JesperOlsenLab
@jesperolsenlab.bsky.social
Mass spectrometry for quantitative proteomics. The Olsen group at the Center for Protein Research, University of Copenhagen.
With a 40% reduction in analysis time and >12,000 proteins covered in 2.7 hours, it's setting new benchmarks for proteome studies.
July 19, 2025 at 9:22 AM
With a 40% reduction in analysis time and >12,000 proteins covered in 2.7 hours, it's setting new benchmarks for proteome studies.
The new Astral Zoom MS overcomes previous MS limitations and is now achieving ultra-fast scans up to 270 Hz. It allows to identity > 100,000 peptides with short LC gradients.
July 19, 2025 at 9:22 AM
The new Astral Zoom MS overcomes previous MS limitations and is now achieving ultra-fast scans up to 270 Hz. It allows to identity > 100,000 peptides with short LC gradients.
The combination of pre accumulation and faster scans significantly improves peptide/protein IDs on short LC gradients and boosts sensitivity for high-throughput workflows 📈
The benefits are even higher with ΦSDM, especially in fast, low-resolution Orbitrap runs.
The benefits are even higher with ΦSDM, especially in fast, low-resolution Orbitrap runs.
July 1, 2025 at 12:29 PM
The combination of pre accumulation and faster scans significantly improves peptide/protein IDs on short LC gradients and boosts sensitivity for high-throughput workflows 📈
The benefits are even higher with ΦSDM, especially in fast, low-resolution Orbitrap runs.
The benefits are even higher with ΦSDM, especially in fast, low-resolution Orbitrap runs.
Florian Harking & Ulises H. Guzman made it happen by preaccumulating ions in the bent flatapole and applying phase-constrained spectrum deconvolution method (ΦSDM).
July 1, 2025 at 12:29 PM
Florian Harking & Ulises H. Guzman made it happen by preaccumulating ions in the bent flatapole and applying phase-constrained spectrum deconvolution method (ΦSDM).
Knocking down CAVIN1 in a 3D model reveals its connection with tumour invasiveness. Hybrid-DIA based phosphoproteomics profiling reveals an intriguing link between mTOR-signalling and its potential association to CAVIN1.
April 25, 2025 at 9:45 AM
Knocking down CAVIN1 in a 3D model reveals its connection with tumour invasiveness. Hybrid-DIA based phosphoproteomics profiling reveals an intriguing link between mTOR-signalling and its potential association to CAVIN1.
The mesenchymal-like subtype was shown to be marked by increased CAVIN1 and PRELP. Higher CAVIN1 correlates with higher relapse risk in two independent cohorts. We confirmed this in a second cohort and were able to link this to Epithelial to Mesenchymal Transition.
April 25, 2025 at 9:45 AM
The mesenchymal-like subtype was shown to be marked by increased CAVIN1 and PRELP. Higher CAVIN1 correlates with higher relapse risk in two independent cohorts. We confirmed this in a second cohort and were able to link this to Epithelial to Mesenchymal Transition.
We stratified 412 CRC tumors into 4 distinct subtypes using quantitative proteomics. Our results show clear links to transcriptomics CMS, immune infiltration, tumor purity, and relapse.
April 25, 2025 at 9:45 AM
We stratified 412 CRC tumors into 4 distinct subtypes using quantitative proteomics. Our results show clear links to transcriptomics CMS, immune infiltration, tumor purity, and relapse.
We also identified aberrant PDGF receptor (PDGFR) activation as a key feature of OCSCs.
When we treated patient-derived ovarian cancer cells with a PDGFR inhibitor, their stemness potential dropped (sphere formation ↓).
When we treated patient-derived ovarian cancer cells with a PDGFR inhibitor, their stemness potential dropped (sphere formation ↓).
April 24, 2025 at 8:57 AM
We also identified aberrant PDGF receptor (PDGFR) activation as a key feature of OCSCs.
When we treated patient-derived ovarian cancer cells with a PDGFR inhibitor, their stemness potential dropped (sphere formation ↓).
When we treated patient-derived ovarian cancer cells with a PDGFR inhibitor, their stemness potential dropped (sphere formation ↓).
Our stemness signature correlates with chemo-refractoriness in clinical proteomics data.
That’s huge: it means this signature might help predict therapy resistance.
That’s huge: it means this signature might help predict therapy resistance.
April 24, 2025 at 8:57 AM
Our stemness signature correlates with chemo-refractoriness in clinical proteomics data.
That’s huge: it means this signature might help predict therapy resistance.
That’s huge: it means this signature might help predict therapy resistance.
Stemness-associated proteins were involved in extracellular matrix remodeling.
This points to a link between the stem-like state and the tumor microenvironment.
This points to a link between the stem-like state and the tumor microenvironment.
April 24, 2025 at 8:57 AM
Stemness-associated proteins were involved in extracellular matrix remodeling.
This points to a link between the stem-like state and the tumor microenvironment.
This points to a link between the stem-like state and the tumor microenvironment.
To validate our stemness signature, we used single-sample GSEA on published proteomics data from embryonic stem cell differentiation.
April 24, 2025 at 8:57 AM
To validate our stemness signature, we used single-sample GSEA on published proteomics data from embryonic stem cell differentiation.
We profiled the proteome and phosphoproteome of 3D spheres enriched for OCSCs from 10 treatment-naive patient-derived lines.
This revealed a shared stemness-related signature across patients, despite high inter-patient heterogeneity.
This revealed a shared stemness-related signature across patients, despite high inter-patient heterogeneity.
April 24, 2025 at 8:57 AM
We profiled the proteome and phosphoproteome of 3D spheres enriched for OCSCs from 10 treatment-naive patient-derived lines.
This revealed a shared stemness-related signature across patients, despite high inter-patient heterogeneity.
This revealed a shared stemness-related signature across patients, despite high inter-patient heterogeneity.
We confirmed this observation and exploited it to compare different modalities of cell division arrest in human foreskin fibroblasts.
March 31, 2025 at 3:12 PM
We confirmed this observation and exploited it to compare different modalities of cell division arrest in human foreskin fibroblasts.
Histone turnover enables distinguishing dividing cells from slow/non-dividing ones, due to the extremely slow core histone turnover in non-dividing cells.
March 31, 2025 at 3:12 PM
Histone turnover enables distinguishing dividing cells from slow/non-dividing ones, due to the extremely slow core histone turnover in non-dividing cells.
Protein turnover provides an orthogonal measurement to protein abundance, revealing functional differences between cell types and states, and improving protein co-regulation analysis to determine members of protein complexes.
March 31, 2025 at 3:12 PM
Protein turnover provides an orthogonal measurement to protein abundance, revealing functional differences between cell types and states, and improving protein co-regulation analysis to determine members of protein complexes.
We then performed a large-scale SC-pSILAC experiment to study the undirected differentiation of human induced pluripotent stem cells through embryoid body induction in >1000 individual single cells.
Our comprehensive dataset shows protein turnover dynamics during cell differentiation over 2 months.
Our comprehensive dataset shows protein turnover dynamics during cell differentiation over 2 months.
March 31, 2025 at 3:12 PM
We then performed a large-scale SC-pSILAC experiment to study the undirected differentiation of human induced pluripotent stem cells through embryoid body induction in >1000 individual single cells.
Our comprehensive dataset shows protein turnover dynamics during cell differentiation over 2 months.
Our comprehensive dataset shows protein turnover dynamics during cell differentiation over 2 months.
We first studied treatments altering global protein turnover including proteasome(bortezomib), protein translation (cycloheximide), and beta-cathenin inhibitions for altered turnover of a specific protein(GSK3 inhibitor).
SC-pSILAC revealed treatment-related changes in single cells.
SC-pSILAC revealed treatment-related changes in single cells.
March 31, 2025 at 3:12 PM
We first studied treatments altering global protein turnover including proteasome(bortezomib), protein translation (cycloheximide), and beta-cathenin inhibitions for altered turnover of a specific protein(GSK3 inhibitor).
SC-pSILAC revealed treatment-related changes in single cells.
SC-pSILAC revealed treatment-related changes in single cells.
Finally fixed cells showed altered morphology vs. non fixed cells. Yet, after freezing the morphological changes in fixed cells are reduced compared to non fixed cells. Fixed frozen single cells have significantly lower CVs than non fixed frozen cells, enhancing data quality and reproducibility.
February 4, 2025 at 8:15 AM
Finally fixed cells showed altered morphology vs. non fixed cells. Yet, after freezing the morphological changes in fixed cells are reduced compared to non fixed cells. Fixed frozen single cells have significantly lower CVs than non fixed frozen cells, enhancing data quality and reproducibility.
We treated 20 cells and single cells with 5-FU and MTX and demonstrated that fixation doesnt affect drug induced changes. While 20 cells provide deeper coverage single cell analysis still identifies key protein targets proving fixation is viable for SCP.
February 4, 2025 at 8:15 AM
We treated 20 cells and single cells with 5-FU and MTX and demonstrated that fixation doesnt affect drug induced changes. While 20 cells provide deeper coverage single cell analysis still identifies key protein targets proving fixation is viable for SCP.
We tested bulk, OneTip and single cell proteomics with 2% formaldehyde and we found: no major effect on protein recovery, limited effect on digestion efficiency, lower CVs, and unaffected multiplexing potential.
February 4, 2025 at 8:15 AM
We tested bulk, OneTip and single cell proteomics with 2% formaldehyde and we found: no major effect on protein recovery, limited effect on digestion efficiency, lower CVs, and unaffected multiplexing potential.
Lastly we applied the workflow to analyse undirected stem cell differentiation enabling the accurate quantification of stem cells and lineage markers.
January 17, 2025 at 7:54 AM
Lastly we applied the workflow to analyse undirected stem cell differentiation enabling the accurate quantification of stem cells and lineage markers.
We further investigated the effect of 5-FU treatments on spheroids with the whisper 80SPD gradient, highlighting differential regulation of some 5-FU targets.
January 17, 2025 at 7:54 AM
We further investigated the effect of 5-FU treatments on spheroids with the whisper 80SPD gradient, highlighting differential regulation of some 5-FU targets.
The improved sensitivity and peptide coverage allows for the detection of abundance PTM sites harboring phosphorylations and glycosylation without prior enrichment, opening new opportunities for SCP analysis.
January 17, 2025 at 7:54 AM
The improved sensitivity and peptide coverage allows for the detection of abundance PTM sites harboring phosphorylations and glycosylation without prior enrichment, opening new opportunities for SCP analysis.
We benchmarked the SCP workflow using Spectronaut and DIA-NN including estimation of the error rate of identifications using a shuffled human mimic protein database.
January 17, 2025 at 7:54 AM
We benchmarked the SCP workflow using Spectronaut and DIA-NN including estimation of the error rate of identifications using a shuffled human mimic protein database.
Throughput is crucial in LFQ-SCP! We tested the recently introduced Whisper Zoom 80 and 120 SPD providing impressive proteome coverage at up to 3x increased throughput.
January 17, 2025 at 7:54 AM
Throughput is crucial in LFQ-SCP! We tested the recently introduced Whisper Zoom 80 and 120 SPD providing impressive proteome coverage at up to 3x increased throughput.