Rapid and cost effective bacterial and yeast identification using Maldi-TOF mass spectrometry and validated VITEK®MS database workflow.
BaseClear provides microbial identification services using Maldi-TOF MS (Matrix Assisted Laser Desorption Ionization Time of Flight), a rapid protein based identification technology for bacteria and yeast. This method generates a characteristic mass spectrum of abundant cellular proteins, which acts as a molecular fingerprint for each microorganism. By comparing this spectrum against the validated VITEK® MS database, accurate identification at species, genus, or family level can be achieved within minutes after measurement.
This service is designed for client in pharmaceutical, food, environment, and industrial microbiology who require fast and cost efficient identification of microbial isolates. It is particularly suitable for routine quality control, environmental monitoring and contamination screening where short turnaround times are essential. Maldi-TOF is often used as a first-line identification method before applying more detailed molecular techniques when needed.
The Maldi-TOF workflow is based on ionization and mass analysis of microbial proteins. Samples are applied to a target plate and introduced into a high-vacuum system. A laser pulse ionizes the sample, releasing a cloud of charged protein molecules that are accelerated in an electric field. The time these ions take to reach the detector (time-of-flight) is measured and translated into a mass spectrum.
The resulting spectrum contains a series of peaks representing the protein composition of the organism. These peaks are compared against the VITEK® MS database, which is CE-marked and FDA-cleared for bacterial and yeast identification. Identification is based on pattern matching between the sample spectrum and reference spectra, enabling reliable classification.
It is important to note that this method is applicable to bacterial and yeast isolates only, mould samples cannot be analyzed using Maldi-TOF.
Clients receive a concise identification report including the best database match generated by the MALDI-TOF analysis. The VITEK® MS system reports identifications at a fixed confidence value of 99.9%, representing the best match to the reference database. Only identifications with this confidence value are reported.
If no identification at 99.9% confidence is obtained, due to insufficient spectrum quality or because the species is not represented in the database, no identification is reported. In such cases, the client is contacted with recommendations for alternative identification methods, such as sequencing-based approaches, including associated timelines and costs.
Standard turnaround time is 3 working days after sample receipt, with a fast-track option delivering results within 1 working day.
You submit your samples through our online order portal, including the required sample information.
Upon arrival, samples are logged, checked for completeness and condition and prepared for analysis according to standardized Maldi-TOF Vitek MS workflow.
A subculture is performed to obtain fresh microbial growth (18-72 hours), ensuring optimal and reproducible Maldi-TOF results
Fresh colonies are applied to the target slide and analyzed by Maldi-TOF MS to generate a protein spectrum.
The generated spectrum is matched against the VITEK® MS database, and an identification report is released and uploaded to the order portal within the agreed turnaround time.
Working day fast track turnaround available
End-to-end Maldi-TOF workflow
Maldi-TOF can reliably identify bacteria and yeast isolates but not moulds. The method relies on protein spectra that are well-characterized for these organism groups.
If no identification is obtained, it is usually due to insufficient spectral quality or absence of a matching reference in the database. In such cases, alternative methods such as DNA sequencing are recommended.
Mixed cultures cannot be reliably identified using Maldi-TOF. The presence of multiple organisms leads to overlapping spectra, preventing accurate pattern matching.
Maldi-TOF is faster and more cost-effective for routine identification, while MicroSEQ® sequencing provides higher resolution and is better suited for ambiguous or complex cases. The two methods are often complementary.
Spectrum quality is determined by the number, intensity, and reproducibility of detected protein peaks. Poor sample preparation or insufficient growth can result in weak or incomplete spectra.
Liquids are not suitable for direct Maldi-TOF identification. The technique relies on co-crystallization of the sample with a matrix on the target plate, which cannot be properly achieved with liquid samples. If obtaining a solid colony on an agar plate is not possible, liquid samples may instead be analyzed using MicroSEQ® sequencing, provided the sample does not contain mixed cultures.
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