The response to stress is crucial for the adaptation of cells and microorganisms to their environments. Research in this field has continued for more than 30 years, especially in terms of the heat shock response, focusing mainly on the bacterium Escherichia coli^1,2. In the early stages of this research, researchers identified individual factors and analyzed the regulatory mechanisms, with a particular focus on heat shock factors. However, in the last decade, this research has come to be seen as a problem of cellular system responses, which have been investigated using “-omics” techniques, such as proteomics and transcriptomics^3,4. A recent study focused on the process of heat shock recovery in mouse cells⁵. With a liquid chromatography–tandem mass spectrometry analysis using timsTOF Pro, the present study provides quantitative time-series data for 3,193 proteins of E. coli, which had been cultured at 30 °C, subjected to an extremely severe heat shock at 50 °C for 90 min, and then returned to culture at 30 °C (11 sampling points). As a control, we added proteome data from the period of the E. coli growth phase, when it was cultured at a constant temperature of 30 °C (seven sampling points).

Effect of age on the vascular proteome in middle cerebral arteries and small mesenteric arteries in mice.

Trapped ion mobility spectrometry (TIMS) has been considered as a promising tool in structural biology, proteomics and many other analytical applications. This dataset consists of cell lysates digested with each of seven proteases (trypsin, LysargiNase, Lys-C, Lys-N, Glu-C, Asp-N, and chymotrypsin), fractionated using SCX-StageTip, and analyzed by nanoLC/TIMS/Q/TOF. The data accompanying this paper have been deposited to jPOST with the identifiers JPST000959, JPST001017 and JPST001176.

To analyze deep protein profiling of cells and tissues with ease, it is required to expand the proteome coverage by single-shot proteome analysis. We established optimal FAIMS parameters for DIA-MS and successfully observed up to 10,044 proteins from HEK293 cell digests by single-shot proteome analysis¹.