Int. J. Mol. Sci. 2014, 15(5), 7266-7280; doi:10.3390/ijms15057266

Review
Recent Advances in Bacteria Identification by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Using Nanomaterials as Affinity Probes
Tai-Chia Chiu
Department of Applied Science, National Taitung University, 684 Section 1, Chunghua Road, Taitung 95002, Taiwan; E-Mail: tcchiu@nttu.edu.tw; Tel.: +886-89-353840; Fax: +886-89-342539
Received: 5 March 2014; in revised form: 14 April 2014 / Accepted: 16 April 2014 /
Published: 28 April 2014

Abstract

: Identifying trace amounts of bacteria rapidly, accurately, selectively, and with high sensitivity is important to ensuring the safety of food and diagnosing infectious bacterial diseases. Microbial diseases constitute the major cause of death in many developing and developed countries of the world. The early detection of pathogenic bacteria is crucial in preventing, treating, and containing the spread of infections, and there is an urgent requirement for sensitive, specific, and accurate diagnostic tests. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is an extremely selective and sensitive analytical tool that can be used to characterize different species of pathogenic bacteria. Various functionalized or unmodified nanomaterials can be used as affinity probes to capture and concentrate microorganisms. Recent developments in bacterial detection using nanomaterials-assisted MALDI-MS approaches are highlighted in this article. A comprehensive table listing MALDI-MS approaches for identifying pathogenic bacteria, categorized by the nanomaterials used, is provided.
Keywords:
affinity probes; bacteria; matrix-assisted laser desorption/ionization mass spectrometry; nanomaterials

1. Introduction

Worldwide, infectious diseases cause nearly 40% of the total 50 million deaths annually [1]. According to the World Health Organization, microbial hazards are the primary concern [2] because microbial diseases are a major cause of death in many developing and developed countries of the world [3,4]. Therefore, the development of rapid, accurate, and sensitive methods for bacterial identification is important for the clinical diagnosis, efficient treatment and prevention of diseases, environmental monitoring and food safety [58]. In clinical laboratories, bacterial identification is typically based on phenotypic tests, including Gram staining, culture and growth characteristics, and biochemical patterns. A number of methods are currently employed to detect and identify pathogenic agents, and these mainly rely on specific microbiological and biochemical identification methods [911]. These methods include culturing the microbes and counting the bacterial colonies, immunology-based methods, antigen–antibody interaction methods, and the polymerase chain reaction method, which involves DNA analysis. These methods can be sensitive and inexpensive, and can provide both qualitative and quantitative information about the test microorganisms; however, they are often time-consuming and laborious because each involves a pathogen amplification step. At present, most bacteria can be identified between a few hours to 1–2 days using these methods, with slow-growing microorganisms requiring additional time or supplementary tests [12]. Consequently, there is an urgent requirement for developing a rapid, sensitive, and selective detection method for such pathogens to treat individuals at risk, to improve public health surveillance and epidemiology, which is essential for ensuring the safety of food supplies, and to diagnose infectious bacterial diseases accurately.

There are challenges associated with identifying various types of pathogenic bacteria in a wide range of samples. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been used to analyze various biomolecules, including peptides, proteins, DNA, RNA, oligonucleotides, oligosaccharides, and polymers [1316]. This approach was first introduced by Tanaka and Karas in the late 1980s [17,18], and is a soft ionization method that provides mass spectra of the analytes with a minimum amount of fragmentation. MALDI-MS has a number of advantages over conventional methods including ease of operation, providing structural information of molecules with high throughput, speed, sensitivity, accuracy, and reproducibility [19,20]. Therefore, it has become a powerful tool for rapid characterization, differentiation, and identification of microorganism species [2127]. For example, the mass-spectral profiling of whole cells can indicate the presence of unique biomarkers that can serve as the basis for identifying microbes [28,29]. In general, mass spectra of microbes isolated from a sample may contain unique patterns that can be automatically matched with spectra in a well-established reference library of microorganisms that have been characterized using appropriate sample preparation protocols. Matching the spectra allow the microbes to be identified as well as evaluated.

A sufficient number of bacterial cells (typically ~104 cells per well) are required to generate detectable MALDI-MS ion signals. However, samples obtained from infectious biological fluids or food poisoning samples are difficult to characterize directly by MALDI-MS because the ions generated from the bacterial cells may be seriously suppressed by the complex sample matrices. This led to the idea of using nanoparticles as affinity probes, to enhance the ability of MALDI-MS to detect bacteria [30,31]. Nanoparticles provide a high surface to volume ratio, giving them high binding and capture efficiencies for bacteria. Affinity separation approaches are methods of selectively concentrating trace amounts of bacteria from complex biological and food samples before they are characterized using MALDI-MS. When inorganic nanoparticles are used in MALDI-MS, instead of organic matrices, the method is called surface-assisted laser desorption and ionization MS (SALDI-MS) [3236]. SALDI-MS was originally proposed by Sunner and Chen as early as 1995, and graphite particles were originally used as ion emitters [37]. This method was called SALDI-MS to emphasize that the surfaces and surface structures are critical to not only sample preparation but also desorption and ionization processes [38]. Numerous types of nanoparticles such as gold (Au) nanoparticles [3941], silver (Ag) nanoparticles [42,43], magnetic nanoparticles [44,45], titanium dioxide (TiO2) nanoparticles [46,47], carbon nanotubes [48,49], carbon nanoparticles [50], nanodiamonds [51], and graphene and graphene oxide [52] have been successfully used as matrices in SALDI-MS. The nanomaterials used in SALDI-MS play similar roles to the organic matrices used in MALDI-MS, absorbing energy from the laser irradiating them and efficiently transferring the energy to the analytes, causing the analytes to be desorbed and ionized [30]. The method provides several advantages including lower background noise in the low mass region, high surface areas, simple sample preparation, flexibility in sample desorption under different conditions, and high UV absorptivity [34]. Nanoparticles can also act as affinity probes, making it easy to concentrate the analytes, and offering good sensitivity and reproducibility [34].

In this review article, we focused on the overview of the recent advancements in the use of nanoparticles as affinity probes to enhance the detection sensitivity and selectivity of bacteria using MALDI-MS. Several examples of successful MALDI-MS approaches for detecting pathogenic bacteria have been provided to illustrate the advantages of this approach with respect to simplicity, sensitivity, and reproducibility. Furthermore, this article also provides some examples for the identification of bacteria in real samples using nanomaterials-assisted MALDI-MS approaches.

2. Bacterial Identification Using MALDI-MS

MALDI-MS is a very sensitive method where a single bacteria colony is sufficient for analysis, while other methods typically require culturing or enrichment of bacteria to obtain sufficient materials. Therefore, in clinical microbiological laboratories, the MALDI-MS is increasingly used for bacterial identification through the determination of the exact molecular masses of numerous peptides and small proteins, many of which are ribosomal. Conventional biochemical differentiation methods [24] have already been replaced by MALDI-MS. Because MALDI-MS is primarily applicable for analyzing clonal isolates, cultivation of the microorganism is still required. Moreover, for accurate identification, MALDI-MS can be used directly on the clinical samples that contain very few bacteria for accurate identification. In 2010, Ferreira et al. [53] introduced a MALDI-MS method for direct analysis of urine samples (4 mL) and observed that the inoculum level in the samples must be greater than 105 cfu/mL (colony-forming unit/mL). In 2010, a protocol for direct analysis of blood was introduced by Stevenson et al. [54], who separate bacteria from the red blood cells and plasma proteins via several centrifugation steps. A total of 212 positive cultures representing 32 genera and 60 species or groups were examined. Besides urine and blood, Barreiro et al. [55] inoculated pasteurized and homogenized samples of whole milk with the bacterial loads of 103–108 cfu. Sepsityper™ Kit (Bruker, Billerica, MA, USA) was used to for the testing milk sample and then analyzed by the Bruker BioTyper database. For a slightly contaminated (104 cfu/mL bacteria) milk sample, bacterial identification could be performed after initial incubation at 37 °C for 4 h. The detection limits for bacteria were in the range of 106–107 cfu/mL.

3. Nanoparticles Used as Affinity Probes

Nanoparticles are clusters of a few hundred to a few thousand atoms, and range from 1 to 100 nm in diameter. The chemical and physical properties of nanoparticles depend on their surfaces; therefore, these properties are highly dependent on the sizes, shapes, and compositions of the nanoparticles [5658]. Nanoparticles have high surface-to-volume ratios, and those with excellent optical, magnetic, and electronic properties have been employed in sensing, imaging, catalysis, electronics, optics, and optoelectronics applications [5965]. Nanoparticles can play an important role in determining the sensitivity of MALDI-MS and provide a high surface-to-volume ratio to give a high binding efficiency for bacteria. The affinity separation approach has been used to attempt to selectively concentrate trace amounts of bacteria from biological and food samples. Nanoparticles (functionalized or unmodified) that have been used as affinity probes to increase the sensitivity of MALDI-MS for detecting microbes are summarized in Table 1.

3.1. Magnetic Nanoparticles

Ho et al. [66] immobilized human immunoglobulin (IgG) onto the surfaces of magnetic Fe3O4 nanoparticles through covalent bonding (Figure 1). The functionalized magnetic nanoparticles were used as affinity probes to selectively concentrate pathogens, such as Staphylococcus aureus (S. aureus) and Staphylococcus saprophyticus (S. saprophyticus), from sample solutions. The bacteria were then characterized using MALDI-MS. The lowest bacterial concentration detected in an aqueous sample solution (0.5 mL) was 3 × 105 cfu/mL, for both S. aureus and S. saprophyticus, and the lowest detectable S. saprophyticus concentration in a urine sample was 3 × 107 cfu/mL.

Vancomycin-modified 11 nm magnetic (Fe3O4) nanoparticles were used as affinity probes to selectively bind to the surface walls of Gram-positive bacteria (S. aureus and S. saprophyticus), as shown in Figure 2, allowing the bacteria to then be directly characterized using MALDI-MS [67]. Vancomycin is one of the most potent antibiotics, and has a high specificity for the D-Alanine (Ala) (D-Ala) moieties on the cell walls of Gram-positive bacteria. The lowest cell concentrations that could be detected in a urine sample (3 mL) were 7.4 × 104 cfu/mL for S. aureus and 7.8 × 104 cfu/mL for S. saprophyticus.

IgG- and vancomycin-modified magnetic nanoparticles have been demonstrated to exhibit effective affinities for selectively concentrating traces of bacteria from the sample solutions. However, because interferences from the urine matrix affect the binding capacity of these nanoprobes, further improvements are required to reduce the matrix effects in the analysis of biological samples.

A combination of membrane filtration and vancomycin-modified magnetic (Fe3O4) 15–20 nm nanoparticles has been used to selectively concentrate Gram-positive bacteria from tap water and reservoir water, allowing the bacteria to be rapidly analyzed using whole-cell MALDI-MS [68]. The capture efficiency for Gram-positive bacteria using these vancomycin-modified magnetic nanoparticles was 26.7%–33.3%, and the analysis time was approximately 2 h. This approach enhanced the sensitivity of the method by a factor of approximately 6 × 104, giving a limit of detection of 5 × 102 cfu/mL for Bacillus cereus (B. cereus), Enterococcus faecium (E. faecium), and S. aureus in water samples (2 L).

3.2. Silver (Ag) Nanoparticles

The bifunctional properties of Ag nanoparticles allowed them to be used as affinity probes for Escherichia coli (E. coli) and Serratia marcescens (S. marcescens), by Gopal et al. [69], to increase the sensitivity of MALDI-MS when characterizing the bacteria. The critical concentration of affinity probes for Ag nanoparticles was 1 mL/L in the case of E. coli and 0.5 mL/L in the case of S. marcescens. Ag nanoparticle concentrations higher than these values showed pronounced bactericidal activities.

The same research group also observed that an ionic solution (CrO42−) and 0.035 mg of Ag nanoparticles could be used to capture yogurt bacteria (Bifidobacterium lactis (B. lactis), Lactobacillus acidophilus (L. acidophilus), Streptococcus thermophilus (S. thermophilus), and Lactobacillus bulgaricus (L. bulgaricus) from AB yogurt and L. acidophilus, Bifidobacterium longum (B. longum), L. bulgaricus, and S. thermophilus from Lin yogurt), improving the sensitivity achieved for detecting bacteria in yogurt samples [70]. This method has demonstrated a rapid, selective and sensitive means of bacterial detection using MALDI-MS for food microbiology.

3.3. Cadmium Sulfide (CdS) Quantum Dots (QDs)

Gopal et al. [71] has reported that CdS QDs can degrade the extracellular polysaccharides of E. coli cells when using MALDI-MS. Adding 20 μL/L of CdS QDs was observed to enhance the extracellular polymeric substance (EPS) peaks using an incubation time of up to 3 h. The authors confirmed that CdS QDs can function as more than just affinity probes, being able to degrade EPSs. CdS QDs can, therefore, be used to inactivate pathogenic E. coli and also inhibit the growth of E. coli biofilms.

Manikandan and Wu [72] observed that CdS QDs (10 mg/L) with particle sizes of 1–7 nm performed fungicidal roles and functioned as protein signal enhancement probes in the MALDI-MS analysis of the fungi Saccharomyces cerevisiae (S. cerevisiae) and Candida utilis (C. utilis). From their MALDI-MS results, the authors proposed the mechanism involving the CdS QDs interacting with the EPSs and removing small molecules from the EPS layers. The MALDI-MS protein signals were enhanced at all of the CdS QD concentrations that were tested (10–30 mg).

Chitosan-modified CdS QDs have been used as effective bacterial biosensors because of the strong affinities between chitosan molecules and bacterial membranes [73]. In that study, Pseudomonas aeruginosa (P. aeruginosa) and S. aureus cells were detected at low concentrations, 200 and 150 cfu/mL, respectively, after an extremely short time (1 min). MALDI-MS and transmission electron microscopy were used to confirm the interactions and the biocompatibility of the chitosan-modified CdS QDs with bacterial cells.

3.4. Platinum (Pt) Nanoparticles

Ahmad and Wu [74] employed a single drop microextraction technique, using an ionic liquid (1-butyl-3-methylimidazolium hexafluorophosphate) drop mixed with Pt nanoparticles, to extract bacterial proteins from aqueous samples to characterize pathogenic bacteria using MALDI-MS. This approach is based on surface changes in the ionic liquid and the membrane proteins of the bacteria, and it was successfully used to detect E. coli and S. marcescens at concentrations as low as 106 cfu/mL.

A rapid method for detecting bacteria associated with plants by an on-particle ionization and enrichment approach using IgG-functionalized Pt nanoparticle-assisted MALDI-MS was reported by Ahmad et al. [75]. The approach was successfully used to detect Bacillus thuringiensis (B. thuringiensis) and Bacillus subtilis (B. subtilis) isolated from rhizospheric soil and carrot plant roots. This study proved that bacteria can be directly detected even at low concentrations.

A rapid and sensitive approach to studying interactions between an affinity probe and a bacterial wall was introduced by Ahmad and Wu [76]. IgG was immobilized on Pt nanoparticles and MALDI-MS was used to detect the specific surface proteins of the bacteria S. marcescens and E. coli. This approach enabled the rapid detection of bacterial proteins, at a high resolution and with good sensitivity, without the need for tedious washing and separation procedures, and can be used to detect approximately 105 cfu/mL of S. marcescens and E. coli.

3.5. Other Nanomaterials

Chan et al. [77] demonstrated that pathogenic bacteria, including E. coli, Klebsiella pneumonia (K. pneumoniae), P. aeruginosa, pandrug-resistant Acinetobacter baumannii (A. baumannii), S. aureus, E. faecalis, and vancomycin-resistant E. faecalis, can be concentrated by lysozyme-encapsulated gold nanoclusters (AuNCs) that photoluminesce red, and distinguished by the results combining MALDI-MS and principal component analysis. Figure 3A shows photographs of sample tubes after the lysozyme-AuNCs were used as probes for E. coli J96 in urine samples containing different concentrations of the E. coli. Photographs of the control experiment sample tubes are shown in Figure 3B for comparison. Figure 3C shows the MALDI-MS spectra of the conjugates containing E. coli J96, in which the peaks at m/z 6177 and 6237 correspond to E. coli J96. The lowest E. coli concentration that could be detected using this approach was approximately 106 cfu/mL. The advantages of this method include speed (without cell culturing) and simplicity, and it can be used as universal affinity probes for Gram-positive/negative and antibiotic-resistant bacteria.

Abdelhamid and Wu [78] demonstrated that multifunctional graphene magnetic nanosheets modified with chitosan (GMCS) can be used in MALDI-MS for the sensitive detection of pathogenic bacteria (P. aeruginosa and S. aureus). The GMCS were observed to act as efficient separation and preconcentration nanoprobes for SALDI and enhance the ionization of bacterial biomolecules. GMCS have been used in the direct detection of low concentrations of P. aeruginosa and S. aureus in blood samples, demonstrating their practical applicability. This approach offers many advantages such as robustness, simplicity, and the capability for fluorescence based real-sample monitoring.

The heat stress response of E. coli (at 107 cfu/mL) at different temperatures has been studied using nickel oxide (NiO) nanoparticle-assisted MALDI-MS by Hasan et al. [79]. MALDI-MS was successfully used to detect 10 kDa chaperonin proteins produced by E. coli under heat stress at temperatures between 40 and 80 °C in the absence or presence of NiO nanoparticles. Dramatic decreases in the viability of E. coli in the presence of NiO were confirmed from the MALDI-MS results. This technique is a rapid, sensitive, and efficient approach for bacterial detection under extremely harsh conditions.

Gopal et al. [80] demonstrated that S. aureus isolated from the human nasal passage can be directly detected using MALDI-MS assisted by TiO2 nanoparticles, without any culturing steps or sample pretreatment being required. TiO2 nanoparticles were used to enhance the bacterial signals in the direct MALDI-MS analysis.

MALDI-MS has been used to evaluate bactericidal activity, by detecting proteins produced because of the inactivation of E. coli cells by zinc oxide (ZnO) nanoparticles [81]. The results showed that at concentrations of 1 and 5 g/L ZnO nanoparticles can be used as affinity probes to improve the signal intensities in the MS spectra. The significant differences in the spectral patterns confirmed that MALDI-MS was successfully used to evaluate the bactericidal activity of ZnO nanoparticles.

Gopal et al. [82] proposed mechanisms for the interactions between five nanoparticles (Ag, NiO, Pt, TiO2, and ZnO) and two bacteria (S. aureus and P. aeruginosa) from studies using transmission electron microscopy, ultra spectrometry, and MALDI-MS. Two mechanisms (Figure 4) were proposed for the interactions: (1) Mechanism A was proposed for Pt and NiO nanoparticles, the function of which is based on their affinities for bacterial walls; and (2) Mechanism B was proposed for bactericidal nanoparticles, such as TiO2, ZnO, and Ag nanoparticles.

4. Conclusions

MALDI-MS is an emerging analytical tool for detecting and identifying microorganisms. It offers high sensitivity, simple sample preparation processes, low sample consumption volumes, and the possibility of automated and high-throughput analyses. In this review, we have described several MALDI-MS approaches for detecting pathogenic bacteria using nanomaterials (such as AuNCs, Ag, magnetic, and Pt nanoparticles and CdS QDs) as affinity probes. The nanomaterials described here act as concentration probes for the selective capture of unique biomarkers from microorganisms, and as surfaces to absorb energy from the laser irradiation, thereby inducing desorption and ionization of the analytes.

As mentioned above, the most important advantage of the affinity-based nanoparobe methods is their ability to selectively concentrate and purify microorganisms from complex samples, such as urine and blood, and allow the further identification of microorganisms without microbial culturing using MALDI-MS. For the nanomaterials-assisted MALDI-MS, Direct analysis of microorganisms at low microbial levels can be performed using the nanomaterials-based MALDI-MS. Numerous nanomaterials have been demonstrated to be useful as affinity probes for targeting bacteria. However, some nanoparticles such as Ag, TiO2 and ZnO, also exhibit bactericidal activity, and therefore might not be good affinity probes at higher nanoparticles concentrations. Controlling of the nanoparticle concentration will be a key factor. All these nanomaterials-assisted MALDI-MS methods also encounter challenges with respect to the enrichment of unknown target bacterial species from the urine, blood, and cerebrospinal fluid. Thus, a limiting factor in MALDI-MS analysis is insufficient database entries. The addition of certain species to the database has been demonstrate significantly improve MALDI-MS precision in bacterial identification.

The broad adoption of nanomaterials-assisted MALDI-MS methods for bacterial identification will require a substantial improvement in performance compared with the existing methods, such as conventional MALDI-MS and biochemical tests. Thus, the standardization of terminology is required. Advances in nanomaterials-assisted MALDI-MS methods will support the simple and accurate means of bacterial identification for food safety, environmental monitoring and clinical diagnosis.

Acknowledgments

This work was supported by the Ministry of Science and Technology of Taiwan under contract No. NSC 102-2113-M-143-001.

Conflicts of Interest

The author declares no conflict of interest.

References

  1. Ivnitski, D.; Abdel-Hamid, I.; Atanasov, P.; Wilkins, E. Biosensors for detection of pathogenic bacteria. Biosens. Bioelectron 1999, 14, 599–624.
  2. WHO Guidelines for Drinking-Water Quality, Available online: http://www.who.int/water_sanitation_health/dwq/guidelines/en/ , accessed on 7 May 2014.
  3. Jahid, I.K.; Ha, S.-D. A review of microbial biofilms of produce: Future challenge to food safety. Food Sci. Biotechnol 2012, 21, 299–316.
  4. Velusamy, V.; Arshak, K.; Korostynska, O.; Oliwa, K.; Adley, C. An overview of foodborne pathogen detection: In the perspective of biosensors. Biotechnol. Adv 2010, 28, 232–254.
  5. Tallury, P.; Malhotra, A.; Byrne, L.M.; Santra, S. Nanobioimaging and sensing of infectious diseases. Adv. Drug Deliv. Rev 2010, 62, 424–437.
  6. Kim, J.; Yoon, M.-Y. Recent advances in rapid and ultrasensitive biosensors for infectious agents: Lesson from Bacillus anthracis diagnostic sensors. Analyst 2010, 135, 1182–1190.
  7. Sekhon, S.S.; Kim, S.-G.; Lee, S.-H.; Jang, A.; Min, J.; Ahn, J.-Y.; Kim, Y.-H. Advances in pathogen-associated molecules detection using aptamer based biosensors. Mol. Cell. Toxicol 2013, 9, 311–317.
  8. Sharma, H.; Mutharasan, R. Review of biosensors for foodborne pathogens and toxins. Sens. Actuators B 2013, 183, 535–549.
  9. Quilliam, R.S.; Williams, A.P.; Avery, L.M.; Malham, S.K.; Jones, D.L. Unearthing human pathogens at the agricultural–environment interface: A review of current methods for the detection of Escherichia coli O157 in freshwater ecosystems. Agric. Ecosyst. Environ 2011, 140, 354–360.
  10. Kirsch, J.; Siltanen, C.; Zhou, Q.; Revzin, A.; Simonian, A. Biosensor technology: Recent advances in threat agent detection and medicine. Chem. Soc. Rev 2013, 42, 8733–8768.
  11. Bridle, H.; Miller, B.; Desmulliez, M.P.Y. Application of microfluidics in waterborne pathogen monitoring: A review. Water Res 2014, 55, 256–271.
  12. Biswas, S.; Rolain, J.-M. Use of MALDI-TOF mass spectrometry for identification of bacteria that are difficult to culture. J. Microbiol. Methods 2013, 92, 14–24.
  13. Sandrin, T.R.; Goldstein, J.E.; Schumaker, S. MALDI TOF MS profiling of bacteria at the strain level: A review. Mass Spectrom. Rev 2013, 32, 188–217.
  14. Bakry, R.; Rainer, M.; Huck, C.W.; Bonn, G.K. Protein profiling for cancer biomarker discovery using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and infrared imaging: A review. Anal. Chim. Acta 2011, 690, 26–34.
  15. Cho, Y.-T.; Su, H.; Huang, T.-L.; Chen, H.-C.; Wu, W.-J.; Wu, P.-C.; Wu, D.-C.; Shiea, J. Matrix-assisted laser desorption ionization/time-of-flight mass spectrometry for clinical diagnosis. Clin. Chim. Acta 2013, 415, 266–275.
  16. Bergman, N.; Shevchenko, D.; Bergquist, J. Approaches for the analysis of low molecular weight compounds with laser desorption/ionization techniques and mass spectrometry. Anal. Bioanal. Chem 2014, 406, 49–61.
  17. Karas, M.; Hillenkamp, F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem 1988, 60, 2299–2301.
  18. Tanaka, K.; Waki, H.; Ido, Y.; Akita, S.; Yoshida, Y.; Yoshida, T. Protein and polymer analyses up to m/z 100,000 by laser ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom 1988, 2, 151–153.
  19. Dingle, T.C.; Butler-Wu, S.M. MALDI-TOF mass spectrometry for microorganism identification. Clin. Lab. Med 2013, 33, 589–609.
  20. Chalupová, J.; Raus, M.; Sedlářová, M.; Šebela, M. Identification of fungal microorganisms by MALDI-TOF mass spectrometry. Biotechnol. Adv 2014, 32, 230–241.
  21. Ho, Y.-P.; Reddy, P.M. Advances in mass spectrometry for the identification of pathogens. Mass Spectrom. Rev 2011, 30, 1203–1224.
  22. Wieser, A.; Schneider, L.; Jung, J.; Schubert, S. MALDI-TOF MS in microbiological diagnostics—Identification of microorganisms and beyond (mini review). Appl. Microbiol. Biotechnol 2012, 93, 965–974.
  23. Krásný, L.; Hynek, R.; Hochel, I. Identification of bacteria using mass spectrometry techniques. Int. J. Mass Spectrom 2013, 353, 67–79.
  24. Lartigue, M.-F. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for bacterial strain characterization. Infect. Genet. Evol 2013, 13, 230–235.
  25. Kostrzewa, M.; Sparbier, K.; Maier, T.; Schubert, S.; MALDI-TOF, M.S. An upcoming tool for rapid detection of antibiotic resistance in microorganisms. Proteomics Clin. Appl 2013, 7, 767–778.
  26. Havlicek, V.; Lemr, K.; Schug, K.A. Current trends in microbial diagnostics based on mass spectrometry. Anal. Chem 2013, 85, 790–797.
  27. Del Chierico, F.; Petrucca, A.; Vernocchi, P.; Bracaglia, G.; Fiscarelli, E.; Bernaschi, P.; Muraca, M.; Urbani, A.; Putignani, L. Proteomics boosts translational and clinical microbiology. J. Proteomics 2014, 97, 69–87.
  28. Welker, M.; Moore, E.R.B. Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst. Appl. Microbiol 2011, 34, 2–11.
  29. Intelicato-Young, J.; Fox, A. Mass spectrometry and tandem mass spectrometry characterization of protein patterns, protein markers and whole proteomes for pathogenic bacteria. J. Microbiol. Methods 2013, 92, 381–386.
  30. Chiu, T.-C.; Huang, L.-S.; Lin, P.-C.; Chen, Y.-C.; Chen, Y.-J.; Lin, C.-C.; Chang, H.-T. Nanomaterials based affinity matrix-assisted laser desorption/ionization mass spectrometry for biomolecules and pathogenic bacteria. Recent Pat. Nanotechnol 2007, 1, 99–111.
  31. Wu, F.-H.; Gopal, J.; Manikandan, M. Future perspective of nanoparticle interaction-assisted laser desorption/ionization mass spectrometry for rapid, simple, direct and sensitive detection of microorganisms. J. Mass Spectrom 2012, 47, 355–363.
  32. Chen, W.-T.; Tomalová, I.; Preisler, J.; Chang, H.-T. Analysis of biomolecules through surface-assisted laser desorption/ionization mass spectrometry employing nanomaterials. J. Chin. Chem. Soc 2011, 58, 769–778.
  33. Rainer, M.; Qureshi, M.N.; Bonn, G.K. Matrix-free and material-enhanced laser desorption/ionization mass spectrometry for the analysis of low molecular weight compounds. Anal. Bioanal. Chem 2011, 400, 2281–2288.
  34. Chiang, C.-K.; Chen, W.-T.; Chang, H.-T. Nanoparticle-based mass spectrometry for the analysis of biomolecules. Chem. Soc. Rev 2011, 40, 1269–1281.
  35. Law, K.P.; Larkin, J.R. Recent advances in SALDI-MS techniques and their chemical and bioanalytical applications. Anal. Bioanal. Chem 2011, 399, 2597–2622.
  36. Lim, A.Y.; Ma, J.; Boey, Y.C.F. Development of nanomaterials for SALDI-MS analysis in forensics. Adv. Mater 2012, 24, 4211–4216.
  37. Sunner, J.; Dratz, E.; Chen, Y.-C. Graphite surface-assisted laser desorption/ionization time-of-flight mass spectrometry of peptides and proteins from liquid solutions. Anal. Chem 1995, 67, 4335–4342.
  38. Han, M.; Sunner, J. An activated carbon substrate surface for laser desorption mass spectrometry. J. Am. Soc. Mass Spectrom 2000, 11, 644–649.
  39. Chiang, C.-K.; Lin, Y.-W.; Chen, W.-T.; Chang, H.-T. Accurate quantitation of glutathione in cell lysates through surface-assisted laser desorption/ionization mass spectrometry using gold nanoaprticles. Nanomedicine 2010, 6, 530–537.
  40. Hsieh, Y.-T.; Chen, W.-T.; Tomalová, I.; Preisler, J.; Chang, H.-T. Detection of melamine in infant formula and grain powder by surface-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom 2012, 26, 1393–1398.
  41. Pilolli, R.; Ditaranto, N.; di Franco, C.; Palmisano, F.; Cioffi, N. Thermally annealed gold nanoparticles for surface-assisted laser desorption ionisation–mass spectrometry of low molecular weight analytes. Anal. Bioanal. Chem 2012, 404, 1703–1711.
  42. Chiu, T.-C.; Chang, L.-C.; Chiang, C.-K.; Chang, H.-T. Determining estrogens using surface-assisted laser desorption/ionization mass spectrometry with silver nanoparticles as the matrix. J. Am. Soc. Mass Spectrom 2008, 19, 1343–1346.
  43. Nizioł, J.; Rode, W.; Zieliński, Z.; Ruman, T. Matrix-free laser desorption–ionization with silver nanoparticle-enhanced steel targets. Int. J. Mass Spectrom 2013, 335, 22–32.
  44. Lin, P.-C.; Yu, C.-C.; Wu, H.-T.; Lu, Y.-W.; Han, C.-L.; Su, A.-K.; Chen, Y.-J.; Lin, C.-C. A chemically functionalized magnetic nanoplatform for rapid and specific biomolecular recognition and separation. Biomacromolecules 2013, 14, 160–168.
  45. Huang, S.-Y.; Chen, Y.-C. Magnetic nanoparticle-based platform for characterization of histidine-rich proteins and peptides. Anal. Chem 2013, 85, 3347–3354.
  46. Chiu, T.-C. Steroid hormones analysis with surface-assisted laser desorption/ionization mass spectrometry using catechin-modified titanium dioxide nanoparticles. Talanta 2011, 86, 415–420.
  47. Radisavljević, M.; Kamčeva, T.; Vukićević, I.; Radoičić, M.; Šaponjić, Z.; Petković, M. Colloidal TiO2 nanoparticles as substrates for M(S)ALDI mass spectrometry of transition metal complexes. Rapid Commun. Mass Spectrom 2012, 26, 2041–2050.
  48. Hsu, W.-Y.; Lin, W.-D.; Hwu, W.-L.; Lai, C.-C.; Tsai, F.-J. Screening assay of very long chain fatty acids in human plasma with multiwalled carbon nanotube-based surface-assisted laser desorption/ionization mass spectrometry. Anal. Chem 2010, 82, 6814–6820.
  49. Cegłowski, M.; Schroeder, G. Laser desorption/ionization mass spectrometric analysis of surfactants on functionalized carbon nanotubes. Rapid Commun. Mass Spectrom 2012, 27, 258–264.
  50. Ng, E.W.Y.; Lam, H.S.; Ng, P.C.; Poon, T.C.W. Quantification of citrulline by parallel fragmentation monitoring—A novel method using graphitized carbon nanoparticles and MALDI-TOF/TOF mass spectrometry. Clin. Chim. Acta 2013, 420, 121–127.
  51. Wei, L.-M.; Shen, Q.; Lu, H.-J.; Yang, P.-Y. Pretreatment of low-abundance peptides on detonation nanodiamond for direct analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Chromatogr. B 2009, 877, 3631–3637.
  52. Liu, Y.; Liu, J.; Deng, C.; Zhang, X. Graphene and graphene oxide: Two ideal choices for the enrichment and ionization of long-chain fatty acids free from matrix-assisted laser desorption ionization matrix interference. Rapid Commun. Mass Spectrom 2011, 25, 3223–3234.
  53. Ferreira, L.; Sánchez-Juanes, F.; González-Ávila, M.; Cembrero-Fuciños, D.; Herrero-Hernández, A.; González-Buitrago, J.M.; Muñoz-Bellido, J.L. Direct identification of urinary tract pathogens from urine samples by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol 2010, 48, 2110–2115.
  54. Stevenson, L.G.; Drake, S.K.; Murray, P.R. Rapid identification of bacteria in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol 2010, 48, 444–447.
  55. Barreiro, J.R.; Braga, P.A.C.; Ferreira, C.R.; Kostrzewa, M.; Maier, T.; Wegemann, B.; Böettcher, V.; Eberlin, M.N.; dos Santos, M.V. Nonculture-based identification of bacteria in milk by protein fingerprinting. Proteomics 2012, 12, 2739–2745.
  56. Burda, C.; Chen, X.; Narayana, R.; El-Sayed, M.A. Chemistry and properties of nanocrystals of different shapes. Chem. Rev 2005, 105, 1025–1102.
  57. An, K.; Somorjai, G.A. Size and shape control of metal nanoparticles for reaction selectivity in catalysis. ChemCatChem 2012, 4, 1512–1524.
  58. Lohse, S.E.; Murphy, C.A. Applications of colloidal inorganic nanoparticles: From medicine to energy. J. Am. Chem. Soc 2012, 134, 15607–15620.
  59. Sanvicens, N.; Pastells, C.; Pascual, N.; Marco, M.-P. Nanoparticle-based biosensors for detection of pathogenic bacteria. Trends Anal. Chem 2009, 28, 1243–1252.
  60. Coto-García, A.M.; Sotelo-González, E.; Fernández-Argüelles, M.T.; Pereiro, R.; Costa-Fernández, J.M.; Sanz-Medel, A. Nanoparticles as fluorescent labels for optical imaging and sensing in genomics and proteomics. Anal. Bioanal. Chem 2011, 399, 29–42.
  61. Veerapandian, M.; Yun, K. Functionalization of biomolecules on nanoparticles: Specialized for antibacterial applications. Appl. Microbiol. Biotechnol 2011, 90, 1655–1667.
  62. Gilmartin, N.; O’Kennedy, R. Nanobiotechnologies for the detection and reduction of pathogens. Enzym. Microb. Technol 2012, 50, 87–95.
  63. Burris, K.P.; Stewart, C.N., Jr. Fluorescent nanoparticles: Sensing pathogens and toxins in foods and crops. Trends Food Sci. Technol 2012, 28, 143–152.
  64. Shinde, S.B.; Fernandes, C.B.; Patravale, V.B. Recent trends in in vitro nanodiagnostics for detection of pathogens. J. Control. Release 2012, 159, 164–180.
  65. Zamborini, F.P.; Bao, L.; Dasari, R. Nanoparticles in measurement science. Anal. Chem 2012, 84, 541–576.
  66. Ho, K.-C.; Tsai, P.-J.; Lin, Y.-S.; Chen, Y.-C. Using biofunctionalized nanoparticles to probe pathogenic bacteria. Anal. Chem 2004, 76, 7162–7168.
  67. Lin, Y.-S.; Tsai, P.-J.; Weng, M.-F.; Chen, Y.-C. Affinity capture using vancomycin-bound magnetic nanoparticles for the MALDI-MS analysis of bacteria. Anal. Chem 2005, 77, 1753–1760.
  68. Li, S.; Guo, Z.; Wu, H.-F.; Liu, Y.; Yang, Z.; Woo, C.H. Rapid analysis of Gram-positive bacteria in water via membrane filtration coupled with nanoprobe-based MALDI-MS. Anal. Bioanal. Chem 2010, 397, 2465–2476.
  69. Gopal, J.; Wu, H.-F.; Lee, C.-H. The biofunctional role of Ag nanoparticles on bacteria— A MALDI-MS perspective. Analyst 2011, 136, 5077–5083.
  70. Lee, C.-H.; Gopal, J.; Wu, F.-H. Ionic solution and nanoparticle assisted MALDI-MS as bacterial biosensors for rapid analysis of yogurt. Biosens. Bioelectron 2012, 31, 77–83.
  71. Gopal, J.; Wu, F.-H.; Gangaraju, G. Quantifying the degradation of extracellular polysaccharides of Escherichia coli by CdS quantum dots. J. Mater. Chem 2011, 21, 13445–13451.
  72. Manikandan, M.; Wu, H.-F. Probing the fungicidal properties of CdS quantum dots on Saccharomyces cerevisiae and Candida utilis using MALDI-MS. J. Nanopart. Res 2013, 15, 1728.
  73. Abdelhamid, H.N.; Wu, F.-H. Probing the interactions of chitosan capped CdS quantum dots with pathogenic bacteria and their biosensing application. J. Mater. Chem. B 2013, 1, 6094–6106.
  74. Ahmad, F.; Wu, F.-H. Characterization of pathogenic bacteria using ionic liquid via single drop microextraction combined with MALDI-TOF MS. Analyst 2011, 136, 4020–4027.
  75. Amhad, F.; Siddiqui, M.A.; Babalola, O.O.; Wu, F.-H. Biofunctionalization of nanoparticle assisted mass spectrometry as biosensors for rapid detection of plant associated bacteria. Biosens. Bioelectron 2012, 35, 235–242.
  76. Ahmad, F.; Wu, F.-H. Rapid and sensitive detection of bacteria via platinum-labeled antibodies and on-particle ionization and enrichment prior to MALDI-TOF mass spectrometry. Microchim. Acta 2013, 180, 485–492.
  77. Chan, P.-H.; Wong, S.-Y.; Lin, S.-H.; Chen, Y.-C. Lysozyme-encapsulated gold nanocluster-based affinity mass spectrometry for pathogenic bacteria. Rapid Commun. Mass Spectrom 2013, 27, 2143–2148.
  78. Abdelhamid, H.N.; Wu, H.-F. Multifunctional graphene magnetic nanosheet decorated with chitosan for highly sensitive detection of pathogenic bacteria. J. Mater. Chem. B 2013, 1, 3950–3961.
  79. Hasan, N.; Ahmad, F.; Wu, F.-H. Monitoring the heat stress response of Escherichia coli via NiO nanoparticle assisted MALDI–TOF mass spectrometry. Talanta 2013, 103, 38–46.
  80. Gopal, J.; Narayana, J.L.; Wu, F.-H. TiO2 nanoparticle assisted mass spectrometry as biosensors of Staphylococcus aureus, key pathogen in nosocomial infections from air, skin surface and human nasal passage. Biosens. Bioelectron 2011, 27, 201–206.
  81. Gopal, J.; Wu, F.-H.; Lee, Y.-H. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry as a rapid and reliable technique for directly evaluating bactericidal activity: Probing the critical concentration of ZnO nanoparticles as affinity probes. Anal. Chem 2010, 82, 9617–9621.
  82. Gopal, J.; Manikandan, M.; Hasan, N.; Lee, C.-H.; Wu, H.-F. A comparative study on the mode of interaction of different nanoparticles during MALDI-MS of bacterial cells. J. Mass Spectrom 2013, 48, 119–127.
Ijms 15 07266f1 200
Figure 1. Synthetic route for immobilizing immunoglobulin (IgG) onto the surfaces of Fe3O4 magnetic nanoparticles. Reprinted with permission from [66]. Copyright (2014) American Chemical Society.

Click here to enlarge figure

Figure 1. Synthetic route for immobilizing immunoglobulin (IgG) onto the surfaces of Fe3O4 magnetic nanoparticles. Reprinted with permission from [66]. Copyright (2014) American Chemical Society.
Ijms 15 07266f1 1024
Ijms 15 07266f2 200
Figure 2. Cartoon illustrations of the proposed method for anchoring vancomycin-immobilized magnetic nanoparticles onto the surface of a Gram-positive bacterial cell and the binding of vancomycin to the terminal of D-Alanine (D-Ala)–D-Ala units of the peptides on the cell wall of a Gram-positive bacterium. Reprinted with permission from [67]. Copyright (2014) American Chemical Society.

Click here to enlarge figure

Figure 2. Cartoon illustrations of the proposed method for anchoring vancomycin-immobilized magnetic nanoparticles onto the surface of a Gram-positive bacterial cell and the binding of vancomycin to the terminal of D-Alanine (D-Ala)–D-Ala units of the peptides on the cell wall of a Gram-positive bacterium. Reprinted with permission from [67]. Copyright (2014) American Chemical Society.
Ijms 15 07266f2 1024
Ijms 15 07266f3 200
Figure 3. Photographs obtained by vortex-mixing (A) the lysozyme-AuNCs with E. coli J96 at different cell concentrations and (B) E. coli J96 alone for 1 h at different cell concentrations, followed by centrifugation at 3500 rpm for 5 min. The samples were prepared in urine that was diluted 50-fold with PBS solution (pH 7.4) containing BSA (~10 μM). The photographs were taken under illumination of UV light (λmax = 365 nm); (C) Examination of the limit of detection. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) obtained after using the lysozyme-AuNCs (1.36 mg/mL, 0.1 mL) as affinity probes to concentrate target species from a urine sample (0.90 mL) containing E. coli J96 (1.59 × 106 cells/mL) for 1 h. The urine sample was diluted 50-fold with PBS solution (pH 7.4) containing BSA (~10 μM) prior to bacterial spiking. Reprinted with permission from [77].

Click here to enlarge figure

Figure 3. Photographs obtained by vortex-mixing (A) the lysozyme-AuNCs with E. coli J96 at different cell concentrations and (B) E. coli J96 alone for 1 h at different cell concentrations, followed by centrifugation at 3500 rpm for 5 min. The samples were prepared in urine that was diluted 50-fold with PBS solution (pH 7.4) containing BSA (~10 μM). The photographs were taken under illumination of UV light (λmax = 365 nm); (C) Examination of the limit of detection. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) obtained after using the lysozyme-AuNCs (1.36 mg/mL, 0.1 mL) as affinity probes to concentrate target species from a urine sample (0.90 mL) containing E. coli J96 (1.59 × 106 cells/mL) for 1 h. The urine sample was diluted 50-fold with PBS solution (pH 7.4) containing BSA (~10 μM) prior to bacterial spiking. Reprinted with permission from [77].
Ijms 15 07266f3 1024
Ijms 15 07266f4 200
Figure 4. Schematic diagram showing the mechanisms (Mechanism A and Mechanism B) for interactions of five nanoparticles with two pathogenic bacteria postulated in the study. Reprinted with permission from [82].

Click here to enlarge figure

Figure 4. Schematic diagram showing the mechanisms (Mechanism A and Mechanism B) for interactions of five nanoparticles with two pathogenic bacteria postulated in the study. Reprinted with permission from [82].
Ijms 15 07266f4 1024
Table Table 1. Nanomaterials used as affinity probes in MALDI-MS.

Click here to display table

Table 1. Nanomaterials used as affinity probes in MALDI-MS.
NanomaterialsFunctionalized moleculePathogenApplicationLOD (cfu/mL)Ref.
Fe3O4 NPsIgGS. aureus; S. saprophyticus3.0 × 105[66]
Fe3O4 NPsIgGS. saprophyticusUrine3.0×107[66]
Fe3O4 NPsVancomycinS. aureus; S. saprophyticusUrine7.8 × 104; 7.4 × 104[67]
Fe3O4 NPsVancomycinB. cereus; E. faecium; S. aureusTap water, reservoir water5.0 × 102[68]
Ag NPsE. coli; S. marcescenN.D.[69]
Ag NPsB. lactis; L. acidophilus; S. thermophilus; L. bulgaricusYogurtN.D.[70]
Ag NPsL. acidophilus; B. longum; L. bulgaricus; S. thermophilusYogurtN.D.[70]
CdS QDsE. coliN.D.[71]
CdS QDsS. cerevisiae; C. utilisN.D.[72]
CdS QDsChitosanP. aeruginosa; S. aureus2.0 × 102; 1.5 × 102[73]
Pt NPsMixed with ionic liquid (1-butyl-3-methylimidazolium hexafluorophosphate)E. coli; S. marcescens106[74]
Pt NPsIgGB. thuringiensis; B. subtilisRhizospheric soil and rootN.D.[75]
Pt NPsIgGS. marcescens; E. coli105[76]
AuNCsLysozymeE. coli; K. pneumoniae; P. aeruginosa; pandrug-resistant A. baumannii; S. aureus; E. faecalis; vancomycin-resistant E. faecalisFetal bovine serum; urineN.D.; 106[77]
Graphene magnetic nanosheetsChitosanP. aeruginosa; S. aureusBlood6.0 × 102; 5.0 × 102[78]
NiO NPsE. coli107[79]
TiO2 NPsS. aureusHuman nasal passageN.D.[80]
ZnO NPsE. coliN.D.[81]
Ag, Pt, NiO, TiO2, ZnO NPsS. aureus; P. saeruginosaN.D.[82]

Ref., Reference; Ag, silver; AuNCs, gold nanoclusters; CdS, cadmium sulfide; IgG, immunoglobulin; LOD, limit of detection; N.D., not determined; NiO, nickel oxide; NPs, nanoparticles; Pt, platinum; QDs, quantum dots; TiO2, titanum dioxide; ZnO, zinc oxide.

Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert