Nuclear p97/Valosin-containing protein (VCP)-like 2 (NVL2) is a nucleolus-localized chaperone-like protein that belongs to the type II class of ATPases associated with diverse cellular activities (AAA) family. In the nucleolus, NVL2 is involved in the maturation of pre-60S particles in an ATP hydrolysis-dependent manner by associating with transactivating factors involved in ribosome biogenesis or the RNA degradation/processing complex, RNA exosome. To perform a comparative analysis of NVL2-associated protein complexes based on their ATP hydrolysis activity, NVL2 (wild-type or ATP hydrolysis-deficient)-associated protein complexes were analyzed. FLAG-tagged NVL2 (wild-type or ATP hydrolysis-deficient mutant, E365Q/E682Q) inducible Flp-In T-REx 293 cell lines were established, and affinity-purifications of the NVL2-associated protein complexes using FLAG tag were performed. NVL2 (wild-type or ATP hydrolysis-deficient)-associated proteins were identified by IP-MS with data dependent acquisition method.

Myh1 and Myh4 encode the adult fast myosin heavy chains (MyHC-IIx and MyHC-IIb). The simultaneous loss of MyHC-IIx and MyHC-IIb causes severe skeletal muscle hypoplasia in postnatal mice. Proteomic analysis using high-resolution mass spectrometry documented changes in protein abundance in skeletal muscle tissues of Myh1 and Myh4 double knockout (dKO) mice. The dataset provides detailed information for further investigation into skeletal muscle characteristics associated with MyHC-IIx and MyHC-IIb deficiency.

We analyzed the alteration of the host cell proteome upon the SARS-CoV-2 infection in the absence and presence of cysteine protease inhibitor, calpeptin, which is effective to virus protease Mpro and host cysteine proteases including L-cathepsin and calpain. The present data was obtained using human lung adenocarcinoma cell line Calu-3 cells (HTB-55, ATCC^®) and SARS-CoV-2 strain JPN/TY/WK-521 (GISAID_ID: EPI_ISL_408667).

This dataset was utilized to investigate the temporal proteomic changes in an oleic acid-induced acute lung injury rat model. Tissue extracts were analyzed by mass spectrometry using a data-independent acquisition approach. The data described in this paper have been deposited to jPOST with the identifiers JPST003445.

To compare the difference and similarities in proteomic features between our established patient-derived sarcoma cell lines and their original tumor tissues, we conducted 18 LC-MS/MS runs for nine sarcoma patient-derived cell lines (PDCs) and their corresponding tumor tissues. The numbers of identified peptides and proteins were nearly identical between the two proteomic datasets in the sarcoma cell lines. Drug-targeted proteins in cancer-related genes were identified using these datasets.

To explore both differences and similarities in proteomic characteristics between patient-derived sarcoma cell lines and their corresponding tumor tissues, we performed 62 LC-MS/MS analyses on 31 sarcoma patient-derived cell lines (PDCs) and their tumor samples. The number of peptides and proteins identified was highly comparable between the two datasets. These comprehensive proteomic profiles also identified druggable cancer-related proteins, offering potential insights into therapeutic targeting.

To investigate the proteomic similarities and differences between patient-derived sarcoma cell lines (PDCs) and their corresponding tumor tissues, we performed 70 LC-MS/MS analyses on 35 matched sample pairs. The number of identified peptides and proteins were highly comparable between the two groups. These comprehensive proteomic profiles enabled the identification of druggable cancer-related proteins, providing potential insights into therapeutic targeting.

Phosphoproteomic data for signal transduction dynamics induced by modified cell-penetrating peptide (Pas2r12) or Pas2r12–enhanced green fluorescent protein (EGFP) complex in human embryonic kidney-derived (HEK293) cells.

The T790M secondary mutation in epidermal growth factor receptor (EGFR) drives resistance to tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC), posing a significant therapeutic challenge. To investigate the molecular basis linking acquired mutation to TKI resistance, affinity purification coupled with mass spectrometry (AP-MS) was used to explore the EGFR protein-protein interaction (PPI) networks (interactomes) in TKI-sensitive versus TKI-resistant patient-derived NSCLC cells, which harbored different EGFR mutants. High-resolution mass spectrometry–based proteomics analysis offers robust insights into the PPI network associated with the secondary T790M mutation.

We analyzed our newly devised polyamine precipitation method (PA method) for EV recovery by LC-MS/MS using the culture supernatants of the cell lines K562 and NCI-N87. The results were compared to those obtained using the gold standard method of recovery by ultracentrifugation (UC) method. Our results confirmed the recovery of common EV content. The data described in this paper have been deposited to jPOST with the identifiers JPOST003025 and JPOST003429.