Effects of varied pH, growth rate and temperature using controlled fermentation and batch culture on Matrix Assisted Laser Desorption/Ionization whole cell protein fingerprints

Wunschel, David S.; Hill, Eric A.; McLean, Jeffrey S.; Jarman, Kristin H.; Gorby, Yuri A.; Valentine, Nancy B.; Wahl, Karen L.

doi:10.1016/j.mimet.2005.04.033

Cited by 65 publications

(56 citation statements)

References 30 publications

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“…Protein expression depends on a variety of environmental factors, such as culture conditions, including different growth phases, agar plates, pH and temperature, and may also have contributed to this effect. Although several studies have pointed out that differences in peak profile are dependent on environmental conditions (Longo et al, 1999;Bernardo et al, 2002;Valentine et al, 2005;Wunschel et al, 2005), the identifying algorithm and detection range of the MALDI Biotyper database allow reliable identification from a variety of agar media. A large number of clonally different strains should be analysed to get a peak profile that is reliable and appropriate for one species.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of species-specific score cut-off values for various Staphylococcus species using a MALDI Biotyper-based identification

Richter

Hollstein

Woloszyn

et al. 2012

Journal of Medical Microbiology

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Although previous studies investigating the MALDI Biotyper database (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based identification) have proven its high accuracy for bacterial identification, the studies differed in sample preparation, number of replicates, quantity of shots and target types used. In particular, the score cut-off values of special importance for reliable species identification varied. The aim of the present study was to identify species-specific differences in the mean score values for staphylococci. Cut-off values recommended by the manufacturer were adapted using the 20th percentile to rule out unknown score-modifying factors, even though the specificity was high and the lowest cut-off values would also yield an accurate result. Whilst correct species diagnosis was obtained in 97.32 % of samples (1382/1420), only 220 of all duplicates (15.49 %) revealed a score of ¢2.3, whilst 968 (68.17 %) had a score between 2.0 and 2.299, and 194 (13.66 %) had a score of ,2.0. Ten of 21 species had a calculated 20th percentile of ,2.0 and one species of ,1.7. In conclusion, the use of species-specific cut-off values improves the relative sensitivity of species identification in staphylococci.

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Section: Discussionmentioning

confidence: 99%

Evaluation of species-specific score cut-off values for various Staphylococcus species using a MALDI Biotyper-based identification

Richter

Hollstein

Woloszyn

et al. 2012

Journal of Medical Microbiology

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“…MALDI-TOF MS is an accurate method for routine bacterial identification, even with changing conditions such as culture medium or pH, and interlaboratory comparison is usually good, provided that minimal common reagents are used (35,(58)(59)(60). Most errors in published reports are attributed to an incomplete population of databases associated with the instruments, clerical error in database assembly or during data acquisition, or an inability of the MS spectra to differentiate similar species.…”

Section: Performance and Comparison Of Commercial Methods In Routine mentioning

confidence: 99%

Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: a Fundamental Shift in the Routine Practice of Clinical Microbiology

et al. 2013

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SUMMARY Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the “nuts and bolts” of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.

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“…2) in order to discriminate on the subspecies level revealed that about 10 times more proteins can be detected than with classical MALDI-TOF MS. The number of proteins found by classical MALDI biotyping ranged from 51 to 59 in a mass range of 3 to 14 kDa, including many ribosomal proteins (7). Applying the HIFU-assisted proteomics workflow clearly extended the mass range and type of possible biomarker target peptides, e.g., the S. enterica subsp.…”

Section: Discussionmentioning

confidence: 99%

“…The resulting fingerprints of these constantly expressed and highly abundant proteins are highly reproducible and mostly independent of the culture medium, incubation temperature, and growth state (6)(7)(8). MALDI biotyping has gained much attention in recent years due to its speed, simple handling, cost-effectiveness, and high-throughput capabilities (9).…”

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confidence: 99%

Beyond the Matrix-Assisted Laser Desorption Ionization (MALDI) Biotyping Workflow: in Search of Microorganism-Specific Tryptic Peptides Enabling Discrimination of Subspecies

Gekenidis

Studer

Wüthrich

et al. 2014

Appl Environ Microbiol

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A well-accepted method for identification of microorganisms uses matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) coupled to analysis software which identifies and classifies the organism according to its ribosomal protein spectral profile. The method, called MALDI biotyping, is widely used in clinical diagnostics and has partly replaced conventional microbiological techniques such as biochemical identification due to its shorter time to result (minutes for MALDI biotyping versus hours or days for classical phenotypic or genotypic identification). Besides its utility for identifying bacteria, MS-based identification has been shown to be applicable also to yeasts and molds. A limitation to this method, however, is that accurate identification is most reliably achieved on the species level on the basis of reference mass spectra, making further phylogenetic classification unreliable. Here, it is shown that combining tryptic digestion of the acid/organic solvent extracted (classical biotyping preparation) and resolubilized proteins, nano-liquid chromatography (nano-LC), and subsequent identification of the peptides by MALDI-tandem TOF (MALDI-TOF/TOF) mass spectrometry increases the discrimination power to the level of subspecies. As a proof of concept, using this targeted proteomics workflow, we have identified subspeciesspecific biomarker peptides for three Salmonella subspecies, resulting in an extension of the mass range and type of proteins investigated compared to classical MALDI biotyping. This method therefore offers rapid and cost-effective identification and classification of microorganisms at a deeper taxonomic level.

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Effects of varied pH, growth rate and temperature using controlled fermentation and batch culture on Matrix Assisted Laser Desorption/Ionization whole cell protein fingerprints

Cited by 65 publications

References 30 publications

Evaluation of species-specific score cut-off values for various Staphylococcus species using a MALDI Biotyper-based identification

Evaluation of species-specific score cut-off values for various Staphylococcus species using a MALDI Biotyper-based identification

Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: a Fundamental Shift in the Routine Practice of Clinical Microbiology

Beyond the Matrix-Assisted Laser Desorption Ionization (MALDI) Biotyping Workflow: in Search of Microorganism-Specific Tryptic Peptides Enabling Discrimination of Subspecies

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