Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics.

A plethora of software suites and multiple classes of spectral libraries have been developed to enhance the depth and robustness of data-independent acquisition (DIA) data processing. However, how the combination of a DIA software tool and a spectral library impacts the outcome of DIA proteomics and phosphoproteomics data analysis has been rarely investigated using benchmark data that mimics biological complexity. In this study, we create DIA benchmark data sets simulating the regulation of thousands of proteins in a complex background, which are collected on both an Orbitrap and a timsTOF instruments. We evaluate four commonly used software suites (DIA-NN, Spectronaut, MaxDIA and Skyline) combined with seven different spectral libraries in global proteome analysis. Moreover, we assess their performances in analyzing phosphopeptide standards and TNF-α-induced phosphoproteome regulation. Our study provides a practical guidance on how to construct a robust data analysis pipeline for different proteomics studies implementing the DIA technique.

[Effects of glucose on photosynthesis and growth of Chloralla sp. HN08 cells].

Objective: To study the potential of using glucose as carbon source to produce microalgae biomass and biochemical components, such as photosynthetic pigments, lipids, carbohydrates and proteins by tropical marine microalgae Chloralla sp. HN08. Methods: We compared the growth characteristics of Chloralla sp. HN08 cells under photoautotrophic and mixotrophic (10 g/L glucose was added into the medium) conditions. The photosynthesis, specific growth rates, cell densities, and the content of cell's major components including lipids, starch, soluble sugar, and soluble protein were determined and compared. Results: Glucose (10 g/L in medium) could promote Chlorella growth and increase the final cell density under light condition. However, cells declined gradually under heterotrophic condition. Under mixotrophic condition, the specific growth rate and the final cell density were 6.8 and 1.3 times as that of cells under photoautotrophic condition, respectively. The content of soluble sugar, starch, and lipids in mixotrophic cells was also significantly higher (P<0.05) than that in photoautotrophic cells. However, the content of soluble protein and photosynthetic pigments of mixotrophic cells was significantly lower (P<0.05) than that of autotrophic cells. Algae culture with glucose addition showed a higher light saturation as well as respiration rate. No significant difference in net photosynthesis rate was found between autotrophic and mixotrophic cultures (P>0.05). Conclusion: Under light condition, glucose as a carbon source can promote lipids and starch accumulation, as well as biomass production.