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Article: Recent advances in the field of single-cell proteomics.

Petrosius, Valdemaras / Schoof, Erwin M

2022 Volume 27, Page(s) 101556

Abstract: The field of single-cell omics is rapidly progressing. Although DNA and RNA sequencing-based methods have dominated the field to date, global proteome profiling has also entered the main stage. Single-cell proteomics was facilitated by advancements in ... ...

Abstract	The field of single-cell omics is rapidly progressing. Although DNA and RNA sequencing-based methods have dominated the field to date, global proteome profiling has also entered the main stage. Single-cell proteomics was facilitated by advancements in different aspects of mass spectrometry (MS)-based proteomics, such as instrument design, sample preparation, chromatography and ion mobility. Single-cell proteomics by mass spectrometry (scp-MS) has moved beyond being a mere technical development, and is now able to deliver actual biological application and has been successfully applied to characterize different cell states. Here, we review some key developments of scp-MS, provide a background to the field, discuss the various available methods and foresee possible future directions.
Language	English
Publishing date	2022-10-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2443840-6
ISSN	1936-5233
ISSN	1936-5233
DOI	10.1016/j.tranon.2022.101556
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Article ; Online: A proteomics-based survey reveals thrombospondin-4 as a ligand regulated by the mannose receptor in the injured lung.

Nørregaard, Kirstine S / Jürgensen, Henrik J / Heltberg, Signe S / Gårdsvoll, Henrik / Bugge, Thomas H / Schoof, Erwin M / Engelholm, Lars H / Behrendt, Niels

The Journal of biological chemistry

2024 , Page(s) 107284

Abstract: Receptor-mediated cellular uptake of specific ligands constitutes an important step in the dynamic regulation of individual protein levels in extracellular fluids. With a focus on the inflammatory lung, we here performed a proteomics-based search for ... ...

Abstract	Receptor-mediated cellular uptake of specific ligands constitutes an important step in the dynamic regulation of individual protein levels in extracellular fluids. With a focus on the inflammatory lung, we here performed a proteomics-based search for novel ligands regulated by the mannose receptor (MR), a macrophage-expressed endocytic receptor. Wildtype and MR-deficient mice were exposed to lipopolysachharide (LPS), after which the protein content in their lung epithelial lining fluid (ELF) was compared by tandem mass tag-based mass spectrometry. More than 1200 proteins were identified in the ELF using this unbiased approach, but only six showed a statistically different abundance. Among these, an unexpected potential new ligand, thrombospondin-4 (TSP-4), displayed a striking 17-fold increased abundance in the MR-deficient mice. Experiments using exogenous addition of TSP-4 to MR-transfected CHO cells or MR-positive alveolar macrophages confirmed that TSP-4 is a ligand for MR-dependent endocytosis. Similar studies revealed that the molecular interaction with TSP-4 depends on both the lectin activity and the fibronectin type-II domain of MR and that a closely related member of the thrombospondin family, TSP-5, is also efficiently internalized by the receptor. This was unlike the other members of this protein family, including TSPs -1 and -2, which are ligands for a close MR homologue known as uPARAP. Our study shows that MR takes part in the regulation of TSP-4, an important inflammatory component in the injured lung, and that two closely related endocytic receptors, expressed on different cell types, undertake the selective endocytosis of distinct members of the thrombospondin family.
Language	English
Publishing date	2024-04-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2024.107284
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Article ; Online: Optimizing Linear Ion-Trap Data-Independent Acquisition toward Single-Cell Proteomics.

Phlairaharn, Teeradon / Ye, Zilu / Krismer, Elena / Pedersen, Anna-Kathrine / Pietzner, Maik / Olsen, Jesper V / Schoof, Erwin M / Searle, Brian C

Analytical chemistry

2023 Volume 95, Issue 26, Page(s) 9881–9891

Abstract: A linear ion trap (LIT) is an affordable, robust mass spectrometer that provides fast scanning speed and high sensitivity, where its primary disadvantage is inferior mass accuracy compared to more commonly used time-of-flight or orbitrap (OT) mass ... ...

Abstract	A linear ion trap (LIT) is an affordable, robust mass spectrometer that provides fast scanning speed and high sensitivity, where its primary disadvantage is inferior mass accuracy compared to more commonly used time-of-flight or orbitrap (OT) mass analyzers. Previous efforts to utilize the LIT for low-input proteomics analysis still rely on either built-in OTs for collecting precursor data or OT-based library generation. Here, we demonstrate the potential versatility of the LIT for low-input proteomics as a stand-alone mass analyzer for all mass spectrometry (MS) measurements, including library generation. To test this approach, we first optimized LIT data acquisition methods and performed library-free searches with and without entrapment peptides to evaluate both the detection and quantification accuracy. We then generated matrix-matched calibration curves to estimate the lower limit of quantification using only 10 ng of starting material. While LIT-MS1 measurements provided poor quantitative accuracy, LIT-MS2 measurements were quantitatively accurate down to 0.5 ng on the column. Finally, we optimized a suitable strategy for spectral library generation from low-input material, which we used to analyze single-cell samples by LIT-DIA using LIT-based libraries generated from as few as 40 cells.
MeSH term(s)	Proteomics/methods ; Tandem Mass Spectrometry/methods ; Peptides/chemistry
Chemical Substances	Peptides
Language	English
Publishing date	2023-06-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c00842
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Article: Optimizing linear ion trap data independent acquisition towards single cell proteomics.

Phlairaharn, Teeradon / Ye, Zilu / Krismer, Elena / Pedersen, Anna-Kathrine / Pietzner, Maik / Olsen, Jesper V / Schoof, Erwin M / Searle, Brian C

bioRxiv : the preprint server for biology

2023

Abstract: A linear ion trap (LIT) is an affordable, robust mass spectrometer that proves fast scanning speed and high sensitivity, where its primary disadvantage is inferior mass accuracy compared to more commonly used time-of-flight (TOF) or orbitrap (OT) mass ... ...

Abstract	A linear ion trap (LIT) is an affordable, robust mass spectrometer that proves fast scanning speed and high sensitivity, where its primary disadvantage is inferior mass accuracy compared to more commonly used time-of-flight (TOF) or orbitrap (OT) mass analyzers. Previous efforts to utilize the LIT for low-input proteomics analysis still rely on either built-in OTs for collecting precursor data or OT-based library generation. Here, we demonstrate the potential versatility of the LIT for low-input proteomics as a stand-alone mass analyzer for all mass spectrometry measurements, including library generation. To test this approach, we first optimized LIT data acquisition methods and performed library-free searches with and without entrapment peptides to evaluate both the detection and quantification accuracy. We then generated matrix-matched calibration curves to estimate the lower limit of quantification using only 10 ng of starting material. While LIT-MS1 measurements provided poor quantitative accuracy, LIT-MS2 measurements were quantitatively accurate down to 0.5 ng on column. Finally, we optimized a suitable strategy for spectral library generation from low-input material, which we used to analyze single-cell samples by LIT-DIA using LIT-based libraries generated from as few as 40 cells.
Language	English
Publishing date	2023-02-21
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.02.21.529444
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Article ; Online: Evidence for an RNAi-independent role of Arabidopsis DICER-LIKE2 in growth inhibition and basal antiviral resistance.

Nielsen, Carsten Poul Skou / Arribas-Hernández, Laura / Han, Lijuan / Reichel, Marlene / Woessmann, Jakob / Daucke, Rune / Bressendorff, Simon / López-Márquez, Diego / Andersen, Stig Uggerhøj / Pumplin, Nathan / Schoof, Erwin M / Brodersen, Peter

The Plant cell

2024

Abstract: Flowering plant genomes encode four or five DICER-LIKE (DCL) enzymes that produce small interfering RNAs (siRNAs) and microRNAs which function in RNA interference (RNAi). Different RNAi pathways in plants effect transposon silencing, antiviral defense ... ...

Abstract	Flowering plant genomes encode four or five DICER-LIKE (DCL) enzymes that produce small interfering RNAs (siRNAs) and microRNAs which function in RNA interference (RNAi). Different RNAi pathways in plants effect transposon silencing, antiviral defense and endogenous gene regulation. DCL2 acts genetically redundantly with DCL4 to confer basal antiviral defense. However, DCL2 may also counteract DCL4, since knockout of DCL4 causes growth defects that are suppressed by DCL2 inactivation. Current models maintain that RNAi via DCL2-dependent siRNAs is the biochemical basis of both effects. Here, we report that DCL2-mediated antiviral resistance and growth defects cannot be explained by the silencing effects of DCL2-dependent siRNAs. Both functions are defective in genetic backgrounds that maintain high levels of DCL2-dependent siRNAs, either with specific point mutations in DCL2 or with reduced DCL2 dosage because of heterozygosity for dcl2 knockout alleles. Intriguingly, all DCL2 functions require its catalytic activity, and the penetrance of DCL2-dependent growth phenotypes in dcl4 mutants correlates with DCL2 protein levels, but not with levels of major DCL2-dependent siRNAs. We discuss this requirement and correlation with catalytic activity, but not with resulting siRNAs, in light of other findings that reveal a DCL2 function in innate immunity activation triggered by cytoplasmic double-stranded RNA.
Language	English
Publishing date	2024-03-11
Publishing country	England
Document type	Journal Article
ZDB-ID	623171-8
ISSN	1532-298X ; 1040-4651
ISSN (online)	1532-298X
ISSN	1040-4651
DOI	10.1093/plcell/koae067
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Article ; Online: Assessing the Role of Trypsin in Quantitative Plasma and Single-Cell Proteomics toward Clinical Application

Woessmann, Jakob / Petrosius, Valdemaras / Üresin, Nil / Kotol, David / Aragon-Fernandez, Pedro / Hober, Andreas / auf dem Keller, Ulrich / Edfors, Fredrik / Schoof, Erwin M.

Analytical Chemistry. 2023 Aug. 28, v. 95, no. 36 p.13649-13658

2023

Abstract: Mass spectrometry-based bottom-up proteomics is rapidly evolving and routinely applied in large-scale biomedical studies. Proteases are a central component of every bottom-up proteomics experiment, digesting proteins into peptides. Trypsin has been the ... ...

Abstract	Mass spectrometry-based bottom-up proteomics is rapidly evolving and routinely applied in large-scale biomedical studies. Proteases are a central component of every bottom-up proteomics experiment, digesting proteins into peptides. Trypsin has been the most widely applied protease in proteomics due to its characteristics. With ever-larger cohort sizes and possible future clinical application of mass spectrometry-based proteomics, the technical impact of trypsin becomes increasingly relevant. To assess possible biases introduced by trypsin digestion, we evaluated the impact of eight commercially available trypsins in a variety of bottom-up proteomics experiments and across a range of protease concentrations and storage times. To investigate the universal impact of these technical attributes, we included bulk HeLa cell lysate, human plasma, and single HEK293 cells, which were analyzed over a range of selected reaction monitoring (SRM), data-independent acquisition (DIA), and data-dependent acquisition (DDA) instrument methods on three LC-MS instruments. The quantification methods employed encompassed both label-free approaches and absolute quantification utilizing spike-in heavy-labeled recombinant protein fragment standards. Based on this extensive data set, we report variations between commercial trypsins, their source, and their concentration. Furthermore, we provide suggestions on the handling of trypsin in large-scale studies.
Keywords	analytical chemistry ; data collection ; digestion ; human cell lines ; humans ; mass spectrometry ; peptides ; proteomics ; recombinant proteins ; trypsin
Language	English
Dates of publication	2023-0828
Size	p. 13649-13658.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c02543
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Article ; Online: Optimizing Linear Ion-Trap Data-Independent Acquisition toward Single-Cell Proteomics

Phlairaharn, Teeradon / Ye, Zilu / Krismer, Elena / Pedersen, Anna-Kathrine / Pietzner, Maik / Olsen, Jesper V. / Schoof, Erwin M. / Searle, Brian C.

Analytical Chemistry. 2023 June 20, v. 95, no. 26 p.9881-9891

2023

Abstract	A linear ion trap (LIT) is an affordable, robust mass spectrometer that provides fast scanning speed and high sensitivity, where its primary disadvantage is inferior mass accuracy compared to more commonly used time-of-flight or orbitrap (OT) mass analyzers. Previous efforts to utilize the LIT for low-input proteomics analysis still rely on either built-in OTs for collecting precursor data or OT-based library generation. Here, we demonstrate the potential versatility of the LIT for low-input proteomics as a stand-alone mass analyzer for all mass spectrometry (MS) measurements, including library generation. To test this approach, we first optimized LIT data acquisition methods and performed library-free searches with and without entrapment peptides to evaluate both the detection and quantification accuracy. We then generated matrix-matched calibration curves to estimate the lower limit of quantification using only 10 ng of starting material. While LIT-MS1 measurements provided poor quantitative accuracy, LIT-MS2 measurements were quantitatively accurate down to 0.5 ng on the column. Finally, we optimized a suitable strategy for spectral library generation from low-input material, which we used to analyze single-cell samples by LIT-DIA using LIT-based libraries generated from as few as 40 cells.
Keywords	analytical chemistry ; data collection ; mass spectrometry ; peptides ; proteomics ; spectrometers
Language	English
Dates of publication	2023-0620
Size	p. 9881-9891.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c00842
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Article ; Online: Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics.

Furtwängler, Benjamin / Üresin, Nil / Motamedchaboki, Khatereh / Huguet, Romain / Lopez-Ferrer, Daniel / Zabrouskov, Vlad / Porse, Bo T / Schoof, Erwin M

Molecular & cellular proteomics : MCP

2022 Volume 21, Issue 4, Page(s) 100219

Abstract: In the young field of single-cell proteomics (scMS), there is a great need for improved global proteome characterization, both in terms of proteins quantified per cell and quantitative performance thereof. The recently introduced real-time search (RTS) ... ...

Abstract	In the young field of single-cell proteomics (scMS), there is a great need for improved global proteome characterization, both in terms of proteins quantified per cell and quantitative performance thereof. The recently introduced real-time search (RTS) on the Orbitrap Eclipse Tribrid mass spectrometer in combination with SPS-MS3 acquisition has been shown to be beneficial for the measurement of samples that are multiplexed using isobaric tags. Multiplexed scMS requires high ion injection times and high-resolution spectra to quantify the single-cell signal; however, the carrier channel facilitates peptide identification and thus offers the opportunity for fast on-the-fly precursor filtering before committing to the time-intensive quantification scan. Here, we compared classical MS2 acquisition against RTS-SPS-MS3, both using the Orbitrap Eclipse Tribrid MS with the FAIMS Pro ion mobility interface and present a new acquisition strategy termed RETICLE (RTS enhanced quant of single cell spectra) that makes use of fast real-time searched linear ion trap scans to preselect MS1 peptide precursors for quantitative MS2 Orbitrap acquisition. We show that classical MS2 acquisition is outperformed by both RTS-SPS-MS3 through increased quantitative accuracy at similar proteome coverage, and RETICLE through higher proteome coverage, with the latter enabling the quantification of over 1000 proteins per cell at an MS2 injection time of 750 ms using a 2 h gradient.
MeSH term(s)	Mass Spectrometry ; Peptides ; Proteome ; Proteomics
Chemical Substances	Peptides ; Proteome
Language	English
Publishing date	2022-02-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2022.100219
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Article ; Online: High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps.

Phlairaharn, Teeradon / Grégoire, Samuel / Woltereck, Lukas R / Petrosius, Valdemaras / Furtwängler, Benjamin / Searle, Brian C / Schoof, Erwin M

Journal of proteome research

2022 Volume 21, Issue 11, Page(s) 2815–2826

Abstract: In recent years, the concept of cell heterogeneity in biology has gained increasing attention, concomitant with a push toward technologies capable of resolving such biological complexity at the molecular level. For single-cell proteomics using Mass ... ...

Abstract	In recent years, the concept of cell heterogeneity in biology has gained increasing attention, concomitant with a push toward technologies capable of resolving such biological complexity at the molecular level. For single-cell proteomics using Mass Spectrometry (scMS) and low-input proteomics experiments, the sensitivity of an orbitrap mass analyzer can sometimes be limiting. Therefore, low-input proteomics and scMS could benefit from linear ion traps, which provide faster scanning speeds and higher sensitivity than an orbitrap mass analyzer, however at the cost of resolution. We optimized an acquisition method that combines the orbitrap and linear ion trap, as implemented on a tribrid instrument, while taking advantage of the high-field asymmetric waveform ion mobility spectrometry (FAIMS) pro interface, with a prime focus on low-input applications. First, we compared the performance of orbitrap- versus linear ion trap mass analyzers. Subsequently, we optimized critical method parameters for low-input measurement by data-independent acquisition on the linear ion trap mass analyzer. We conclude that linear ion traps mass analyzers combined with FAIMS and Whisper flow chromatography are well-tailored for low-input proteomics experiments, and can simultaneously increase the throughput and sensitivity of large-scale proteomics experiments where limited material is available, such as clinical samples and cellular subpopulations.
MeSH term(s)	Proteomics/methods ; Peptides/analysis ; Mass Spectrometry/methods ; Ion Mobility Spectrometry
Chemical Substances	Peptides
Language	English
Publishing date	2022-10-26
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.2c00376
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Article ; Online: Proteomics identifies differences in fibrotic potential of extracellular vesicles from human tendon and muscle fibroblasts.

Yeung, Ching-Yan Chloé / Schoof, Erwin M / Tamáš, Michal / Mackey, Abigail L / Kjaer, Michael

Cell communication and signaling : CCS

2020 Volume 18, Issue 1, Page(s) 177

Abstract: Background: Fibroblasts are the powerhouses responsible for the production and assembly of extracellular matrix (ECM). Their activity needs to be tightly controlled especially within the musculoskeletal system, where changes to ECM composition affect ... ...

Abstract	Background: Fibroblasts are the powerhouses responsible for the production and assembly of extracellular matrix (ECM). Their activity needs to be tightly controlled especially within the musculoskeletal system, where changes to ECM composition affect force transmission and mechanical loading that are required for effective movement of the body. Extracellular vesicles (EVs) are a mode of cell-cell communication within and between tissues, which has been largely characterised in cancer. However, it is unclear what the role of healthy fibroblast-derived EVs is during tissue homeostasis. Methods: Here, we performed proteomic analysis of small EVs derived from primary human muscle and tendon cells to identify the potential functions of healthy fibroblast-derived EVs. Results: Mass spectrometry-based proteomics revealed comprehensive profiles for small EVs released from healthy human fibroblasts from different tissues. We found that fibroblast-derived EVs were more similar than EVs from differentiating myoblasts, but there were significant differences between tendon fibroblast and muscle fibroblast EVs. Small EVs from tendon fibroblasts contained higher levels of proteins that support ECM synthesis, including TGFβ1, and muscle fibroblast EVs contained proteins that support myofiber function and components of the skeletal muscle matrix. Conclusions: Our data demonstrates a marked heterogeneity among healthy fibroblast-derived EVs, indicating shared tasks between EVs of skeletal muscle myoblasts and fibroblasts, whereas tendon fibroblast EVs could play a fibrotic role in human tendon tissue. These findings suggest an important role for EVs in tissue homeostasis of both tendon and skeletal muscle in humans. Video abstract.
MeSH term(s)	Adult ; Exosomes/metabolism ; Exosomes/ultrastructure ; Extracellular Matrix Proteins/metabolism ; Extracellular Vesicles/metabolism ; Extracellular Vesicles/ultrastructure ; Female ; Fibroblasts/metabolism ; Fibroblasts/pathology ; Fibroblasts/ultrastructure ; Fibrosis ; Humans ; Male ; Models, Biological ; Muscle, Skeletal/pathology ; Proteomics ; Tendons/pathology
Chemical Substances	Extracellular Matrix Proteins
Language	English
Publishing date	2020-11-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1478-811X
ISSN (online)	1478-811X
DOI	10.1186/s12964-020-00669-9
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