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Thielert M, Itang ECM, Ammar C, Rosenberger FA, Bludau I, Schweizer L, Nordmann TM, Skowronek P, Wahle M, Zeng W, Zhou X, Brunner A, Richter S, Levesque MP, Theis FJ, Steger M, Mann M. Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. Mol Syst Biol 2023; 19:e11503. [PMID: 37602975 PMCID: PMC10495816 DOI: 10.15252/msb.202211503] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/22/2023] Open
Abstract
Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, and robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated and complete dimethyl labeling of bulk or single-cell samples, without losing proteomic depth. Lys-N digestion enables five-plex quantification at MS1 and MS2 level. Because the multiplexed channels are quantitatively isolated from each other, mDIA accommodates a reference channel that does not interfere with the target channels. Our algorithm RefQuant takes advantage of this and confidently quantifies twice as many proteins per single cell compared to our previous work (Brunner et al, PMID 35226415), while our workflow currently allows routine analysis of 80 single cells per day. Finally, we combined mDIA with spatial proteomics to increase the throughput of Deep Visual Proteomics seven-fold for microdissection and four-fold for MS analysis. Applying this to primary cutaneous melanoma, we discovered proteomic signatures of cells within distinct tumor microenvironments, showcasing its potential for precision oncology.
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Affiliation(s)
- Marvin Thielert
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Ericka CM Itang
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Constantin Ammar
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Florian A Rosenberger
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Isabell Bludau
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Lisa Schweizer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Thierry M Nordmann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Patricia Skowronek
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Maria Wahle
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Wen‐Feng Zeng
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Xie‐Xuan Zhou
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Andreas‐David Brunner
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery SciencesBiberach an der RissGermany
| | - Sabrina Richter
- Helmholtz Zentrum München – German Research Center for Environmental HealthInstitute of Computational BiologyNeuherbergGermany
- TUM School of Life Sciences WeihenstephanTechnical University of MunichFreisingGermany
| | - Mitchell P Levesque
- Department of DermatologyUniversity of Zurich, University of Zurich HospitalZurichSwitzerland
| | - Fabian J Theis
- Helmholtz Zentrum München – German Research Center for Environmental HealthInstitute of Computational BiologyNeuherbergGermany
- TUM School of Life Sciences WeihenstephanTechnical University of MunichFreisingGermany
| | - Martin Steger
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- New address: NEOsphere Biotechnologies GmbHPlaneggGermany
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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Lkhagva A, Tai HC. Dimethylcysteine (DiCys)/ o-Phthalaldehyde Derivatization for Chiral Metabolite Analyses: Cross-Comparison of Six Chiral Thiols. Molecules 2021; 26:7416. [PMID: 34946495 DOI: 10.3390/molecules26247416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
Metabolomics profiling using liquid chromatography-mass spectrometry (LC-MS) has become an important tool in biomedical research. However, resolving enantiomers still represents a significant challenge in the metabolomics study of complex samples. Here, we introduced N,N-dimethyl-l-cysteine (dimethylcysteine, DiCys), a chiral thiol, for the o-phthalaldehyde (OPA) derivatization of enantiomeric amine metabolites. We took interest in DiCys because of its potential for multiplex isotope-tagged quantification. Here, we characterized the usefulness of DiCys in reversed-phase LC-MS analyses of chiral metabolites, compared against five commonly used chiral thiols: N-acetyl-l-cysteine (NAC); N-acetyl-d-penicillamine (NAP); isobutyryl-l-cysteine (IBLC); N-(tert-butoxycarbonyl)-l-cysteine methyl ester (NBC); and N-(tert-butylthiocarbamoyl)-l-cysteine ethyl ester (BTCC). DiCys and IBLC showed the best overall performance in terms of chiral separation, fluorescence intensity, and ionization efficiency. For chiral separation of amino acids, DiCys/OPA also outperformed Marfey’s reagents: 1-fluoro-2-4-dinitrophenyl-5-l-valine amide (FDVA) and 1-fluoro-2-4-dinitrophenyl-5-l-alanine amide (FDAA). As proof of principle, we compared DiCys and IBLC for detecting chiral metabolites in aqueous extracts of rice. By LC–MS analyses, both methods detected twenty proteinogenic l-amino acids and seven d-amino acids (Ala, Arg, Lys, Phe, Ser, Tyr, and Val), but DiCys showed better analyte separation. We conclude that DiCys/OPA is an excellent amine-derivatization method for enantiomeric metabolite detection in LC-MS analyses.
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Makjaroen J, Somparn P, Hodge K, Poomipak W, Hirankarn N, Pisitkun T. Comprehensive Proteomics Identification of IFN-λ3-regulated Antiviral Proteins in HBV-transfected Cells. Mol Cell Proteomics 2018; 17:2197-2215. [PMID: 30097535 PMCID: PMC6210224 DOI: 10.1074/mcp.ra118.000735] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/10/2018] [Indexed: 12/16/2022] Open
Abstract
Interferon lambda (IFN-λ) is a relatively unexplored, yet promising antiviral agent. IFN-λ has recently been tested in clinical trials of chronic hepatitis B virus infection (CHB), with the advantage that side effects may be limited compared with IFN-α, as IFN-λ receptors are found only in epithelial cells. To date, IFN-λ's downstream signaling pathway remains largely unelucidated, particularly via proteomics methods. Here, we report that IFN-λ3 inhibits HBV replication in HepG2.2.15 cells, reducing levels of both HBV transcripts and intracellular HBV DNA. Quantitative proteomic analysis of HBV-transfected cells was performed following 24-hour IFN-λ3 treatment, with parallel IFN-α2a and PBS treatments for comparison using a dimethyl labeling method. The depth of the study allowed us to map the induction of antiviral proteins to multiple points of the viral life cycle, as well as facilitating the identification of antiviral proteins not previously known to be elicited upon HBV infection (e.g. IFITM3, XRN2, and NT5C3A). This study also shows up-regulation of many effectors involved in antigen processing/presentation indicating that this cytokine exerted immunomodulatory effects through several essential molecules for these processes. Interestingly, the 2 subunits of the immunoproteasome cap (PSME1 and PSME2) were up-regulated whereas cap components of the constitutive proteasome were down-regulated upon both IFN treatments, suggesting coordinated modulation toward the antigen processing/presentation mode. Furthermore, in addition to confirming canonical activation of interferon-stimulated gene (ISG) transcription through the JAK-STAT pathway, we reveal that IFN-λ3 restored levels of RIG-I and RIG-G, proteins known to be suppressed by HBV. Enrichment analysis demonstrated that several biological processes including RNA metabolism, translation, and ER-targeting were differentially regulated upon treatment with IFN-λ3 versus IFN-α2a. Our proteomic data suggests that IFN-λ3 regulates an array of cellular processes to control HBV replication.
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Affiliation(s)
- Jiradej Makjaroen
- From the ‡Medical Microbiology Interdisciplinary Program, Graduate School, Chulalongkorn University, Bangkok, Thailand
- §Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- ¶Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Poorichaya Somparn
- §Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- ¶Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kenneth Hodge
- ¶Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Witthaya Poomipak
- ¶Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nattiya Hirankarn
- §Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Trairak Pisitkun
- ¶Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Jiang H, Zhang L, Zhang Y, Xie L, Wang Y, Lu H. HST-MRM-MS: A Novel High-Sample-Throughput Multiple Reaction Monitoring Mass Spectrometric Method for Multiplex Absolute Quantitation of Hepatocellular Carcinoma Serum Biomarker. J Proteome Res 2018; 18:469-477. [PMID: 30346787 DOI: 10.1021/acs.jproteome.8b00790] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Absolute quantification of clinical biomarkers by mass spectrometry (MS) has been challenged due to low sample-throughput of current multiple reaction monitoring (MRM) methods. For this problem to be overcome, in this work, a novel high-sample-throughput multiple reaction monitoring mass spectrometric (HST-MRM-MS) quantification approach is developed to achieve simultaneous quantification of 24 samples. Briefly, triplex dimethyl reagents (L, M, and H) and eight-plex iTRAQ reagents were used to label the N- and C-termini of the Lys C-digested peptides, respectively. The triplex dimethyl labeling produces three coelute peaks in MRM traces, and the iTRAQ labeling produces eight peaks in MS2, resulting in 24 (3×8) channels in a single experiment. HST-MRM-MS has shown good accuracy ( R2 > 0.98 for absolute quantification), reproducibility (RSD < 15%), and linearity (2-3 orders of magnitude). Moreover, the novel method has been successfully applied in quantifying serum biomarkers in hepatocellular carcinoma (HCC)-related serum samples. In conclusion, HST-MRM-MS is an accurate, high-sample-throughput, and broadly applicable MS-based absolute quantification method.
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Liang HC, Liu YC, Chen H, Ku MC, Do QT, Wang CY, Tzeng SF, Chen SH. In Situ Click Reaction Coupled with Quantitative Proteomics for Identifying Protein Targets of Catechol Estrogens. J Proteome Res 2018; 17:2590-2599. [PMID: 29897771 DOI: 10.1021/acs.jproteome.8b00021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Catechol estrogens (CEs) are metabolic electrophiles that actively undergo covalent interaction with cellular proteins, influencing molecular function. There is no feasible method to identify their binders in a living system. Herein, we developed a click chemistry-based approach using ethinylestradiol (EE2) as the precursor probe coupled with quantitative proteomics to identify protein targets of CEs and classify their binding strengths. Using in situ metabolic conversion and click reaction in liver microsomes, CEs-protein complex was captured by the probe, digested by trypsin, stable isotope labeled via reductive amination, and analyzed by liquid chromatography-mass spectrometry (LC-MS). A total of 334 liver proteins were repeatedly identified ( n ≥ 2); 274 identified proteins were classified as strong binders based on precursor mass mapping. The binding strength was further scaled by D/H ratio (activity probe/solvent): 259 strong binders had D/H > 5.25; 46 weak binders had 5.25 > D/H > 1; 5 nonspecific binders (keratins) had D/H < 1. These results were confirmed using spiked covalent control (strong binder) and noncovalent control (weak binder), as well as in vitro testing of cytochrome c (D/H = 5.9), which showed covalent conjugation with CEs. Many identified strong binders, such as glutathione transferase, catechol-O-methyl transferase, superoxide dismutase, catalase, glutathione peroxidase, and cytochrome c, are involved in cellular redox processes or detoxification activities. CE conjugation was shown to suppress the superoxide oxidase activity of cytochrome c, suggesting that CEs modification may alter the redox action of cellular proteins. Due to structural similarity and inert alkyne group, EE2 probe is very likely to capture protein targets of CEs in general. Thus, this strategy can be adopted to explore the biological impact of CEs modification in living systems.
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Hubner NC, Nguyen LN, Hornig NC, Stunnenberg HG. A quantitative proteomics tool to identify DNA-protein interactions in primary cells or blood. J Proteome Res 2015; 14:1315-29. [PMID: 25546135 DOI: 10.1021/pr5009515] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interactions between transcription factors and genomic DNA, and in particular their impact on disease and cell fate, have been extensively studied on a global level using techniques based on next-generation sequencing. These approaches, however, do not allow an unbiased study of protein complexes that bind to certain DNA sequences. DNA pulldowns from crude lysates combined with quantitative mass spectrometry were recently introduced to close this gap. Established protocols, however, are restricted to cell lines because they are based on metabolic labeling or require large amounts of material. We introduce a high-throughput-compatible DNA pulldown that combines on-bead digestion with direct dimethyl labeling or label-free protein quantification. We demonstrate that our method can efficiently identify transcription factors binding to their consensus DNA motifs in extracts from primary foreskin fibroblasts and peripheral blood mononuclear cells (PBMCs) freshly isolated from human donors. Nuclear proteomes with absolute quantification of nearly 7000 proteins in K562 cells and PBMCs clearly link differential interactions to differences in protein abundance, hence stressing the importance of selecting relevant cell extracts for any interaction in question. As shown for rs6904029, a SNP highly associated with chronic lymphocytic leukemia, our approach can provide invaluable functional data, for example, through integration with GWAS.
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Affiliation(s)
- Nina C Hubner
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen , Nijmegen 6525 GA, The Netherlands
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Abstract
Determination of a protein's N-terminal sequence can be important for the characterization of protein processing. To increase the confidence of protein N-terminal identification, chemical derivatization of the N-terminal amine group by (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) or dimethyl labeling followed by mass spectrometric analysis is commonly performed. Using this approach, proteins can be separated by SDS-PAGE, and the protein N-terminus of interest is labeled by TMPP or dimethyl in-gel before tryptic digestion and LC-MS analysis. The N-terminus of a protein can thus be easily identified because the N-terminal tryptic peptides are preferentially labeled. Peptides with N-terminal derivatization produce a better fragmentation pattern during tandem mass spectrometric analysis, which significantly facilitates sequencing of these peptides.
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Abstract
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Temperature changes influence the
reaction rates of all biological
processes, which can pose dramatic challenges to cold-blooded organisms,
and the capability to adapt to temperature fluctuations is crucial
for the survival of these animals. In order to understand the roles
that neuropeptides play in the temperature stress response, we employed
a mass spectrometry-based approach to investigate the neuropeptide
changes associated with acute temperature elevation in three neural
tissues from the Jonah crab Cancer borealis. At high temperature, members from two neuropeptide families, including
RFamide and RYamide, were observed to be significantly reduced in
one of the neuroendocrine structures, the pericardial organ, while
several orcokinin peptides were detected to be decreased in another
major neuroendocrine organ, the sinus gland. These results implicate
that the observed neuropeptides may be involved with temperature perturbation
response via hormonal regulation. Furthermore, a temperature stress
marker peptide with the primary sequence of SFRRMGGKAQ (m/z 1137.7) was detected and de novo sequenced in
the circulating fluid (hemolymph) from animals under thermal perturbation.
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Affiliation(s)
- Ruibing Chen
- Research Center of Basic Medical Sciences, Tianjin Medical University , Tianjin 300070, China
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Shan B, Xu C, Zhang Y, Xu T, Gottesfeld JM, Yates JR. Quantitative proteomic analysis identifies targets and pathways of a 2-aminobenzamide HDAC inhibitor in Friedreich's ataxia patient iPSC-derived neural stem cells. J Proteome Res 2014; 13:4558-66. [PMID: 24933366 PMCID: PMC4227551 DOI: 10.1021/pr500514r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Members
of the 2-aminobenzamide class of histone deacetylase (HDAC) inhibitors
show promise as therapeutics for the neurodegenerative diseases Friedreich’s
ataxia (FRDA) and Huntington’s disease (HD). While it is clear
that HDAC3 is one of the important targets of the 2-aminobenzamide
HDAC inhibitors, inhibition of other class I HDACs (HDACs 1 and 2)
may also be involved in the beneficial effects of these compounds
in FRDA and HD, and other HDAC interacting proteins may be impacted
by the compound. To this end, we synthesized activity-based profiling
probe (ABPP) versions of one of our HDAC inhibitors (compound 106),
and in the present study we used a quantitative proteomic method coupled
with multidimensional protein identification technology (MudPIT) to
identify the proteins captured by the ABPP 106 probe. Nuclear proteins
were extracted from FRDA patient iPSC-derived neural stem cells, and
then were reacted with control and ABPP 106 probe. After reaction,
the bound proteins were digested on the beads, and the peptides were
modified using stable isotope-labeled formaldehyde to form dimethyl
amine. The selectively bound proteins determined by mass spectrometry
were subjected to functional and pathway analysis. Our findings suggest
that the targets of compound 106 are involved not only in transcriptional
regulation but also in posttranscriptional processing of mRNA.
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Affiliation(s)
- Bing Shan
- Department of Chemical Physiology, ‡Department of Cell and Molecular biology, The Scripps Research Institute , La Jolla, California 92037, United States
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