Pectra remains a challenging task. The major cleavage and fragmentation pathways, as well as the mass resolution and accuracy of each ion that is detected, are often instrument-dependent. Every instrument also provides different intensity ranges for acquired spectra. Thus, spectra interpretation software is usually custom-designed for a certain mass spectrometer and/or acquisition method. In fact, there are several MS instruments, and nearly each company that commercializes them has developed its own and unique proprietary data format and software for storing and handling data. The software packages available for lipid MS data analysis, both commercial and freeware, were developed for specific types of applications and data acquisition modes. Specialized software packages such as LipidViewTM (Sciex) [151] have been developed for a multiple precursor ion and neutral loss scanning. LipidSearchTM (Thermo Scientific), on the other hand, was developed jointly by academic staff and MKI (Tokyo, Japan) [152] and holds a set of tools specifically aimed for LC/(Z)-4-Hydroxytamoxifen web MS-based lipidomics data, including high-resolution accurate-mass data generated by OrbitrapTM-based mass Necrosulfonamide site spectrometers. In addition to commercially available software packages, there are several free and open-source software tools and libraries that can be used for helping in MS data analysis nowadays. These software packages use open-source data formats, allowing researchers to overcome the problem of data file type incompatibility and the use of proprietary software. Among the most popular freeware package are LipidXplorer, ALEX, Lipid Blast and MS-DIAL. They are open-source software that allows for the qualitative and quantitative analysis of lipid spectra acquired using different approaches and different mass spectrometers. Both LipidXplorer [153] and ALEX [154] were designed for shotgun lipidomics using high-resolution mass spectrometers. The MS-DIAL was developed to deal with both data dependent and independent MS/MS experiments [155], while LipidBlast was developed for polar lipid analysis through MS/MS experiments and mass spectral library search, using either lowor high-resolution instruments [156]. For further processing, retrieved data are usually normalized and subjected to statistical analysis, with a number of different statistical tests. These include, MANOVA, PERMANOVA, similarity percentages (SIMPER), principal component analysis (PCA), principal coordinates analysis (PCO) and partial least-squares discriminant analysis (PLS/DA), often using different and specialized statistics packages or available freeware. 6. Future Perspectives Current improvements in MS-based lipidomics open an unprecedented window of opportunity to unravel the true richness of polar lipids molecular species in marine macrophytes. It is paramount that high-throughput techniques available to screen the polar lipidome of target organisms are accompanied by reliable bioinformatics pipelines that efficiently manage generated data, so that the constraints commonly faced by other omics (e.g., metabolomics, metagenomics) can be avoided.Mar. Drugs 2016, 14,21 ofThese bioinformatics pipelines will allow a more efficient data mining and effective use of generated data, thus improving our ability to detect new MNP. Innovative applications and products will naturally emerge as we continue to gain in-depth knowledge on polar lipidomics of marine organisms (including macrophytes). Nevertheless, it is important to h.Pectra remains a challenging task. The major cleavage and fragmentation pathways, as well as the mass resolution and accuracy of each ion that is detected, are often instrument-dependent. Every instrument also provides different intensity ranges for acquired spectra. Thus, spectra interpretation software is usually custom-designed for a certain mass spectrometer and/or acquisition method. In fact, there are several MS instruments, and nearly each company that commercializes them has developed its own and unique proprietary data format and software for storing and handling data. The software packages available for lipid MS data analysis, both commercial and freeware, were developed for specific types of applications and data acquisition modes. Specialized software packages such as LipidViewTM (Sciex) [151] have been developed for a multiple precursor ion and neutral loss scanning. LipidSearchTM (Thermo Scientific), on the other hand, was developed jointly by academic staff and MKI (Tokyo, Japan) [152] and holds a set of tools specifically aimed for LC/MS-based lipidomics data, including high-resolution accurate-mass data generated by OrbitrapTM-based mass spectrometers. In addition to commercially available software packages, there are several free and open-source software tools and libraries that can be used for helping in MS data analysis nowadays. These software packages use open-source data formats, allowing researchers to overcome the problem of data file type incompatibility and the use of proprietary software. Among the most popular freeware package are LipidXplorer, ALEX, Lipid Blast and MS-DIAL. They are open-source software that allows for the qualitative and quantitative analysis of lipid spectra acquired using different approaches and different mass spectrometers. Both LipidXplorer [153] and ALEX [154] were designed for shotgun lipidomics using high-resolution mass spectrometers. The MS-DIAL was developed to deal with both data dependent and independent MS/MS experiments [155], while LipidBlast was developed for polar lipid analysis through MS/MS experiments and mass spectral library search, using either lowor high-resolution instruments [156]. For further processing, retrieved data are usually normalized and subjected to statistical analysis, with a number of different statistical tests. These include, MANOVA, PERMANOVA, similarity percentages (SIMPER), principal component analysis (PCA), principal coordinates analysis (PCO) and partial least-squares discriminant analysis (PLS/DA), often using different and specialized statistics packages or available freeware. 6. Future Perspectives Current improvements in MS-based lipidomics open an unprecedented window of opportunity to unravel the true richness of polar lipids molecular species in marine macrophytes. It is paramount that high-throughput techniques available to screen the polar lipidome of target organisms are accompanied by reliable bioinformatics pipelines that efficiently manage generated data, so that the constraints commonly faced by other omics (e.g., metabolomics, metagenomics) can be avoided.Mar. Drugs 2016, 14,21 ofThese bioinformatics pipelines will allow a more efficient data mining and effective use of generated data, thus improving our ability to detect new MNP. Innovative applications and products will naturally emerge as we continue to gain in-depth knowledge on polar lipidomics of marine organisms (including macrophytes). Nevertheless, it is important to h.
