Proteomics analysis dataset for Pseudomonas aeruginosa PAO1 37°C vs. 43°C

The data in this item includes raw proteomics data from post-43°C exposure and during the recovery period to assess protein-level effect.Sample preparation: Overall, 18 samples including 3 replicates of Pseudomonas aeruginosa after exposure to 37 °C (control) or 43 °C (heat shock), at 3 time points (T=0hr, T=18hr, and T=54hr). Samples from the T=0 groups are simply labeled “37” or “43”.The samples were subjected in-solution tryptic digestion using suspension trapping (S-trap method by Protifi).Liquid chromatography mass spectrometry: The resulting peptides were analyzed using nanoflow liquid chromatography (nanoAcquity) coupled to high resolution, high mass accuracy mass spectrometry (Q-Exactive HF). Each sample was analyzed on the instrument separately in a random order in discovery mode.Data processing: Raw data was processed with MaxQuant v1.6.6.0. The data was searched with the Andromeda search engine against the Pseudomonas aeruginosa PAO1 database as downloaded from Uniprot, appended with common lab protein contaminants. Search parameters included the following modifications: Fixed modification- cysteine carbamidomethylation. Variable modifications- methionine oxidation. The quantitative comparisons were calculated using Perseus v1.6.0.7. Decoy hits were filtered out and only proteins that were identified in at least two replicates of at least one experimental group were kept.

本数据集包含43°C暴露后及恢复期间的原生蛋白质组学数据，旨在评估蛋白质水平效应。样本制备方面，总计18个样本，其中包括铜绿假单胞菌在37°C（对照组）或43°C（热冲击）暴露下的3个重复样本，分别在3个时间点（T=0小时、T=18小时和T=54小时）采集。T=0时间点的样本简单标记为“37”或“43”。这些样本经Protifi公司所采用的悬浮捕获法（S-trap方法）进行溶液中赖氨酸酶消化。采用液相色谱-质谱联用技术对所得肽段进行分析，具体为纳米流液相色谱（nanoAcquity）与高分辨率、高质量精度质谱（Q-Exactive HF）的联用。每个样本均在发现模式下，以随机顺序单独在仪器上进行分析。数据处理方面，原始数据经MaxQuant v1.6.6.0软件处理，利用Andromeda搜索引擎对从Uniprot下载的铜绿假单胞菌PAO1数据库进行搜索，并附加了常见的实验室蛋白质污染物。搜索参数包括以下修饰：固定修饰-半胱氨酸羧甲基化。可变修饰-蛋氨酸氧化。定量比较使用Perseus v1.6.0.7软件计算。去除了假阳性命中结果，仅保留至少在一个实验组中至少两个重复样本中识别出的蛋白质。