2
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Ma W, Ang IL, Lei KMK, Lam MMT, Zhang P, Poon TCW. Pitfalls and Solutions in Mass Spectrometry-Based Identification of Protein Glycation. Anal Chem 2023; 95:1829-1837. [PMID: 36630282 DOI: 10.1021/acs.analchem.2c01261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Emerging evidence suggests that advanced glycation end-products (AGEs) such as Nε-(carboxymethyl)lysine (CML) and Nε-(carboxymethyl)lysine (CEL) may play important roles in certain human diseases. Reliable analytical methods are needed for their characterizations and measurements. Pitfalls have been reported for applications of LC-MS/MS to identify various types of post-translational modifications, but not yet for the case of AGEs. Here, we showed that in the absence of manual inspection, cysteine alkylation with 2-iodoacetamide (IAA) can result in false-positive/ambiguous identifications of CML >20%. They were attributed to offsite alkylation together with incorrect monoisotopic peak assignment (pitfall 1) or together with deamidation (pitfall 2). For pitfall 1, false-positive identifications can be alleviated using a peptide mass error tolerance ≤5 ppm during the database search. Pitfall 2 results in ambiguous modification assignments, which may be overcome by using other alkylation reagents. According to calculations of theoretical mass shifts, the use of other common alkylation reagents (iodoacetic acid, 2-chloroacetamide, and acrylamide) should face similar pitfalls. The use of acrylamide can result in false-positive identifications of CEL instead of CML. Subsequently, we showed that compared to IAA, the use of N-isopropylacrylamide (NIPAM) as an alkylation reagent achieved similar levels of proteome coverage, while reducing the offsite alkylation reactions at lysine by more than five times. Furthermore, false-positive/ambiguous identifications of CML due to the two types of pitfalls were absent when using NIPAM. NIPAM alkylation results in a unique mass shift that allows reliable identifications of CML and most likely other AGEs, such as CEL.
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Affiliation(s)
- Wendong Ma
- Pilot Laboratory, MOE Frontier Science Centre for Precision Oncology, Centre for Precision Medicine Research and Training, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Irene Ling Ang
- Pilot Laboratory, MOE Frontier Science Centre for Precision Oncology, Centre for Precision Medicine Research and Training, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Kate M K Lei
- Pilot Laboratory, MOE Frontier Science Centre for Precision Oncology, Centre for Precision Medicine Research and Training, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Melody Man Ting Lam
- Proteomics Core, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Pengwei Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, China
| | - Terence Chuen Wai Poon
- Pilot Laboratory, MOE Frontier Science Centre for Precision Oncology, Centre for Precision Medicine Research and Training, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
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3
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Cui G, Gao Z, Chang S, Narwade N, Chen Y, Poudel B, Lei KMK, Zhang W, Li G, Poon TCW, Cheung E. TRIM37 Augments AP-2γ Transcriptional Activity and Cellular Localization via K63-linked Ubiquitination to Drive Breast Cancer Progression. Int J Biol Sci 2022; 18:4316-4328. [PMID: 35864973 PMCID: PMC9295074 DOI: 10.7150/ijbs.69466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Received: 11/26/2021] [Accepted: 05/09/2022] [Indexed: 11/26/2022] Open
Abstract
Activator Protein 2 gamma (AP-2γ) is a master transcription factor that plays a critical role in the development and progression of breast cancer. However, the underlying mechanism is still unclear. Herein, using a proteomics approach, we identified Tripartite motif-containing 37 (TRIM37) as a novel coactivator of AP-2γ-mediated transcription in breast cancer cells. We demonstrate that TRIM37 facilitates AP-2γ chromatin binding to directly regulate the AP-2γ mediated transcriptional program. We also show that TRIM37 achieves this by stimulating K63 chain-linked ubiquitination of AP-2γ, promoting protein localization from the cytoplasm to the nucleus. In clinical analyses, we find TRIM37 is upregulated in multiple breast cancer datasets, supporting our findings that the TRIM37-AP-2γ interaction is essential for breast cancer tumor growth. Overall, our work reveals that TRIM37 is an oncogenic coactivator of AP-2γ in breast cancer and provides a novel therapeutic target for treating the disease.
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Affiliation(s)
- Guimei Cui
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.,MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China.,Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Zhuoran Gao
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.,MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China.,Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Shiehong Chang
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Nitin Narwade
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.,MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China.,Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Yitian Chen
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.,MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China.,Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Barun Poudel
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Kate M K Lei
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.,MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China.,Pilot Laboratory, University of Macau, Macau SAR, China.,Institute of Translational Medicine, University of Macau, Macau SAR, China.,Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Weibo Zhang
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.,MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China.,Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Gang Li
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.,MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China.,Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Terence C W Poon
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.,MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China.,Pilot Laboratory, University of Macau, Macau SAR, China.,Institute of Translational Medicine, University of Macau, Macau SAR, China.,Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Edwin Cheung
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China.,Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.,MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China.,Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
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4
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Zhang P, Chan W, Ang IL, Wei R, Lam MMT, Lei KMK, Poon TCW. Revisiting Fragmentation Reactions of Protonated α-Amino Acids by High-Resolution Electrospray Ionization Tandem Mass Spectrometry with Collision-Induced Dissociation. Sci Rep 2019; 9:6453. [PMID: 31015571 PMCID: PMC6478932 DOI: 10.1038/s41598-019-42777-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/08/2019] [Indexed: 12/23/2022] Open
Abstract
Fragmentation reactions of protonated α-amino acids (AAs) were studied previously using tandem mass spectrometry (MS/MS) of unit mass resolution. Isobaric fragmentation products and minor fragmentation products could have been overlooked or misannotated. In the present study, we examined the fragmentation patterns of 19 AAs using high-resolution electrospray ionization MS/MS (HR-ESI-MS/MS) with collision-induced dissociation (CID). Isobaric fragmentation products from protonated Met and Trp were resolved and identified for the first time. Previously unreported fragmentation products from protonated Met, Cys, Gln, Arg, and Lys were observed. Additionally, the chemical identity of a fragmentation product from protonated Trp that was incorrectly annotated in previous investigations was corrected. All previously unreported fragmentation products and reactions were verified by pseudo MS3 experiments and/or MS/MS analyses of deuterated AAs. Clearer pictures of the fragmentation reactions for Met, Cys, Trp, Gln, Arg and Lys were obtained in the present study.
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Affiliation(s)
- Pengwei Zhang
- Pilot Laboratory, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Wan Chan
- Department of Chemistry, Hong Kong University of Science and Technology, Hong Kong, China
| | - Irene L Ang
- Pilot Laboratory, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Rui Wei
- Pilot Laboratory, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Melody M T Lam
- Proteomics Core, Faculty of Health Sciences, University of Macau, Macau, China
| | - Kate M K Lei
- Pilot Laboratory, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Terence C W Poon
- Pilot Laboratory, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China.
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5
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Zhang P, Chan W, Ang IL, Wei R, Lam MMT, Lei KMK, Poon TCW. Gas-Phase Fragmentation Reactions of Protonated Cystine using High-Resolution Tandem Mass Spectrometry. Molecules 2019; 24:E747. [PMID: 30791449 PMCID: PMC6412553 DOI: 10.3390/molecules24040747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 11/16/2022] Open
Abstract
Cystine is an important biomolecule in living systems. Although collision-induced dissociation (CID)-based tandem mass spectrometry (MS/MS) is commonly applied for identification and quantification of cystine in both biomedical and nutritional studies, gas-phase fragmentation reactions of cystine in CID has remained unclear. This may lead to improper assay design, which may in turn result in inaccurate test results. In the present study, gas-phase fragmentation reactions of protonated cystine in CID were characterized using high-resolution MS/MS and pseudo MS³. Fragmentations started from cleavages of disulfide bond (S⁻S) and carbon⁻sulfur bond (C⁻S). When cleaving at the S⁻S, protonated cysteine was generated as one of the predominant fragmentation products. Minor fragmentations started from the loss of H₂O + CO and the loss of NH₃. Our results reveal that the m/z 74 fragment ion, which is commonly used as a product ion of the transition (precursor/product ion pair) in selected reaction monitoring (SRM) assay for quantifying cystine, comprises two isobaric fragments originating from different parts of cystine. This indicates the need for careful selection of a stable isotope-labeled cystine molecule as an internal standard for SRM assays. Here, we provide a clear picture of the fragmentation reactions of protonated cystine in CID. It can serve as a useful guidance for designing MS/MS-based assays for cystine testing.
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Affiliation(s)
- Pengwei Zhang
- Pilot Laboratory, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China.
| | - Wan Chan
- Department of Chemistry, Hong Kong University of Science and Technology, Hong Kong, China.
| | - Irene L Ang
- Pilot Laboratory, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China.
| | - Rui Wei
- Pilot Laboratory, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China.
| | - Melody M T Lam
- Proteomics Core, Faculty of Health Sciences, University of Macau, Macau, China.
| | - Kate M K Lei
- Pilot Laboratory, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China.
| | - Terence C W Poon
- Pilot Laboratory, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China.
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