system converts to digital information, displaying it as a mass spectrum.
From page 217...
... TIER 1: 2012 TO 2016 Currently there are two MS-based systems that may be viewed as having parameters that come close to satisfying the proposed figures of merit for the autonomous detection system using mass spectrometry. The relevant characteristics include actual system size, performance, and quantitative figures of merit, such as the probability of false-positives approaching one false-positive per year.
From page 218...
... There is a resident database, and the system can produce an output with the likeliest bacteria present. It is the 20 to 30 derivatized fatty acids that are the fundamental data used to describe, analyze, and identify the biological sample.
From page 219...
... Bioaerosol Mass Spectrometer The bioaerosol mass spectrometer (BAMS) produces low-end bacterial biochemical information such as basic dipicolinic acid spore information.
From page 220...
... Different bacterial growth media for both spores saw minimal mass spectral differences within each species. Determination of individual particles was made in real time in two steps.
From page 221...
... Identification of a particle occurs by mass spectral pattern matching with a database. The tested substances produce significantly different experimental mass spectra, and no false identification or false alarms have been observed with sequential challenges of the CBRNE materials.
From page 222...
... The BAMS system has a good chance at performing to and meeting most of the autonomous detection system using mass spectrometry technical requirements but with some false-negatives. This assessment can also be considered for organisms in addition to Bacillus subtilis.
From page 223...
... , but most reports focused on tissue cell capture and rarely refer to airborne bacteria cells captured directly from air. A simple microfluidic device that is capable of fast and efficient airborne bacteria enrichment has recently been reported (Jing et al., 2013)
From page 224...
... When the concentration of E coli bacteria suspension was 104 cell/mL, there were still 130 bacterial particles collected by the microfluidic chip, which is 4 times higher than the 26 cells collected by the plate sedimentation method.
From page 225...
... .  Bottom-up around 1.5 kDa: Bacterial differentiation using prod uct ion mass spectral data of peptide sequences from the trypsin digested proteins is accomplished through the use of search en gines against publicly available sequence databases to infer iden tification (Williams et al., 2002)
From page 226...
... This can be thought of as a miniature "one-pot protein mixture purification avenue." A μTAS is a microfluidic device for sample processing using minimal reagents and water buffer (Dittich et al., 2006)
From page 227...
... MALDI-MS Three general processing procedures are used to generate protein ions for subsequent characterization and identification of bacteria with MALDI-MS. The simplest uses a mixture of the bacterial sample with a matrix deposited onto a metal MALDI target (Bright et al., 2002; Demirev et al., 2001; Gantt et al., 1999; Hettick et al., 2004; Lay, 2001; Lee et al., 2002; Wang et al., 1998)
From page 228...
... Overall, relatively few protein markers desorb from bacteria in MALDI. Very little detail is resident in the MALDI mass spectral signals compared to LC-ESI-ion trap MS-MS.
From page 229...
... Further, different bacterial dilution protocols were performed for low-concentration studies. Dilute bacterial samples were analyzed in order to assess the peptide recovery and bacterial identification ability of the in-house bacterial classification and identification (BACid)
From page 230...
... The approach also characterized double-blind bacterial samples when the experimental organism was not in the database due to its genome not having been sequenced. One experimental sample did not have its genome sequenced, and the peptide experimental record was added into the virtual bacterial proteome database.
From page 231...
... Also, it eliminated inconsistencies observed in publicly available protein databases caused by the utilization of nonstandardized gene-finding programs during the process of constructing the proteome database. Blind Mixture Analysis The BACid analysis of Sample 18 in Figure J-1 is shown in Figure J-2.
From page 232...
... Also shown in Figure J-2 for Sample 18 are six bacterial candidates near the cutoff threshold within the Staphylococcus genus. Staphylococcus aureus ATCC 3359 strain present in the blind sample has not been sequenced and has not been reported in the public domains, and thus was not part of the constructed proteome database.
From page 233...
... Thus, BACid was able to characterize Sample 17 as Clostridium without choosing one of the nine Clostridia strains resident in the database or other bacterial genera. BACid instead matched Clostridia species 1 to the experimental peptides, which indicated that there is sufficient information in the experimental peptides to differentiate Clostridium phytofermentans ISDg from the nine database Clostridia strains.
From page 234...
... Sensitivity Performance of Mass Spectrometry–Based Proteomics The MS proteomics method has shown promising results in specificity and sensitivity. While the latter parameter is highly dependent on the MS physical limit of detection, enhancing the biological sample processing is a crucial step to ease such dependency.
From page 235...
... . There is a market gap in this field, although there are speculations about the renaissance of commercial techniques based on nucleic acid sequencing (Jeng et al., 2012)
From page 236...
... 1998. Direct mass spectrometric analysis of in situ thermally hydrolyzed and methylated lipids from whole bacterial cells.
From page 237...
... 2002. Rapid typing of bacteria using matrix assisted laser desorption ionization time-of-flight mass spectrometry and pattern recognition software.
From page 238...
... 2005. Identification and phenotypic characterization of Sphingomonas wittichii strain RW1 by pep tide mass fingerprinting using matrix-assisted laser desorption ionization time of flight mass spectrometry.
From page 239...
... Field Analytical Chemistry and Technology 4:93–110. Havlicek, V., K
From page 240...
... 2000. Mass spectral in vestigation of microorganisms.
From page 241...
... 2007. Universal sample preparation method for characterization of bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry.
From page 242...
... of biomolecular ions in bioaerosol mass spectrometry. Analytical Chemistry 77:4734-4741.
From page 243...
... 2003. Laser power dependence of mass spectral signatures from individual bacte rial spores in bioaerosol mass spectrometry.
From page 244...
... 2004. Mass spectral analysis in proteomics.


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