Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy

Abstract In mass spectrometry-based untargeted metabolomics, rarely more than 30% of the compounds are identified. Without the true identity of these molecules it is impossible to draw conclusions about the biological mechanisms, pathway relationships and provenance of compounds. The only way at present to address this discrepancy is to use in silico fragmentation software to identify unknown compounds by comparing and ranking theoretical MS/MS fragmentations from target structures to experimental tandem mass spectra (MS/MS). We compared the performance of four publicly available in silico fragmentation algorithms (MetFragCL, CFM-ID, MAGMa+ and MS-FINDER) that participated in the 2016 CASMI challenge. We found that optimizing the use of metadata, weighting factors and the manner of combining different tools eventually defined the ultimate outcomes of each method. We comprehensively analysed how outcomes of different tools could be combined and reached a final success rate of 93% for the training data, and 87% for the challenge data, using a combination of MAGMa+, CFM-ID and compound importance information along with MS/MS matching. Matching MS/MS spectra against the MS/MS libraries without using any in silico tool yielded 60% correct hits, showing that the use of in silico methods is still important

Avian mycoplasmosis update

Avian mycoplasmas occur in a variety of bird species. The most important mycoplasmas for chickens and turkeys are Mycoplasma gallisepticum (MG), M. synoviae (MS), and M. meleagridis. Besides, M. iowe (MI) is an emerging pathogen in turkeys, but of little concern for chickens. Mycoplasmas are bacteria that lack cell wall and belong to the class Mollicutes. Although they have been considered extracellular agents, scientists admit nowadays that some of them are obligatory intracellular microorganisms, whereas all other mycoplasmas are considered facultative intracellular organisms. Their pathogenic mechanism for disease include adherence to host target cells, mediation of apoptosis, innocent bystander damage to host cell due to intimate membrane contact, molecular (antigen) mimicry that may lead to tolerance, and mitotic effect for B and/or T lymphocytes, which could lead to suppressed T-cell function and/or production of cytotoxic T cell, besides mycoplasma by-products, such as hydrogen peroxide and superoxide radicals. Moreover, mycoplasma ability to stimulate macrophages, monocytes, T-helper cells and NK cells, results in the production of substances, such as tumor necrosing factor (TNF-alpha), interleukin (IL-1, 2, 6) and interferon (<FONT FACE=Symbol>a, b, g</FONT>). The major clinical signs seen in avian mycoplasmosis are coughing, sneezing, snicks, respiratory rales, ocular and nasal discharge, decreased feed intake and egg production, increased mortality, poor hatchability, and, primarily in turkeys, swelling of the infraorbital sinus(es). Nevertheless, chronic and unapparent infections are most common and more threatening. Mycoplasmas are transmitted horizontally, from bird to bird, and vertically, from dam to offspring through the eggs. Losses attributed to mycoplasmosis, mainly MG and MS infections, result from decreased egg production and egg quality, poor hatchability (high rate of embryonic mortality and culling of day-old birds), poor feed efficiency, increase in mortality and carcass condemnations, besides medication costs. Mycoplasmas are diagnosed by serologic tests, culture and PCR and are sensitive to antimicrobials whose action sites are other than the bacterial cell wall, such as tetracyclines, macrolides, quinolones and tiamulin. However, mycoplasma control is more efficiently achieved by acquisition of birds free of MG, MS, MM and/or MI, vaccination of layers, and monitoring of breeder flocks, followed by elimination of the infected flocks that are detected