links, descriptions, video tutorials, and contact details for software developers. The new tool comprehensively covers the seven major areas in lipidomics data processing, as follows: (1) lipid-oriented databases; (2) MS data repositories; (3) analysis of targeted lipidomics datasets; (4) lipid identification and (5) quantification from untargeted lipidomics datasets; (6) statistical analysis and visualization; and (7) data integration solutions (Fig. 2). To support informed decision making by lipidomics analysts, for each software, a short description is provided, highlighting the main functionalities and the areas of applications, followed by the specific features listed under 'Technical information' and 'Task specific information' tabs (Figs. 3 and 4). Additionally, users can review simplified, tabular representations of the available functions for each tool in a given section by using the 'Tools Overview' tab.In the 'Technical information' section, users can view the type of the license under which the tool is distributed, the availability of desktop and/or web-based interfaces, data input/output formats, and compatibility with different operating systems (for example, Windows, Linux, macOS). There is also information accessible via clickable links, which allow the downloading of the tool together with related documentation, user guides, and training datasets. Additional fields list how to use the tool through the command line or via API interfaces for advanced users wishing to construct their own customized pipelines. 'Task specific information' tabs navigate users to pages describing functionalities of the software for particular tasks covering the seven areas outlined above (Figs. 1 and 2). Some comprehensive tools have multiple functions integrated into one combined package and can be configured for a wide range of workflows. These tools are assigned to each task with associated descriptions accordingly, and the list of tools is shown in Table 1. In the next section, we provide more details about each area and its associated software and tools.

Bovine milk contains a variety of endogenous peptides, partially formed by milk proteases that may exert diverse bioactive functions. Milk storage allows further protease activities altering the milk peptidome, while processing, e.g., heat treatment can trigger diverse chemical reactions, such as Maillard reactions and oxidations, leading to different posttranslational modifications (PTMs). The influence of processing on the native and modified peptidome was studied by analyzing peptides extracted from raw milk (RM), ultra-high temperature (UHT) milk, and powdered infant formula (IF) by nano reversed-phase liquid chromatography coupled online to electrospray ionization (ESI) tandem mass spectrometry. Only unmodified peptides proposed by two independent software tools were considered as identified. Thus, 801 identified peptides mainly originated from αS- and β-caseins, but also from milk fat globular membrane proteins, such as glycosylation-dependent cell adhesion molecule 1. RM and UHT milk showed comparable unmodified peptide profiles, whereas IF differed mainly due to a higher number of β-casein peptides. When 26 non-enzymatic posttranslational modifications (PTMs) were targeted in the milk peptidomes, 175 modified peptides were identified, i.e., mostly lactosylated and a few hexosylated or oxidized peptides. Most modified peptides originated from αS-caseins. The numbers of lactosylated peptides increased with harsher processing.

Preparation of functionalized cellulose films on SiO2 to introduce protein repellent properties evaluated by spectroscopic in situ ellipsometry.

No abstract