Database for the identification of the human proteome and its use across the scientific community. Users can browse proteins and chromosomes and contribute to the data repository.

ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.

This PXD project contains two projects published on ProteomicsDB (https://www.proteomicsDB.org) as integral part of the publication. The first project entitled 'human body map' (https://www.proteomicsdb.org/#projects/42) involves the analysis of 36 different human tissues and body fluids. The second project entitled 'Cellzome adopted' includes a collection of raw files which comprises identifications of 'missing proteins'.

Accompanying MaxQuant, Percolator and Picked Protein Group FDR files to reproduce resultsin the publication Re-analysis of ProteomicsDB using an accurate, sensitive and scalable false discovery rate estimation approach for protein groups. The code for reproducing Protein Group FDRs is available on GitHub athttps://github.com/kusterlab/picked_group_fdr

Use the unpack.sh bash script included here to unpack all archives, or adapt it to only unpack subsets of the data.

his dataset provides detailed proteomics data focused on the Hemoglobin Subunit Alpha (HBA1) protein.

It contains experimental measurements from various biological samples and conditions.

Data includes quantitative protein expression levels across different tissues and doses.

The dataset is useful for studying hemoglobin function, regulation, and protein interactions.

Researchers can use this data to analyze dose-response relationships for HBA1.

It supports investigations into anemia, oxygen transport, and blood disorders.

Includes both visual and numerical representations of protein responses.

The dataset is curated from reliable proteomics experiments and literature references.

Data is structured to facilitate statistical analysis and machine learning applications.

Ideal for bioinformatics, computational biology, and systems biology studies.

The ProteomeTools project aims to derive molecular and digital tools from the human proteome to facilitate biomedical and life science research. Here, we describe the third iteration of the generation and multimodal LC-MS/MS analysis of >305,000 synthetic non-tryptic peptides representing HLA Class I & II ligands as well as peptides derived from the N-terminal proteases LysN and ApsN. This resource will be extended to 1.4 million peptides and all data will be made available to the public in ProteomicsDB.

List of off-target effects of OTSSP167 occurring at concentrations lower than 50nM, derived from the publicly available phosphoproteomics database at http://proteomicsdb.org.

Mutated KRAS is among the most frequent activating genetic alterations in cancer. Drug discovery efforts have led to inhibitors that block mutant KRAS activity. To better understand the molecular basis of their cytostatic rather than cytotoxic effects, we performed comprehensive dose-dependent proteome-wide target deconvolution, pathway engagement and protein expression characterization in response to KRAS, MEK, ERK, SHP2, and SOS1 inhibitors in pancreatic (KRAS G12C, G12D) and lung cancer (KRAS G12C) cell lines. Analysis of 688,716 dose-response curves available in ProteomicsDB revealed common and cell line-specific signaling networks dominated by KRAS activity. Time-dose experiments separated early ERK-driven from late CDK-mediated signaling leading to exit from the cell cycle. The transition occurred without substantial proteome re-modelling but extensive changes in phosphorylation and ubiquitinylation. Our resource highlights the complexity of KRAS signaling in cancer and places a large number of new proteins and their modifications into this functional context for further exploration.

Here, we provide all curve data processed with internal pipelines or CurveCurator v0.5.0. (https://github.com/kusterlab/curve_curator). All phospho proteome, whole proteome, ubiquitinome, and cysteine profiling data are in separate zip folders. Within these folders, each subexperiment can be interactively reviewed. Next to each data set is the toml parameter file used to generate the curves.txt and dashboard.html files. The data structure and additional information separated by experiment are provided in the ReadMe.xlsx.

Additionally, we provide Supplementary Table S3-S6 as well as the Source Table for the 2D UMAP and the pairwise fold-change comparisons.

The ProteomeTools project aims to derive molecular and digital tools from the human proteome to facilitate biomedical and life science research. Here, we describe the generation and multimodal LC-MS/MS analysis of >350,000 synthetic tryptic peptides representing nearly all canonical human gene products. This resource will be extended to 1.4 million peptides within two years and all data will be made available to the public in ProteomicsDB.

Measuring dose-dependent effects of drugs on post-translational modifications on a proteome-wide scale reveals how these drugs work in cells. Here, we present a quantitative chemical proteomic approach termed decryptM, able to assess target and pathway engagement as well as the mode of action (MoA) of diverse cancer drugs in cells by measuring their dose- (and time-) resolved modulation of PTMs on a proteomic scale. Data collected for 31 drugs, representing six drug classes in 13 human cell lines, demonstrate that the approach is widely applicable. The body of data represents ~1.8 million quantitative cellular drug assays (dose-response curves) including 47502 regulated p-peptides (of 124660 detected on 11982 proteins), 7316 Ubi-peptides (of 9173 detected on 3006 proteins), and 546 Ac-peptides (of 2478 detected on 1377 proteins). Most PTMs were not regulated by most drugs, which is highly valuable information for understanding which pathways are addressed (or not) by each drug in cells. The decryptM data have been incorporated into ProteomicsDB and can be explored interactively. The raw files, searches, curves files, and result PDFs can be downloaded here. For details, have a look at the Experiment_summary.xlsx.

Paper: doi/10.1126/science.ade3925

"The ProteomeTools project aims to derive molecular and digital tools from the human proteome to facilitate biomedical and life science research. Here, we describe the second iteration of the generation and multimodal LC-MS/MS analysis of >220,000 synthetic tryptic peptides representing nearly all canonical human gene products. This resource will be extended to 1.4 million peptides and all data will be made available to the public in ProteomicsDB."