1
|
Li J, Zhan X. Mass spectrometry analysis of phosphotyrosine-containing proteins. MASS SPECTROMETRY REVIEWS 2024; 43:857-887. [PMID: 36789499 DOI: 10.1002/mas.21836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.
Collapse
Affiliation(s)
- Jiajia Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
| |
Collapse
|
2
|
Identification, production and bioactivity of casein phosphopeptides – A review. Food Res Int 2022; 157:111360. [DOI: 10.1016/j.foodres.2022.111360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 01/23/2023]
|
3
|
Kaulich PT, Cassidy L, Bartel J, Schmitz RA, Tholey A. Multi-protease Approach for the Improved Identification and Molecular Characterization of Small Proteins and Short Open Reading Frame-Encoded Peptides. J Proteome Res 2021; 20:2895-2903. [PMID: 33760615 DOI: 10.1021/acs.jproteome.1c00115] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The identification of proteins below approximately 70-100 amino acids in bottom-up proteomics is still a challenging task due to the limited number of peptides generated by proteolytic digestion. This includes the short open reading frame-encoded peptides (SEPs), which are a subset of the small proteins that were not previously annotated or that are alternatively encoded. Here, we systematically investigated the use of multiple proteases (trypsin, chymotrypsin, LysC, LysargiNase, and GluC) in GeLC-MS/MS analysis to improve the sequence coverage and the number of identified peptides for small proteins, with a focus on SEPs, in the archaeon Methanosarcina mazei. Combining the data of all proteases, we identified 63 small proteins and additional 28 SEPs with at least two unique peptides, while only 55 small proteins and 22 SEP could be identified using trypsin only. For 27 small proteins and 12 SEPs, a complete sequence coverage was achieved. Moreover, for five SEPs, incorrectly predicted translation start points or potential in vivo proteolytic processing were identified, confirming the data of a previous top-down proteomics study of this organism. The results show clearly that a multi-protease approach allows to improve the identification and molecular characterization of small proteins and SEPs. LC-MS data: ProteomeXchange PXD023921.
Collapse
Affiliation(s)
- Philipp T Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel 24105, Germany
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel 24105, Germany
| | - Jürgen Bartel
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald 17489, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel, Kiel 24118, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel 24105, Germany
| |
Collapse
|
4
|
Li J, Zhan X. Mass spectrometry-based proteomics analyses of post-translational modifications and proteoforms in human pituitary adenomas. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140584. [PMID: 33321259 DOI: 10.1016/j.bbapap.2020.140584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022]
Abstract
Pituitary adenoma (PA) is a common intracranial neoplasm, which affects the hypothalamus-pituitary-target organ axis systems, and is hazardous to human health. Post-translational modifications (PTMs), including phosphorylation, ubiquitination, nitration, and sumoylation, are vitally important in the PA pathogenesis. The large-scale analysis of PTMs could provide a global view of molecular mechanisms for PA. Proteoforms, which are used to define various protein structural and functional forms originated from the same gene, are the future direction of proteomics research. The global studies of different proteoforms and PTMs of hypophyseal hormones such as growth hormone (GH) and prolactin (PRL) and the proportion change of different GH proteoforms or PRL proteoforms in human pituitary tissue could provide new insights into the clinical value of pituitary hormones in PAs. Multiple quantitative proteomics methods, including mass spectrometry (MS)-based label-free and stable isotope-labeled strategies in combination with different PTM-peptide enrichment methods such as TiO2 enrichment of tryptic phosphopeptides and antibody enrichment of other PTM-peptides increase the feasibility for researchers to study PA proteomes. This article reviews the research status of PTMs and proteoforms in PAs, including the enrichment method, technical limitation, quantitative proteomics strategies, and the future perspectives, to achieve the goals of in-depth understanding its molecular pathogenesis, and discovering effective biomarkers and clinical therapeutic targets for predictive, preventive, and personalized treatment of PA patients.
Collapse
Affiliation(s)
- Jiajia Li
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, Shandong 250117, P. R. China; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 P. R. China; State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Xianquan Zhan
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, Shandong 250117, P. R. China; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 P. R. China; State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China; Department of Oncology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China.
| |
Collapse
|
5
|
Cho HM, Hong JS, Kim YB, Nawarathne SR, Choi I, Yi YJ, Wu D, Lee H, Han SE, Nam KT, Seoung EI, Heo JM. Responses in growth performance and nutrient digestibility to a multi-protease supplementation in amino acid-deficient broiler diets. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:840-853. [PMID: 33987564 PMCID: PMC7721581 DOI: 10.5187/jast.2020.62.6.840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 11/20/2022]
Abstract
The present study was conducted to investigate the effect of a multi-protease on
production indicators of broiler chickens fed a crude protein and amino acid
deficient-diets for 35 days immediately after hatch. A total of 448 one-day-old
Ross 308 male broiler chicks were allocated in a completely randomized design
into one of eight dietary treatments (positive control [PC], negative control
[NC: minus 0.5% from PC, and minus 2% of lysine, methionine, threonine and
methionine plus cysteine], extreme negative control [ENC: minus 1% from PC,
minus 4% of lysine, methionine, threonine and methionine plus cysteine], and
plus multi-protease 150 or 300 g per ton [e. g., PC-150]; PC, PC-150, NC,
NC-150, NC-300, ENC, ENC-150, ENC-300) to give eight replicates with seven birds
in a battery cage. Body weight, average daily gain, average daily feed intake,
feed conversion ratio, and mortality were measured every week. Carcass traits,
proximate analysis of breast meat, and ileum digestibility were analyzed on day
21 and 35. Feeding a multi-protease (i.e., more than 150 g/ton) for 35 days
immediately after hatching improved feed efficiency and ileum digestibility
(i.e., dry matter, crude protein, and energy) compared to their counterparts
(i.e., diets without multi-protease: PC, NC, and ENC). In conclusion, our
results indicated that broiler chickens fed nutrients deficient-diet (i.e.,
crude protein and amino acids) supplemented a multi-protease had an ability to
compensate and (or) improve their growth performance commensurate with increased
ileal digestibility for 35 days immediately after hatch.
Collapse
Affiliation(s)
- Hyun Min Cho
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Jun Sun Hong
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Yu Bin Kim
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Shan Randima Nawarathne
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Inchul Choi
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Young-Joo Yi
- Department of Agricultural Education, College of Education, Sunchon National University, Suncheon 57922, Korea
| | - Di Wu
- Kemin Industries, Inc., 12 Senoko Drive 758200, Singapore
| | - Hans Lee
- Kemin Industries, Inc., 12 Senoko Drive 758200, Singapore
| | - Seung Eun Han
- Kemin Industries, Inc., 12 Senoko Drive 758200, Singapore
| | - Ki Taeg Nam
- Department of Animal Science and Biotechnology, Hankyong National University, Anseong 17579, Korea
| | - Eun Il Seoung
- Department of Animal Science and Biotechnology, Hankyong National University, Anseong 17579, Korea
| | - Jung Min Heo
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| |
Collapse
|
6
|
Arrington JV, Hsu CC, Elder SG, Andy Tao W. Recent advances in phosphoproteomics and application to neurological diseases. Analyst 2018; 142:4373-4387. [PMID: 29094114 DOI: 10.1039/c7an00985b] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphorylation has an incredible impact on the biological behavior of proteins, altering everything from intrinsic activity to cellular localization and complex formation. It is no surprise then that this post-translational modification has been the subject of intense study and that, with the advent of faster, more accurate instrumentation, the number of large-scale mass spectrometry-based phosphoproteomic studies has swelled over the past decade. Recent developments in sample preparation, phosphorylation enrichment, quantification, and data analysis strategies permit both targeted and ultra-deep phosphoproteome profiling, but challenges remain in pinpointing biologically relevant phosphorylation events. We describe here technological advances that have facilitated phosphoproteomic analysis of cells, tissues, and biofluids and note applications to neuropathologies in which the phosphorylation machinery may be dysregulated, much as it is in cancer.
Collapse
|
7
|
Somasundaram P, Koudelka T, Linke D, Tholey A. C-Terminal Charge-Reversal Derivatization and Parallel Use of Multiple Proteases Facilitates Identification of Protein C-Termini by C-Terminomics. J Proteome Res 2016; 15:1369-78. [PMID: 26939532 DOI: 10.1021/acs.jproteome.6b00146] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The identification of protein C-termini in complex proteomes is challenging due to the poor ionization efficiency of the carboxyl group. Amidating the negatively charged C-termini with ethanolamine (EA) has been suggested to improve the detection of C-terminal peptides and allows for a directed depletion of internal peptides after proteolysis using carboxyl reactive polymers. In the present study, the derivatization with N,N-dimethylethylenediamine (DMEDA) and (4-aminobutyl)guanidine (AG) leading to a positively charged C-terminus was investigated. C-terminal charge-reversed peptides showed improved coverage of b- and y-ion series in the MS/MS spectra compared to their noncharged counterparts. DMEDA-derivatized peptides resulted in many peptides with charge states of 3+, which benefited from ETD fragmentation. This makes the charge-reversal strategy particularly useful for the analysis of protein C-termini, which may also be post-translationally modified. The labeling strategy and the indirect enrichment of C-termini worked with similar efficiency for both DMEDA and EA, and their applicability was demonstrated on an E. coli proteome. Utilizing two proteases and different MS/MS activation mechanisms allowed for the identification of >400 C-termini, encompassing both canonical and truncated C-termini.
Collapse
Affiliation(s)
- Prasath Somasundaram
- AG Systematische Proteomforschung & Bioanalytik, Institut für Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel , Niemannsweg 11, 24105 Kiel, Germany
| | - Tomas Koudelka
- AG Systematische Proteomforschung & Bioanalytik, Institut für Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel , Niemannsweg 11, 24105 Kiel, Germany
| | - Dennis Linke
- AG Systematische Proteomforschung & Bioanalytik, Institut für Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel , Niemannsweg 11, 24105 Kiel, Germany
| | - Andreas Tholey
- AG Systematische Proteomforschung & Bioanalytik, Institut für Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel , Niemannsweg 11, 24105 Kiel, Germany
| |
Collapse
|