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Motivation The data independent acquisition (DIA) mass spectrometry (MS) method is increasingly popular in the field of proteomics. But the loss of the correspondence between peptide ions and their spectra in DIA makes the identification challenging. One effective approach to reduce false positive identification is to calculate the deviation between the peptide's estimated retention time (RT) and measured RT. During this process, scaling the spectral library RT into the estimated RT, known as the RT calibration, is a prerequisite for calculating the deviation. Currently, within the DIA algorithm ecosystem, there is a lack of engine-independent and readily usable RT calibration toolkits. Results In this work, we introduce Calib-RT, a RT calibration method tailored to the characteristics of RT data. This method can achieve the nonlinear calibration across various data scales and tolerate a certain level of noise interference. Calib-RT is expected to enrich the open source DIA algorithm toolchain and assist in the development of DIA identification algorithms. Availability and implementation Calib-RT is released as an open source software under the MIT license and can be installed from PyPi as a python module. The source code is available on GitHub at https://github.com/chenghui03/Calib_RT. [ABSTRACT FROM AUTHOR]

Lignin is an important component of plant fiber raw materials, and is a three-dimensional network structure aromatic polymer with abundant resources and a complex structure in nature. Lignin is generally used as industrial waste, and its potential value has not been fully utilized. Modern agriculture extensively uses chemical fertilizers, leading to the gradual degradation of soil fertility and structure, which seriously affects crop growth, nutrient transport, and root respiration function. Based on soil bulk density, porosity, aggregates, and their stability indicators, this study analyzed the effects of aminated industrial lignin and its loading with arbuscular mycorrhizal fungi on soil structure improvement and plant growth. It was hoped that resource-rich lignin could play a beneficial role in improving soil structure and promoting crop growth. The phenolic hydroxyl group of lignin was epoxidized and further aminated to load with arbuscular mycorrhizal fungi. The results indicated that amine-modified lignin could effectively load with arbuscular mycorrhizal fungi. The application of arbuscular mycorrhizal fungi-supported aminated lignin to soil aggregate structure improvement greatly reduced the bulk density of soil, and increased the porosity of soil and the content of large granular soil. Compared with unmodified soil, soil bulk density decreased by 73.08%, the porosity of soil increased by 70.43%, and the content of large granular soil increased by 56.38%. Using the improved soil for corn cultivation efficiently increased the biomass of corn. The plant height was increased by 72.16%, the root–shoot ratio was increased by 156.25%, and other indexes were also improved to varying degrees. The experimental method provides an important basis for the effective utilization of lignin materials in agriculture in the future. [ABSTRACT FROM AUTHOR]