project_tag	record_status	additional_information	created_by_id	date_created	project_status	budget	owner_group_id	project_id	date_modified	name	description	uri	PI_contact_id	comment	modified_by_id	publication_id	
PeptideAtlasPublic	N	\N	358	2004-11-11 13:52:02	\N	N/A	39	475	2014-08-15 14:12:36	PeptideAtlas Public	Permissions-controlling umbrella project for all PeptideAtlas builds that should be publicly available.	\N	2	\N	668	54	
PXD003530	N	\N	668	2025-11-18 14:24:06	N	N/A	1	2860	2025-11-18 14:24:06	Sites of aspirin-mediated lysine acetylation in HeLa cells	Aspirin, or acetylsalicylic acid is widely used to control pain, inflammation and fever. Important to this function is its ability to irreversibly acetylate cyclooxygenases at active site serines. Aspirin has the potential to acetylate other amino-acid side-chains, leading to speculation that aspirin-mediated lysine acetylation could explain some of its drug actions or side-effects. Using a labeled form of aspirin, aspirin-d3, we identified over 12000 sites of lysine acetylation from cultured human cells. Although aspirin amplifies acetylation signals at thousands of sites, cells tolerate aspirin mediated acetylation very well unless endogenous deacetylases are inhibited. Apart from a limited number of cellular proteins that are substantially acetylated under endogenous conditions, aspirin mediated acetylation leads to a large increase in the acetylation of many proteins even although they remain at very low stoichiometry. This reinforces the idea that a major function of cellular deacetylases is the suppression of non-specific or non-enzymatic protein acetylation.	\N	668	\N	668	1456	
PXD005252	N	\N	668	2025-11-18 14:25:27	N	N/A	1	2864	2026-01-13 09:45:25	Time-resolved analysis reveals rapid dynamics and broad scope of the CBP/p300 acetylome	The acetyltransferases CBP and p300 are multifunctional transcriptional co-activators; however, their acetylation targets, site-specific acetylation kinetics, and function in proteome regulation are incompletely understood. We combined quantitative proteomics with novel CBP/p300-specific catalytic inhibitors, bromodomain inhibitor, and gene knockout to show that CBP/p300 acetylates thousands of sites, including signature histone sites, as well as a multitude of sites on signaling effectors and enhancer-associated transcriptional regulators. Kinetic analysis identified a subset of CBP/p300-regulated sites with very rapid (&lt;g30min) acetylation turnover, revealing a dynamic balance between acetylation and deacetylation. Quantification of acetylation, mRNA, and protein abundance after CBP/p300 inhibition reveals a kinetically competent network of gene expression that strictly depends on CBP/p300-catalyzed rapid acetylation. Collectively, our in-depth acetylome analyses reveal systems attributes of CBP/p300 targets, and the resource dataset provides a framework for investigating CBP/p300 functions, as well as for understanding the impact of small molecule inhibitors targeting its catalytic and bromodomain activities.	\N	668	\N	668	1459	
PXD005903	N	\N	668	2025-11-18 14:25:55	N	N/A	1	2866	2025-11-18 14:25:55	Integrated lysine acetylation stoichiometry and proteomics analysis in human cells	Lysine acetylation is a widespread posttranslational modification that targets a large number of biological pathways. Recent studies reveal that lysine acetylation sites exhibit mainly low stoichiometry. Here we explored three sample preparation methods, the use of detergents for the chemical acetylation reaction in combination with stable and efficient alkylating reagent, to analyze the stoichiometry of acetylation in three human cell lines. We identified and determined the acetylation occupancy in about 1500 protein in each cell line. Lysine acetylation is highly dynamic, we determined variations in the acetylation stoichiometry when nearby residues are phosphorylated. The stoichiometric analysis in combination with quantitative proteomics allowed us to better understand the role of this PTM in different cells. We found that high abundance of the deacetylase SIRT1 correlates with less acetylation occupancy and abundance of ribosomes, proteins involved in ribosome biogenesis, rRNA processing, among others. We confirmed through the inhibition of SIRT1 with EX-527, followed by quantitative proteomics and acetylation stoichiometry analyzes, the negative role of this deacetylase on transcription and translation pathways. In addition, we found that SIRT1 positively regulates several metabolic pathways.	\N	668	\N	668	1460	
PXD009839	N	\N	668	2025-11-18 14:25:41	N	N/A	1	2865	2025-11-18 14:25:41	Orchestrating protein acetylation: a toggle for cellular defense versus virus replication	Emerging evidence points to protein acetylation as a nexus at the interface of virus-host interactions. However, global protein acetylation is understudied during infection, and the temporal control and function of acetylation in the context of infection remains poorly understood. Here, we present the first temporal-spatial characterization of acetylation during infection with human cytomegalovirus (HCMV). By using acetyl-peptide immunoaffinity purification, we identified dynamic changes in acetylation events on both cellular and viral proteins over the course of HCMV infection. Our subsequent analyses demonstrated that these acetylations functionally contribute to the progression of infection.	\N	668	\N	668	\N	
PXD009994	N	\N	668	2025-11-18 14:24:27	N	N/A	1	2861	2025-11-18 14:24:27	Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation	Lysine acetylation is a reversible posttranslational modification that occurs at thousands of sites on human proteins. However, the stoichiometry of acetylation remains poorly characterized, and is important for understanding acetylation-dependent mechanisms of protein regulation. Here we provide accurate, validated measurements of acetylation stoichiometry at 6,829 sites on 2,535 proteins in human cervical cancer (HeLa) cells. Most acetylation occurs at very low stoichiometry (median 0.02%), whereas high stoichiometry acetylation occurs on nuclear proteins involved in gene transcription and on acetyltransferases. Analysis of acetylation copy number shows that histones harbor the majority of acetylated lysine residues in human cells. Class I deacetylases target a greater proportion of high stoichiometry acetylation compared to SIRT1 and HDAC6. The acetyltransferases CBP and p300 catalyze a majority (65%) of high stoichiometry acetylation, yet also target sites with low stoichiometry. This resource dataset provides valuable information for understanding the impact of individual acetylation sites on protein function.	\N	668	\N	668	1457	
PXD014453	N	\N	668	2025-11-18 14:24:39	N	N/A	1	2862	2025-11-18 14:24:39	Revealing dynamic protein acetylation across subcellular compartments	Protein acetylation is a widespread post-translational modification implicated in many cellular processes. Recent advances in mass spectrometry have enabled the cataloging of thousands of sites throughout the cell, however identifying regulatory acetylation marks has proven to be a daunting task. Knowledge of the kinetics and stoichiometry of site-specific acetylation are important factors to uncover function. Here, an improved method of quantifying acetylation stoichiometry was developed and validated, providing a detailed landscape of dynamic acetylation stoichiometry within cellular compartments. The dynamic nature of site-specific acetylation in response to serum stimulation was revealed. In two distinct human cell lines, growth factor stimulation led to site-specific, temporal acetylation changes, revealing diverse kinetic profiles that clustered into several groups. Overlap of dynamic acetylation sites among the two cell types suggested similar regulatory control points across major cellular pathways that include splicing, translation, and protein homeostasis. Rapid increases in acetylation on protein translational machinery suggests a positive regulatory role under pro-growth conditions. Lastly, higher median stoichiometry was observed in cellular compartments where active acetyltransferases are well-described.	\N	668	\N	668	\N	
PXD023084	N	\N	668	2024-12-03 16:06:05	N	N/A	1	2643	2024-12-03 16:06:05	High intensity interval training remodels the proteome and acetylome in human skeletal muscle	Exercise is an effective strategy in the prevention and treatment of metabolic diseases. Alterations in the skeletal muscle proteome, including post-translational modifications, regulate its metabolic adaptations to exercise. Here, we examined the effect of high-intensity interval training (HIIT) on the proteome and acetylome of human skeletal muscle, revealing the response of 3168 proteins and 1263 lysine acetyl-sites on 464 acetylated proteins. We identified novel protein adaptations to exercise training involved in metabolism and excitation-contraction coupling. Furthermore, HIIT increased the acetylation of mitochondrial proteins, particularly those of complex V, likely via non-enzymatic mechanisms. We also highlight the regulation of novel exercise-responsive histone acetyl-sites. These data demonstrate the plasticity of the skeletal muscle proteome and acetylome, providing insight into the regulation of contractile, metabolic and transcriptional processes within skeletal muscle. Herein, we provide a substantial hypothesis-generating resource to stimulate further mechanistic research investigating how exercise improves metabolic health.	\N	668	\N	668	1252	
PXD023218	N	\N	668	2024-12-03 15:42:22	N	N/A	1	2574	2024-12-03 15:42:22	Linking post-translational modifications and protein turnover	Proteome-wide measurements of protein turnover have largely ignored the impact of post-translational modifications (PTMs). To address this gap, we employ stable isotope labelling and mass spectrometry to measure the turnover of &gt;120,000 peptidoforms including &gt;33,000 phosphorylated, acetylated and ubiquitinated peptides for &gt;9,000 native proteins. This site-resolved protein turnover (SPOT) profiling discloses global and site-specific differences in turnover associated with the presence or absence of PTMs. While causal relationships may not always be immediately apparent, we hypothesize that PTMs with diverging turnover may distinguish states of differential protein stability, structure, localization, enzymatic activity, or protein-protein interactions. We exemplify how the turnover data may facilitate insights into unknown functions of PTMs and provide a web-tool for the scientific community that allows interrogation and visualisation of all turnover data. Since the methodology is applicable to many cell types and modifications, it has substantial potential to prioritize PTMs for functional investigation in the future.	\N	668	\N	668	\N	
PXD041171	N	\N	668	2025-11-18 14:25:11	N	N/A	1	2863	2025-11-18 14:25:11	Sirtuin 2 Promotes HCMV Replication by Regulating Cell Cycle Progression	The host cell cycle is a major target for manipulation by viral pathogens, which often replicate in certain cell cycle stages. The prevalent pathogen human cytomegalovirus (HCMV), for instance, only replicates during G1 and therefore employs diverse mechanisms for regulating cell cycle progression. Here, we demonstrate that the human enzyme sirtuin 2 (SIRT2) is required for HCMV-mediated cell cycle dysregulation. By combining virology assays with mass pectrometry-based proteome, acetylome, and interactome analyses, we have defined a pro-virus function for SIRT2 in regulating the G1 to S phase transition.	\N	668	\N	668	1458	
