Data as reported in Thomas et al., 2025. Volcano plots depict the relative enrichment of each protein versus non-crosslinked control (x-axis) and the statistical significance of each protein following a Student’s t-test (y-axis, -log10 transformed). The left panel depicts the results of a pulldown using trifunctionalized phosphatidic acid; the right panel depicts the results of the pulldown using trifunctionalized phosphatidylethanolamine. Black proteins are unenriched or depleted in the presence of probe, Purple enriched candidates are defined as proteins with a false discovery rate less than 0.2 and a fold change of at least 1.5-fold, and Orange enriched hits are defined as proteins with a false discovery rate less than 0.05 and a fold change of at least 2-fold in the +UV over the -UV.
Trifunctional Phosphatidic Acid
Structure
Chemical structures drawn by Berit Blume.
Protein Interactome
Journal
Chemical Communications
Abstract
Phosphatidylethanolamine (PE) is a ubiquitous lipid species in higher eukaryotes which resides preferentially in mitochondria. Here, we synthesized a multifunctionalized PE derivative (1) de-signed to identify PE-binding proteins in intact cells through photo-crosslinking and subsequent isolation and proteomic analysis of the PE-protein conjugates. Due to its aromatic caging group, 1 is initially concentrating in perinuclear membranes. After uncaging, rapid translocation to mitochondria was observed. Hence, the tool is useful for tracking PE location and for determining the PE interactome. A trifunctional phosphatidic acid (PA) derivative in compari-son was rapidly metabolized and is hence more limited in its use.
Lipid probes utilized
Cell line analyzed
Uncaging & Crosslinking timeline
| Lipid Probe | Uptake time | Uncaging time | Interaction time | Crosslinking time |
|---|---|---|---|---|
| PA | 60 min | 5 min | 15 min | 5 min |
| PE | 60 min | 5 min | 15 min | 5 min |
Mass spectrometry quantification method
16-channel Tandem Mass Tagging (TMT16)
Additional sample preparation ?
Data visualization
Data as reported in Thomas et al., 2025. Ranked-order plots depict the relative enrichment of each protein versus non-crosslinked control (y-axis) from lowest to highest. The left panel depicts the results of a pulldown using trifunctionalized phosphatidic acid; the right panel depicts the results of the pulldown using trifunctionalized phosphatidylethanolamine. Black proteins are unenriched or depleted in the presence of probe, Purple enriched candidates are defined as proteins with a false discovery rate less than 0.2 and a fold change of at least 1.5-fold, and Orange enriched hits are defined as proteins with a false discovery rate less than 0.05 and a fold change of at least 2-fold in the +UV over the -UV.
[1] "Data not yet provided."Gene Ontology Analysis
In beta: GO analysis still under development
Data exploration and download
Check the boxes below to filter the dataset by which lipid probe was used in the pulldown and by significance thresholds.