A major challenge for a clinical diagnostic bacteriology/mycology laboratory is to identify the causal microorganism to the species level within a limited time frame. Conventional microbiological techniques such as culture, Gram stain, biochemical tests and molecular tests like 16S rRNA analysis can take days to yield the desired result. Matrix-assisted laser desorption ionisation-time of flight (MALDI-TOF) mass spectrometry (MS) system serves as a potential solution as it can provide accurate identification results within minutes. While several MALDI-TOF MS instruments are in the market, choosing the right system and comparing all the relative pros and cons can be difficult. Our present study focuses on this aspect as we have performed an option appraisal between two leading MALDI-TOF MS instruments, namely the MBT Sirius IVD system (Bruker) and the VITEK-MS system (Biomerieux). We have discussed all the parts of MALDI-TOF systems in detail followed by a cost analysis categorising the total cost into capital and consumable cost which will provide clarity of the estimated budget. We have also discussed the principle involved in organism identification and have compared the two systems concerning technology, accuracy, database, optimal operating conditions, etc. This article aims to provide readers with a better understanding of MALDI-TOF systems and facilitate informed decision-making regarding the acquisition of such systems.