Mass spectrometry-based proteomics of the Aurantiochytrium limacinum ATCC MYA-1381 zoospore-to-vegetative cell transition (MaxQuant processed data)

This dataset provides standard MaxQuant proteomic output files generated from an analysis of the Aurantiochytrium limacinum ATCC MYA-1381 zoospore-to-vegetative cell transition. Mass spectrometry data from three biological time-course replicates were analyzed using two separate protein prediction sets: one from a JGI genome annotation and the other from the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) annotation of the A. limacinum proteome. Each biological replicate in the dataset includes protein abundance measurements across five time points, capturing dynamic proteomic changes associated with cellular remodeling, metabolism, and ectoplasmic network formation. Data is provided as outputted from MaxQuant, including quantitative values for protein group identification and peptide-level measurements.

Methods
Aurantiochytrium limacinum ATCC MYA-1381 was cultured at 25°C in GPY medium containing 3% D-glucose, 1.5% peptone, 0.5% yeast extract, and 1.8% Instant Ocean sea salt. After 24 hours, cells were transferred to GPY agar plates and grown for an additional 24 hours. Zoospores were released by flooding plates with artificial seawater (1.8% Instant Ocean) and collected after 2 hours. Zoospores were inoculated into petri dishes containing A1 medium, and samples were collected at five time points: zoospores at 0 hours (T0) and settled cells at 2, 4, 6, and 8 hours post-settlement (T2, T4, T6, T8). Cells were harvested by centrifugation, and pellets were stored at -80°C for protein extraction.

Protein extraction was performed using a lysis buffer containing KCl, MgCl₂, Tris, NP-40, Tween, SDS, and deionized water. Samples were vortexed, centrifuged, and supernatants were collected. Protein concentration was determined using a bicinchoninic acid (BCA) assay. Proteins were digested with trypsin and labeled using iTRAQ-8plex reagents (113–117). Peptides were fractionated by high-performance liquid chromatography (HPLC) and analyzed using an Ultimate 3000 nano UHPLC system coupled to a Q Exactive mass spectrometer (Thermo Fisher Scientific).

Mass spectrometry data were analyzed separately against two predicted A. limacinum proteomes: one from the JGI genome annotation (MycoCosm) and the other from the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) annotation. Searches were conducted using MaxQuant v1.6.2.14 with trypsin enzyme specificity allowing up to two missed cleavages. Carbamidomethylation of cysteine was set as a fixed modification, while oxidation of methionine and iTRAQ-8plex labeling were included as variable modifications. The precursor mass tolerance was set to 10 ppm, and the MS/MS tolerance was 0.6 Da. MaxQuant output included standard protein identification and quantification metrics, with results organized into per-replicate proteinGroups and peptides, as well as summary tables of total reporter intensities and normalized (corrected) values.