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Article ; Online: Phosphoproteomic investigation of targets of protein phosphatases in EGFR signaling.

Eguchi, Akihiro / Olsen, Jesper V

2024 Volume 14, Issue 1, Page(s) 7908

Abstract: Receptor tyrosine kinases (RTKs) initiate cellular signaling pathways, which are regulated through a delicate balance of phosphorylation and dephosphorylation events. While many studies of RTKs have focused on downstream-activated kinases catalyzing the ... ...

Abstract	Receptor tyrosine kinases (RTKs) initiate cellular signaling pathways, which are regulated through a delicate balance of phosphorylation and dephosphorylation events. While many studies of RTKs have focused on downstream-activated kinases catalyzing the site-specific phosphorylation, few studies have focused on the phosphatases carrying out the dephosphorylation. In this study, we analyzed six protein phosphatase networks using chemical inhibitors in context of epidermal growth factor receptor (EGFR) signaling by mass spectrometry-based phosphoproteomics. Specifically, we focused on protein phosphatase 2C (PP2C), involved in attenuating p38-dependent signaling pathways in various cellular responses, and confirmed its effect in regulating p38 activity in EGFR signaling. Furthermore, utilizing a p38 inhibitor, we classified phosphosites whose phosphorylation status depends on PP2C inhibition into p38-dependent and p38-independent sites. This study provides a large-scale dataset of phosphatase-regulation of EGF-responsive phosphorylation sites, which serves as a useful resource to deepen our understanding of EGFR signaling.
MeSH term(s)	ErbB Receptors/metabolism ; Signal Transduction ; Phosphorylation ; Phosphoprotein Phosphatases/metabolism
Chemical Substances	ErbB Receptors (EC 2.7.10.1) ; Phosphoprotein Phosphatases (EC 3.1.3.16)
Language	English
Publishing date	2024-04-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-58619-1
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Article ; Online: Impact of SHP2 tyrosine phosphorylation on the development of acquired resistance to allosteric SHP2 inhibitors.

Franciosa, Giulia / Olsen, Jesper V

Oncotarget

2023 Volume 14, Page(s) 281–283

MeSH term(s)	Humans ; Phosphorylation ; Cell Line, Tumor ; Protein Kinase Inhibitors/pharmacology ; Tyrosine ; Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics ; Protein Tyrosine Phosphatase, Non-Receptor Type 11/metabolism ; Enzyme Inhibitors/pharmacology
Chemical Substances	Protein Kinase Inhibitors ; Tyrosine (42HK56048U) ; Protein Tyrosine Phosphatase, Non-Receptor Type 11 (EC 3.1.3.48) ; Enzyme Inhibitors
Language	English
Publishing date	2023-03-31
Publishing country	United States
Document type	Editorial
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.28392
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Article ; Online: Digging deeper into ancient skeletal proteomes through consecutive digestion with multiple proteases.

Fagernäs, Zandra / Troché, Gaudry / Olsen, Jesper V / Welker, Frido

Journal of proteomics

2024 Volume 298, Page(s) 105143

Abstract: An increasing number of studies utilise the recovery of ancient skeletal proteomes for phylogenetic and evolutionary analysis. Although these studies manage to extract and analyse ancient peptides, the recovered proteomes are generally small in size and ... ...

Abstract	An increasing number of studies utilise the recovery of ancient skeletal proteomes for phylogenetic and evolutionary analysis. Although these studies manage to extract and analyse ancient peptides, the recovered proteomes are generally small in size and with low protein sequence coverage. We expand on previous observations which have shown that the parallel digestion and analysis of Pleistocene skeletal proteomes increases overall proteome size and protein sequence coverage. Furthermore, we demonstrate that the consecutive digestion of a skeletal proteome using two proteases, particularly the combination of Glu-C or chymotrypsin followed by trypsin digestion, enables the recovery of alternative proteome components not reachable through trypsin digestion alone. The proteomes preserved in Pleistocene skeletal specimens are larger than previously anticipated, but unlocking this protein sequence information requires adaptation of extraction and protein digestion protocols. The sequential utilisation of several proteases is, in this regard, a promising avenue for the study of highly degraded but unique hominin proteomes for phylogenetic purposes. SIGNIFICANCE: Palaeoproteomic analysis of archaeological materials, such as hominin skeletal elements, show great promise in studying past organisms and evolutionary relationships. However, as most proteomic methods are inherently destructive, it is essential to aim to recover as much information as possible from every sample. Currently, digestion with trypsin is the standard approach in most palaeoproteomic studies. We find that parallel or consecutive digestion with multiple proteases can improve proteome size and coverage for both Holocene and Pleistocene bone specimens. This allows for recovery of more proteomic data from a sample and maximises the chance of recovering phylogenetically relevant information.
MeSH term(s)	Animals ; Trypsin/chemistry ; Proteome/metabolism ; Peptide Hydrolases/metabolism ; Phylogeny ; Proteomics/methods ; Hominidae/metabolism ; Digestion
Chemical Substances	Trypsin (EC 3.4.21.4) ; Proteome ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2024-02-27
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2024.105143
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Article ; Online: ETD-Based Proteomic Profiling Improves Arginine Methylation Identification and Reveals Novel PRMT5 Substrates.

Lu, Lingzi / Ye, Zilu / Zhang, Rou / Olsen, Jesper V / Yuan, Yanqiu / Mao, Yang

Journal of proteome research

2024 Volume 23, Issue 3, Page(s) 1014–1027

Abstract: Protein arginine methylations are important post-translational modifications (PTMs) in eukaryotes, regulating many biological processes. However, traditional collision-based mass spectrometry methods inevitably cause neutral losses of methylarginines, ... ...

Abstract	Protein arginine methylations are important post-translational modifications (PTMs) in eukaryotes, regulating many biological processes. However, traditional collision-based mass spectrometry methods inevitably cause neutral losses of methylarginines, preventing the deep mining of biologically important sites. Herein we developed an optimized mass spectrometry workflow based on electron-transfer dissociation (ETD) with supplemental activation for proteomic profiling of arginine methylation in human cells. Using symmetric dimethylarginine (sDMA) as an example, we show that the ETD-based optimized workflow significantly improved the identification and site localization of sDMA. Quantitative proteomics identified 138 novel sDMA sites as potential PRMT5 substrates in HeLa cells. Further biochemical studies on SERBP1, a newly identified PRMT5 substrate, confirmed the coexistence of sDMA and asymmetric dimethylarginine in the central RGG/RG motif, and loss of either methylation caused increased the recruitment of SERBP1 to stress granules under oxidative stress. Overall, our optimized workflow not only enabled the identification and localization of extensive, nonoverlapping sDMA sites in human cells but also revealed novel PRMT5 substrates whose sDMA may play potentially important biological functions.
MeSH term(s)	Humans ; HeLa Cells ; Proteomics ; Arginine/metabolism ; Protein Processing, Post-Translational ; Methylation ; Protein-Arginine N-Methyltransferases/genetics ; Protein-Arginine N-Methyltransferases/metabolism
Chemical Substances	Arginine (94ZLA3W45F) ; PRMT5 protein, human (EC 2.1.1.319) ; Protein-Arginine N-Methyltransferases (EC 2.1.1.319)
Language	English
Publishing date	2024-01-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00724
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Article ; Online: Systematic optimization of automated phosphopeptide enrichment for high-sensitivity phosphoproteomics.

Bortel, Patricia / Piga, Ilaria / Koenig, Claire / Gerner, Christopher / Martinez-Val, Ana / Olsen, Jesper V

Molecular & cellular proteomics : MCP

2024 , Page(s) 100754

Abstract: Improving coverage, robustness and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography tandem mass spectrometry (LC-MS/MS) from minimal peptide inputs. Here, we systematically optimized key experimental ... ...

Abstract	Improving coverage, robustness and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography tandem mass spectrometry (LC-MS/MS) from minimal peptide inputs. Here, we systematically optimized key experimental parameters for automated on-beads phosphoproteomics sample preparation with focus on low input samples. Assessing the number of identified phosphopeptides, enrichment efficiency, site localization scores and relative enrichment of multiply-phosphorylated peptides pinpointed critical variables influencing the resulting phosphoproteome. Optimizing glycolic acid concentration in the loading buffer, percentage of ammonium hydroxide in the elution buffer, peptide-to-beads ratio, binding time, sample and loading buffer volumes, allowed us to confidently identify >16,000 phosphopeptides in half-an-hour LC-MS/MS on an Orbitrap Exploris 480 using 30 μg of peptides as starting material. Furthermore, we evaluated how sequential enrichment can boost phosphoproteome coverage and showed that pooling fractions into a single LC-MS/MS analysis increased the depth. We also present an alternative phosphopeptide enrichment strategy based on stepwise addition of beads thereby boosting phosphoproteome coverage by 20%. Finally, we applied our optimized strategy to evaluate phosphoproteome depth with the Orbitrap Astral MS using a cell dilution series and were able to identify >32,000 phosphopeptides from 0.5 million HeLa cells in half-an-hour LC-MS/MS using narrow-window data-independent acquisition (nDIA).
Language	English
Publishing date	2024-03-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2024.100754
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Zs.A 5599: Show issues

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Article ; Online: Recent advances in kinase signaling network profiling by mass spectrometry.

Franciosa, Giulia / Locard-Paulet, Marie / Jensen, Lars J / Olsen, Jesper V

Current opinion in chemical biology

2023 Volume 73, Page(s) 102260

Abstract: Mass spectrometry-based phosphoproteomics is currently the leading methodology for the study of global kinase signaling. The scientific community is continuously releasing technological improvements for sensitive and fast identification of ... ...

Abstract	Mass spectrometry-based phosphoproteomics is currently the leading methodology for the study of global kinase signaling. The scientific community is continuously releasing technological improvements for sensitive and fast identification of phosphopeptides, and their accurate quantification. To interpret large-scale phosphoproteomics data, numerous bioinformatic resources are available that help understanding kinase network functional role in biological systems upon perturbation. Some of these resources are databases of phosphorylation sites, protein kinases and phosphatases; others are bioinformatic algorithms to infer kinase activity, predict phosphosite functional relevance and visualize kinase signaling networks. In this review, we present the latest experimental and bioinformatic tools to profile protein kinase signaling networks and provide examples of their application in biomedicine.
MeSH term(s)	Proteomics/methods ; Phosphorylation ; Protein Kinases/metabolism ; Signal Transduction ; Mass Spectrometry/methods ; Phosphoproteins/chemistry
Chemical Substances	Protein Kinases (EC 2.7.-) ; Phosphoproteins
Language	English
Publishing date	2023-01-18
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1439176-4
ISSN	1879-0402 ; 1367-5931
ISSN (online)	1879-0402
ISSN	1367-5931
DOI	10.1016/j.cbpa.2022.102260
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Zs.A 4986: Show issues

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Article ; Online: Obtaining Complete Human Proteomes.

Martinez-Val, Ana / Guzmán, Ulises H / Olsen, Jesper V

Annual review of genomics and human genetics

2022 Volume 23, Page(s) 99–121

Abstract: Proteins are the molecular effectors of the information encoded in the genome. Proteomics aims at understanding the molecular functions of proteins in their biological context. In contrast to transcriptomics and genomics, the study of proteomes provides ... ...

Abstract	Proteins are the molecular effectors of the information encoded in the genome. Proteomics aims at understanding the molecular functions of proteins in their biological context. In contrast to transcriptomics and genomics, the study of proteomes provides deeper insight into the dynamic regulatory layers encoded at the protein level, such as posttranslational modifications, subcellular localization, cell signaling, and protein-protein interactions. Currently, mass spectrometry (MS)-based proteomics is the technology of choice for studying proteomes at a system-wide scale, contributing to clinical biomarker discovery and fundamental molecular biology. MS technologies are continuously being developed to fulfill the requirements of speed, resolution, and quantitative accuracy, enabling the acquisition of comprehensive proteomes. In this review, we present how MS technology and acquisition methods have evolved to meet the requirements of cutting-edge proteomics research, which is describing the human proteome and its dynamic posttranslational modifications with unprecedented depth. Finally, we provide a perspective on studying proteomes at single-cell resolution.
MeSH term(s)	Genome ; Humans ; Mass Spectrometry/methods ; Protein Processing, Post-Translational ; Proteome/analysis ; Proteome/chemistry ; Proteome/metabolism ; Proteomics/methods
Chemical Substances	Proteome
Language	English
Publishing date	2022-04-19
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2037670-4
ISSN	1545-293X ; 1527-8204
ISSN (online)	1545-293X
ISSN	1527-8204
DOI	10.1146/annurev-genom-112921-024948
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Article ; Online: A deeper look at carrier proteome effects for single-cell proteomics.

Ye, Zilu / Batth, Tanveer S / Rüther, Patrick / Olsen, Jesper V

Communications biology

2022 Volume 5, Issue 1, Page(s) 150

Abstract: Multiplexing approaches using tandem mass tags with a carrier proteome to boost sensitivity have advanced single cell proteomics by mass spectrometry (SCoPE-MS). Here, we probe the carrier proteome effects in single cell proteomics with mixed species ... ...

Abstract	Multiplexing approaches using tandem mass tags with a carrier proteome to boost sensitivity have advanced single cell proteomics by mass spectrometry (SCoPE-MS). Here, we probe the carrier proteome effects in single cell proteomics with mixed species TMTpro-labeled samples. We demonstrate that carrier proteomes, while increasing overall identifications, dictate which proteins are identified. We show that quantitative precision and signal intensity are limited at high carrier levels, hindering the recognition of regulated proteins. Guidelines for optimized mass spectrometry acquisition parameters and best practices for fold-change or protein copy number-based comparisons are provided.
MeSH term(s)	Proteome/metabolism ; Proteomics/methods ; Tandem Mass Spectrometry/methods
Chemical Substances	Proteome
Language	English
Publishing date	2022-02-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-022-03095-4
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Article ; Online: Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT-based multiplexing.

Koenig, Claire / Martinez-Val, Ana / Franciosa, Giulia / Olsen, Jesper V

Proteomics

2022 Volume 22, Issue 19-20, Page(s) e2100245

Abstract: In large-scale quantitative mass spectrometry (MS)-based phosphoproteomics, isobaric labeling with tandem mass tags (TMTs) coupled with offline high-pH reversed-phase peptide chromatographic fractionation maximizes depth of coverage. To investigate to ... ...

Abstract	In large-scale quantitative mass spectrometry (MS)-based phosphoproteomics, isobaric labeling with tandem mass tags (TMTs) coupled with offline high-pH reversed-phase peptide chromatographic fractionation maximizes depth of coverage. To investigate to what extent limited sample amounts affect sensitivity and dynamic range of the analysis due to sample losses, we benchmarked TMT-based fractionation strategies against single-shot label-free quantification with spectral library-free data independent acquisition (LFQ-DIA), for different peptide input per sample. To systematically examine how peptide input amounts influence TMT-fractionation approaches in a phosphoproteomics workflow, we compared two different high-pH reversed-phase fractionation strategies, microflow (MF) and stage-tip fractionation (STF), while scaling the peptide input amount down from 12.5 to 1 μg per sample. Our results indicate that, for input amounts higher than 5 μg per sample, TMT labeling, followed by microflow fractionation (MF) and phospho-enrichment, achieves the deepest phosphoproteome coverage, even compared to single shot direct-DIA analysis. Conversely, STF of enriched phosphopeptides (STF) is optimal for lower amounts, below 5 μg/peptide per sample. As a result, we provide a decision tree to help phosphoproteomics users to choose the best workflow as a function of sample amount.
MeSH term(s)	Phosphopeptides/analysis ; Proteomics/methods ; Tandem Mass Spectrometry/methods ; Proteome ; Chromatography, Reverse-Phase/methods
Chemical Substances	Phosphopeptides ; Proteome
Language	English
Publishing date	2022-07-01
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202100245
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Zs.A 5386: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Proteomics to study cancer immunity and improve treatment.

Franciosa, Giulia / Kverneland, Anders H / Jensen, Agnete W P / Donia, Marco / Olsen, Jesper V

Seminars in immunopathology

2023 Volume 45, Issue 2, Page(s) 241–251

Abstract: Cancer survival and progression depend on the ability of tumor cells to avoid immune recognition. Advances in the understanding of cancer immunity and tumor immune escape mechanisms enabled the development of immunotherapeutic approaches. In patients ... ...

Abstract	Cancer survival and progression depend on the ability of tumor cells to avoid immune recognition. Advances in the understanding of cancer immunity and tumor immune escape mechanisms enabled the development of immunotherapeutic approaches. In patients with otherwise incurable metastatic cancers, immunotherapy resulted in unprecedented response rates with the potential for durable complete responses. However, primary and acquired resistance mechanisms limit the efficacy of immunotherapy. Further therapeutic advances require a deeper understanding of the interplay between immune cells and tumors. Most high-throughput studies within the past decade focused on an omics characterization at DNA and RNA level. However, proteins are the molecular effectors of genomic information; therefore, the study of proteins provides deeper understanding of cellular functions. Recent advances in mass spectrometry (MS)-based proteomics at a system-wide scale may allow translational and clinical discoveries by enabling the analysis of understudied post-translational modifications, subcellular protein localization, cell signaling, and protein-protein interactions. In this review, we discuss the potential contribution of MS-based proteomics to preclinical and clinical research findings in the context of tumor immunity and cancer immunotherapies.
MeSH term(s)	Humans ; Proteomics/methods ; Neoplasms/etiology ; Neoplasms/therapy ; Immunotherapy
Language	English
Publishing date	2023-01-04
Publishing country	Germany
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2316828-6
ISSN	1863-2300 ; 1863-2297
ISSN (online)	1863-2300
ISSN	1863-2297
DOI	10.1007/s00281-022-00980-2
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