Need for proteome molecular mass library to aid peak identification in MALDI-TOF MS microbial identification

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) generates microorganism-specific mass spectrum which has been shown to be useful in microbial identification via the mass spectrum fingerprinting approach. Specifically, the mass spectrum of an unknown microorganism is compared against those catalogued in a reference database of known microbes to aid in positive identification of microbe. However, the rich information encoded in the mass spectrum of microorganism could also be mined for identification purposes through the annotation of most or all of the mass peaks profiled. To do this, a molecular mass library of all profiled proteins in the proteome of the possible microorganism would need to be built.


Essentially, MALDI-TOF MS microbial identification is an informatic challenge both in using the pattern recognition algorithm in comparing between unknown and known mass spectra (i.e., mass spectrum fingerprinting), and in identification of mass peaks for annotating the microbe in the proteome database search approach. To identify an unknown microorganism that could not be identified through the mass spectrum fingerprinting approach due to lack of a corresponding mass spectrum of a known microorganism in the reference database, a proteome molecular mass library of all microorganisms on Earth would need to be built. Given the vast diversity of microbes on the planet and the fact that many microbes could not be cultivated on solid medium yet, such a database could not be built.


Thus, the question asked in microbial identification is necessarily a narrower one: what is the unknown microbe given current information of all known microorganisms from the MALDI-TOF MS microbial identification perspective? To answer this question, a reference library of mass spectra from known microorganisms would be necessary, and the approach for identification would be mass spectrum fingerprinting. But, cases exist where a finer identification is needed to discriminate between closely-related strains. Here comes the need for the annotation of mass peaks for aiding fine-grained microbial identification.


Functional annotation of mass peaks in MALDI-TOF MS microbial identification is essentially a top-down proteomics exercise where molecular mass of proteins in a proteome are matched against mass peaks in a mass spectrum. Such an approach would necessarily require the construction of a proteome molecular mass library where the molecular mass of all proteins profiled in the proteome is calculated. This would significantly aid peak identification in the mass spectrum after the putative microbial species is identified.


Thus, while mass spectrum fingerprinting comparison of mass spectra of unknown microbe with that of known microorganisms in a reference database could identify microorganism via MALDI-TOF MS, the ability to discriminate between closely-related microorganisms would come from the annotation of mass peaks in mass spectrum of the unknown microorganism previously identified to the species level. Such functional annotation of mass peaks would require the support of a library of molecular mass of all proteins in the proteome of the microorganism which has been identified to the species level via mass spectrum fingerprinting.


Category: microbiology, biochemistry, biotechnology, bioengineering, bioinformatics,

Tags: MALDI-TOF MS, microbial identification, mass spectrum fingerprinting, proteome database search, molecular mass, bacteria,



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