1
|
Kovanich D, Low TY, Zaccolo M. Using the Proteomics Toolbox to Resolve Topology and Dynamics of Compartmentalized cAMP Signaling. Int J Mol Sci 2023; 24:4667. [PMID: 36902098 PMCID: PMC10003371 DOI: 10.3390/ijms24054667] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/04/2023] Open
Abstract
cAMP is a second messenger that regulates a myriad of cellular functions in response to multiple extracellular stimuli. New developments in the field have provided exciting insights into how cAMP utilizes compartmentalization to ensure specificity when the message conveyed to the cell by an extracellular stimulus is translated into the appropriate functional outcome. cAMP compartmentalization relies on the formation of local signaling domains where the subset of cAMP signaling effectors, regulators and targets involved in a specific cellular response cluster together. These domains are dynamic in nature and underpin the exacting spatiotemporal regulation of cAMP signaling. In this review, we focus on how the proteomics toolbox can be utilized to identify the molecular components of these domains and to define the dynamic cellular cAMP signaling landscape. From a therapeutic perspective, compiling data on compartmentalized cAMP signaling in physiological and pathological conditions will help define the signaling events underlying disease and may reveal domain-specific targets for the development of precision medicine interventions.
Collapse
Affiliation(s)
- Duangnapa Kovanich
- Center for Vaccine Development, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Manuela Zaccolo
- Department of Physiology, Anatomy and Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford OX1 3PT, UK
| |
Collapse
|
2
|
Tsai CF, Wang YT, Hsu CC, Kitata RB, Chu RK, Velickovic M, Zhao R, Williams SM, Chrisler WB, Jorgensen ML, Moore RJ, Zhu Y, Rodland KD, Smith RD, Wasserfall CH, Shi T, Liu T. A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics. Commun Biol 2023; 6:70. [PMID: 36653408 PMCID: PMC9849344 DOI: 10.1038/s42003-022-04400-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023] Open
Abstract
Effective phosphoproteome of nanoscale sample analysis remains a daunting task, primarily due to significant sample loss associated with non-specific surface adsorption during enrichment of low stoichiometric phosphopeptide. We develop a tandem tip phosphoproteomics sample preparation method that is capable of sample cleanup and enrichment without additional sample transfer, and its integration with our recently developed SOP (Surfactant-assisted One-Pot sample preparation) and iBASIL (improved Boosting to Amplify Signal with Isobaric Labeling) approaches provides a streamlined workflow enabling sensitive, high-throughput nanoscale phosphoproteome measurements. This approach significantly reduces both sample loss and processing time, allowing the identification of >3000 (>9500) phosphopeptides from 1 (10) µg of cell lysate using the label-free method without a spectral library. It also enables precise quantification of ~600 phosphopeptides from 100 sorted cells (single-cell level input for the enriched phosphopeptides) and ~700 phosphopeptides from human spleen tissue voxels with a spatial resolution of 200 µm (equivalent to ~100 cells) in a high-throughput manner. The new workflow opens avenues for phosphoproteome profiling of mass-limited samples at the low nanogram level.
Collapse
Affiliation(s)
- Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Chuan-Chih Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Reta Birhanu Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Marija Velickovic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - William B Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Marda L Jorgensen
- Department of Pathology, Immunology, and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Clive H Wasserfall
- Department of Pathology, Immunology, and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| |
Collapse
|
3
|
Xu C, Li Y, Xiao Z, Yang J, Xue M, Jiang N, Meng Y, Liu W, Fan Y, Zhou Y. Proteomic and Phosphoproteomic Analyses Reveal Gibel Carp Responses to Cyprinid Herpesvirus 2 Infection. J Proteome Res 2022; 21:1961-1973. [DOI: 10.1021/acs.jproteome.2c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chen Xu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yiqun Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Zidong Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
- College of Fisheries, Huazhong Agricultural University, Wuhan 430072, China
| | - Jie Yang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
- College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Mingyang Xue
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Nan Jiang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Wenzhi Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yuding Fan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| |
Collapse
|
4
|
Zhang L, Wang Y, Zhang W, Hsu YI, Asoh TA, Qi B, Uyama H. Robust Dual-Biomimetic Titanium Dioxide-Cellulose Monolith for Enrichment of Phosphopeptides. ACS Biomater Sci Eng 2022; 8:2676-2683. [PMID: 35616239 DOI: 10.1021/acsbiomaterials.2c00385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metal oxide affinity chromatography (MOAC) is considered to be one of the most effective methods for phosphopeptide enrichment. However, most of the materials used in the method are powder; frequent centrifugation is necessitated during the enrichment process, and potential risks of loss of peptides and materials and clogging of the column employed for liquid chromatography-mass spectrometry (LC-MS) arise. Moreover, the reusability of these materials to achieve sustainability was hardly investigated. To overcome these limitations, herein, inorganic titanium dioxide (TiO2) was coated onto the skeletal surface of the organic cellulose monolith (CM) material with a coral-like structure via a sol-gel method. This produced an organic-inorganic hybrid TiO2-CM material, which contained a combination of organic and inorganic substances, making it mimic the mollusk shell in terms of composition. The prepared TiO2-CM material as monolith exhibited excellent mechanical strength and did not break during the enrichment process; thus, the tedious implementation of multiple centrifugation cycles was prevented, thereby streamlining the experimental procedure and avoiding the loss of peptides and materials. Moreover, a large amount of TiO2 was introduced onto the surface of the CM material, and thus, the resultant TiO2-CM material exhibited a large surface area. As a result, the fabricated TiO2-CM material was successfully applied to the enrichment of phosphopeptides obtained from the tryptic digests of a BSA/β-casein (mass ratio, 500/1) mixture. The results were superior to those achieved for commercial TiO2 beads, confirming that TiO2-CM has excellent selectivity for phosphopeptides and reusability. Furthermore, 9287 unique phosphopeptides derived from the 2661 phosphoproteins were successfully identified from two milligrams of tryptic digests of Hela cell exosomes obtained through five independent replications after enriching using the TiO2-CM material. The results indicated that the material has good application prospects in the analysis of protein phosphorylation. Furthermore, TiO2-CM consists of green and cheap cellulose as the skeleton, and its synthesis process is environment-friendly, simple, and inexpensive.
Collapse
Affiliation(s)
- Luwei Zhang
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yan Wang
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Wanjun Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Yu-I Hsu
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Taka-Aki Asoh
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Baoyun Qi
- Department of Neurology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Hiroshi Uyama
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
5
|
Low TY, Mohtar MA, Lee PY, Omar N, Zhou H, Ye M. WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT. MASS SPECTROMETRY REVIEWS 2021; 40:309-333. [PMID: 32491218 DOI: 10.1002/mas.21636] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.
Collapse
Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Nursyazwani Omar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Houjiang Zhou
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Centre, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| |
Collapse
|
6
|
Gaur K, Pérez Otero SC, Benjamín-Rivera JA, Rodríguez I, Loza-Rosas SA, Vázquez Salgado AM, Akam EA, Hernández-Matias L, Sharma RK, Alicea N, Kowaleff M, Washington AV, Astashkin AV, Tomat E, Tinoco AD. Iron Chelator Transmetalative Approach to Inhibit Human Ribonucleotide Reductase. JACS AU 2021; 1:865-878. [PMID: 34240081 PMCID: PMC8243325 DOI: 10.1021/jacsau.1c00078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Indexed: 05/04/2023]
Abstract
Efforts directed at curtailing the bioavailability of intracellular iron could lead to the development of broad-spectrum anticancer drugs given the metal's role in cancer proliferation and metastasis. Human ribonucleotide reductase (RNR), the key enzyme responsible for synthesizing the building blocks of DNA replication and repair, depends on Fe binding at its R2 subunit to activate the catalytic R1 subunit. This work explores an intracellular iron chelator transmetalative approach to inhibit RNR using the titanium(IV) chemical transferrin mimetic (cTfm) compounds Ti(HBED) and Ti(Deferasirox)2. Whole-cell EPR studies reveal that the compounds can effectively attenuate RNR activity though seemingly causing different changes to the labile iron pool that may account for differences in their potency against cells. Studies of Ti(IV) interactions with the adenosine nucleotide family at pH 7.4 reveal strong metal binding and extensive phosphate hydrolysis, which suggest the capacity of the metal to disturb the nucleotide substrate pool of the RNR enzyme. By decreasing intracellular Fe bioavailability and altering the nucleotide substrate pool, the Ti cTfm compounds could inhibit the activity of the R1 and R2 subunits of RNR. The compounds arrest the cell cycle in the S phase, indicating suppressed DNA replication, and induce apoptotic cell death. Cotreatment cell viability studies with cisplatin and Ti(Deferasirox)2 reveal a promising synergism between the compounds that is likely owed to their distinct but complementary effect on DNA replication.
Collapse
Affiliation(s)
- Kavita Gaur
- Department
of Chemistry, University of Puerto Rico
Río Piedras Campus, San Juan, Puerto Rico 00931, United States
| | - Sofia C. Pérez Otero
- Department
of Chemistry, University of Puerto Rico
Río Piedras Campus, San Juan, Puerto Rico 00931, United States
| | - Josué A. Benjamín-Rivera
- Department
of Chemistry, University of Puerto Rico
Río Piedras Campus, San Juan, Puerto Rico 00931, United States
| | - Israel Rodríguez
- Department
of Chemistry, University of Puerto Rico
Río Piedras Campus, San Juan, Puerto Rico 00931, United States
| | - Sergio A. Loza-Rosas
- Department
of Chemistry, University of Puerto Rico
Río Piedras Campus, San Juan, Puerto Rico 00931, United States
| | | | - Eman A. Akam
- Department
of Chemistry and Biochemistry, The University
of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, United States
| | - Liz Hernández-Matias
- Department
of Biology, University of Puerto Rico Río
Piedras Campus, San Juan, Puerto Rico 00931, United States
| | - Rohit K. Sharma
- Department
of Chemistry, University of Puerto Rico
Río Piedras Campus, San Juan, Puerto Rico 00931, United States
| | - Nahiara Alicea
- Department
of Chemistry, University of Puerto Rico
Río Piedras Campus, San Juan, Puerto Rico 00931, United States
| | - Martin Kowaleff
- Department
of Chemistry, University of Puerto Rico
Río Piedras Campus, San Juan, Puerto Rico 00931, United States
| | - Anthony V. Washington
- Department
of Biology, University of Puerto Rico Río
Piedras Campus, San Juan, Puerto Rico 00931, United States
| | - Andrei V. Astashkin
- Department
of Chemistry and Biochemistry, The University
of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, United States
| | - Elisa Tomat
- Department
of Chemistry and Biochemistry, The University
of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, United States
| | - Arthur D. Tinoco
- Department
of Chemistry, University of Puerto Rico
Río Piedras Campus, San Juan, Puerto Rico 00931, United States
| |
Collapse
|
7
|
Uhrig RG, Echevarría‐Zomeño S, Schlapfer P, Grossmann J, Roschitzki B, Koerber N, Fiorani F, Gruissem W. Diurnal dynamics of the Arabidopsis rosette proteome and phosphoproteome. PLANT, CELL & ENVIRONMENT 2021; 44:821-841. [PMID: 33278033 PMCID: PMC7986931 DOI: 10.1111/pce.13969] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 05/11/2023]
Abstract
Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional regulation controls diurnal fluctuations at the protein level. Here, we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 hr light:12 hr dark diurnal cycle and the phosphoproteome immediately before and after the light-to-dark and dark-to-light transitions. We quantified nearly 5,000 proteins and 800 phosphoproteins, of which 288 fluctuated in their abundance and 226 fluctuated in their phosphorylation status. Of the phosphoproteins, 60% were quantified for changes in protein abundance. This revealed six proteins involved in nitrogen and hormone metabolism that had concurrent changes in both protein abundance and phosphorylation status. The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, light perception, photosynthesis, metabolism and transport. The phosphoproteome at the light-dark transitions revealed the dynamics at phosphorylation sites in either anticipation of or response to a change in light regime. Phosphorylation site motif analyses implicate casein kinase II and calcium/calmodulin-dependent kinases among the primary light-dark transition kinases. The comparative analysis of the diurnal proteome and diurnal and circadian transcriptome established how mRNA and protein accumulation intersect in leaves during the diurnal cycle of the plant.
Collapse
Affiliation(s)
- R. Glen Uhrig
- Department of BiologyInstitute of Molecular Plant Biology, ETH ZurichZurichSwitzerland
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Pascal Schlapfer
- Department of BiologyInstitute of Molecular Plant Biology, ETH ZurichZurichSwitzerland
| | - Jonas Grossmann
- Functional Genomics Center ZurichUniversity of ZurichZurichSwitzerland
| | - Bernd Roschitzki
- Functional Genomics Center ZurichUniversity of ZurichZurichSwitzerland
| | - Niklas Koerber
- Institute of Bio‐ and GeosciencesIBG‐2: Plant Sciences, Forschungszentrum Jülich GmbHJülichGermany
| | - Fabio Fiorani
- Institute of Bio‐ and GeosciencesIBG‐2: Plant Sciences, Forschungszentrum Jülich GmbHJülichGermany
| | - Wilhelm Gruissem
- Department of BiologyInstitute of Molecular Plant Biology, ETH ZurichZurichSwitzerland
- Institute of BiotechnologyNational Chung Hsing UniversityTaichungTaiwan
| |
Collapse
|
8
|
Zhou Q, Meng Q, Tan X, Ding W, Ma K, Xu Z, Huang X, Gao H. Protein Phosphorylation Changes During Systemic Acquired Resistance in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:748287. [PMID: 34858456 PMCID: PMC8632492 DOI: 10.3389/fpls.2021.748287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/08/2021] [Indexed: 05/03/2023]
Abstract
Systemic acquired resistance (SAR) in plants is a defense response that provides resistance against a wide range of pathogens at the whole-plant level following primary infection. Although the molecular mechanisms of SAR have been extensively studied in recent years, the role of phosphorylation that occurs in systemic leaves of SAR-induced plants is poorly understood. We used a data-independent acquisition (DIA) phosphoproteomics platform based on high-resolution mass spectrometry in an Arabidopsis thaliana model to identify phosphoproteins related to SAR establishment. A total of 8011 phosphorylation sites from 3234 proteins were identified in systemic leaves of Pseudomonas syringae pv. maculicola ES4326 (Psm ES4326) and mock locally inoculated plants. A total of 859 significantly changed phosphoproteins from 1119 significantly changed phosphopeptides were detected in systemic leaves of Psm ES4326 locally inoculated plants, including numerous transcription factors and kinases. A variety of defense response-related proteins were found to be differentially phosphorylated in systemic leaves of Psm ES4326 locally inoculated leaves, suggesting that these proteins may be functionally involved in SAR through phosphorylation or dephosphorylation. Significantly changed phosphoproteins were enriched mainly in categories related to response to abscisic acid, regulation of stomatal movement, plant-pathogen interaction, MAPK signaling pathway, purine metabolism, photosynthesis-antenna proteins, and flavonoid biosynthesis. A total of 28 proteins were regulated at both protein and phosphorylation levels during SAR. RT-qPCR analysis revealed that changes in phosphorylation levels of proteins during SAR did not result from changes in transcript abundance. This study provides comprehensive details of key phosphoproteins associated with SAR, which will facilitate further research on the molecular mechanisms of SAR.
Collapse
Affiliation(s)
- Qingfeng Zhou
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Qi Meng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an, China
| | - Xiaomin Tan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an, China
| | - Wei Ding
- Shanghai Omicsspace Biotechnology Co., Ltd., Shanghai, China
| | - Kang Ma
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Ziqin Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an, China
| | - Xuan Huang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi’an, China
- *Correspondence: Xuan Huang,
| | - Hang Gao
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
- Hang Gao,
| |
Collapse
|
9
|
Abstract
Phosphopeptide enrichment is a commonly used sample preparation step for investigating phosphorylation. TiO2-based enrichment has been demonstrated to have excellent performance both for large amounts of complex and for small amounts of simple samples. However, it has not yet been studied for complex samples in the nanogram range. Our objective was to develop a methodology applicable for complex samples in the low nanogram range, useful for mass spectrometry analysis of tissue microarrays. The selectivity and performance of two stationary phases (TiO2 nanoparticle-coated monolithic column and spin tip filled with TiO2 microspheres) and several loading solvents were studied. Based on this study, we developed an effective and robust method, based on a spin tip with a non-conventional 50 mM citric acid-based loading solvent. It gave excellent results for phosphopeptide enrichment from samples containing a few nanograms of a complex protein mixture.
Collapse
|
10
|
Schlaffner CN, Kahnert K, Muntel J, Chauhan R, Renard BY, Steen JA, Steen H. FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data. eLife 2020; 9:e58783. [PMID: 33284109 PMCID: PMC7721442 DOI: 10.7554/elife.58783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/23/2020] [Indexed: 12/22/2022] Open
Abstract
Improvements in LC-MS/MS methods and technology have enabled the identification of thousands of modified peptides in a single experiment. However, protein regulation by post-translational modifications (PTMs) is not binary, making methods to quantify the modification extent crucial to understanding the role of PTMs. Here, we introduce FLEXIQuant-LF, a software tool for large-scale identification of differentially modified peptides and quantification of their modification extent without knowledge of the types of modifications involved. We developed FLEXIQuant-LF using label-free quantification of unmodified peptides and robust linear regression to quantify the modification extent of peptides. As proof of concept, we applied FLEXIQuant-LF to data-independent-acquisition (DIA) data of the anaphase promoting complex/cyclosome (APC/C) during mitosis. The unbiased FLEXIQuant-LF approach to assess the modification extent in quantitative proteomics data provides a better understanding of the function and regulation of PTMs. The software is available at https://github.com/SteenOmicsLab/FLEXIQuantLF.
Collapse
Affiliation(s)
- Christoph N Schlaffner
- F.M. Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Konstantin Kahnert
- Department of Pathology, Boston Children’s HospitalBostonUnited States
- Bioinformatics Unit (MF1), Robert Koch InstituteBerlinGermany
- Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität BerlinBerlinGermany
| | - Jan Muntel
- Department of Pathology, Boston Children’s HospitalBostonUnited States
- Department of Pathology, Harvard Medical SchoolBostonUnited States
| | - Ruchi Chauhan
- F.M. Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Bernhard Y Renard
- Bioinformatics Unit (MF1), Robert Koch InstituteBerlinGermany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of PotsdamPotsdamGermany
| | - Judith A Steen
- F.M. Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Hanno Steen
- Department of Pathology, Boston Children’s HospitalBostonUnited States
- Department of Pathology, Harvard Medical SchoolBostonUnited States
- Precision Vaccines Program, Boston Children’s HospitalBostonUnited States
| |
Collapse
|
11
|
Kupcik R, Macak JM, Rehulkova H, Sopha H, Fabrik I, Anitha VC, Klimentova J, Murasova P, Bilkova Z, Rehulka P. Amorphous TiO 2 Nanotubes as a Platform for Highly Selective Phosphopeptide Enrichment. ACS OMEGA 2019; 4:12156-12166. [PMID: 31460330 PMCID: PMC6682070 DOI: 10.1021/acsomega.9b00571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/21/2019] [Indexed: 06/10/2023]
Abstract
This work reports highly selective phosphopeptide enrichment using amorphous TiO2 nanotubes (TiO2NTs) and the same material decorated with superparamagnetic Fe3O4 nanoparticles (TiO2NTs@Fe3O4NPs). TiO2NTs and TiO2NTs@Fe3O4NPs materials were applied for phosphopeptide enrichment both from a simple peptide mixture (tryptic digest of bovine serum albumin and α-casein) and from a complex peptide mixture (tryptic digest of Jurkat T cell lysate). The obtained enrichment efficiency and selectivity for phosphopeptides of TiO2NTs and TiO2NTs@Fe3O4NPs were increased to 28.7 and 25.3%, respectively, as compared to those of the well-established TiO2 microspheres. The enrichment protocol was extended for a second elution step facilitating the identification of additional phosphopeptides. It further turned out that both types of amorphous TiO2 nanotubes provide qualitatively new physicochemical features that are clearly advantageous for highly selective phosphopeptide enrichment. This has been confirmed experimentally resulting in substantial reduction of non-phosphorylated peptides in the enriched samples. In addition, TiO2NTs@Fe3O4NPs combine high selectivity and ease of handling due to the superparamagnetic character of the material. The presented materials and performances are further promising for applications toward a whole range of other types of biomolecules to be treated in a similar fashion.
Collapse
Affiliation(s)
- Rudolf Kupcik
- Department
of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532
10 Pardubice, Czech Republic
| | - Jan M. Macak
- Center
of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice, Nam. Cs. Legii 565, 530 02 Pardubice, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Helena Rehulkova
- Department
of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500
01 Hradec Kralove, Czech Republic
| | - Hanna Sopha
- Center
of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice, Nam. Cs. Legii 565, 530 02 Pardubice, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Ivo Fabrik
- Department
of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500
01 Hradec Kralove, Czech Republic
| | - V. C. Anitha
- Center
of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice, Nam. Cs. Legii 565, 530 02 Pardubice, Czech Republic
| | - Jana Klimentova
- Department
of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500
01 Hradec Kralove, Czech Republic
| | - Pavla Murasova
- Department
of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532
10 Pardubice, Czech Republic
| | - Zuzana Bilkova
- Department
of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532
10 Pardubice, Czech Republic
| | - Pavel Rehulka
- Department
of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500
01 Hradec Kralove, Czech Republic
| |
Collapse
|
12
|
Yi L, Tsai CF, Dirice E, Swensen AC, Chen J, Shi T, Gritsenko MA, Chu RK, Piehowski PD, Smith RD, Rodland KD, Atkinson MA, Mathews CE, Kulkarni RN, Liu T, Qian WJ. Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells. Anal Chem 2019; 91:5794-5801. [PMID: 30843680 PMCID: PMC6596310 DOI: 10.1021/acs.analchem.9b00024] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Comprehensive phosphoproteomic analysis of small populations of cells remains a daunting task due primarily to the insufficient MS signal intensity from low concentrations of enriched phosphopeptides. Isobaric labeling has a unique multiplexing feature where the "total" peptide signal from all channels (or samples) triggers MS/MS fragmentation for peptide identification, while the reporter ions provide quantitative information. In light of this feature, we tested the concept of using a "boosting" sample (e.g., a biological sample mimicking the study samples but available in a much larger quantity) in multiplexed analysis to enable sensitive and comprehensive quantitative phosphoproteomic measurements with <100 000 cells. This simple boosting to amplify signal with isobaric labeling (BASIL) strategy increased the overall number of quantifiable phosphorylation sites more than 4-fold. Good reproducibility in quantification was demonstrated with a median CV of 15.3% and Pearson correlation coefficient of 0.95 from biological replicates. A proof-of-concept experiment demonstrated the ability of BASIL to distinguish acute myeloid leukemia cells based on the phosphoproteome data. Moreover, in a pilot application, this strategy enabled quantitative analysis of over 20 000 phosphorylation sites from human pancreatic islets treated with interleukin-1β and interferon-γ. Together, this signal boosting strategy provides an attractive solution for comprehensive and quantitative phosphoproteome profiling of relatively small populations of cells where traditional phosphoproteomic workflows lack sufficient sensitivity.
Collapse
Affiliation(s)
- Lian Yi
- Biological Sciences Division
| | | | - Ercument Dirice
- Section of Islet Cell Biology and Regenerative Medicine, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02215, United States
| | | | - Jing Chen
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32611, United States
| | | | | | - Rosalie K. Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | | | - Richard D. Smith
- Biological Sciences Division
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | | | - Mark A. Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32611, United States
| | - Clayton E. Mathews
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32611, United States
| | - Rohit N. Kulkarni
- Section of Islet Cell Biology and Regenerative Medicine, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Tao Liu
- Biological Sciences Division
| | | |
Collapse
|
13
|
Chen R, Li J. Enrichment of Phosphorylated MHC Peptides with Immobilized Metal Affinity Chromatography and Titanium Dioxide Particles. Methods Mol Biol 2019; 2024:259-268. [PMID: 31364055 DOI: 10.1007/978-1-4939-9597-4_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phosphorylation is one of the most important forms of posttranslational modification. Dysregulation of phosphorylation is implicated in tumorigenesis, with cancerous signaling pathways activated by kinases. For immunotherapy with neoantigen-based peptides, phosphopeptides derived from aberrantly phosphorylated proteins presented by major histocompatibility complex (MHC) are promising candidates due to their specificity to elicit cytotoxic T-cell responses. Unlike other MHC peptides, phosphorylated MHC peptides cannot be predicted from DNA sequences, and their identification relies on the direct detection of phosphopeptides using mass spectrometry (MS). For MS detection, it is extremely important to enrich phosphorylated peptides from the complex repertoire of MHC peptides. Herein, we describe the combined use of immobilized metal affinity chromatography and titanium dioxide nanoparticles for phosphopeptides enrichment from immunopeptidome.
Collapse
Affiliation(s)
- Rui Chen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Jianjun Li
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada.
| |
Collapse
|
14
|
Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
Collapse
Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| |
Collapse
|
15
|
Zagorac I, Fernandez-Gaitero S, Penning R, Post H, Bueno MJ, Mouron S, Manso L, Morente MM, Alonso S, Serra V, Muñoz J, Gómez-López G, Lopez-Acosta JF, Jimenez-Renard V, Gris-Oliver A, Al-Shahrour F, Piñeiro-Yañez E, Montoya-Suarez JL, Apala JV, Moreno-Torres A, Colomer R, Dopazo A, Heck AJR, Altelaar M, Quintela-Fandino M. In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer. Nat Commun 2018; 9:3501. [PMID: 30158526 PMCID: PMC6115463 DOI: 10.1038/s41467-018-05742-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 07/19/2018] [Indexed: 01/25/2023] Open
Abstract
Triple-negative breast cancer (TNBC) lacks prognostic and predictive markers. Here, we use high-throughput phosphoproteomics to build a functional TNBC taxonomy. A cluster of 159 phosphosites is upregulated in relapsed cases of a training set (n = 34 patients), with 11 hyperactive kinases accounting for this phosphoprofile. A mass-spectrometry-to-immunohistochemistry translation step, assessing 2 independent validation sets, reveals 6 kinases with preserved independent prognostic value. The kinases split the validation set into two patterns: one without hyperactive kinases being associated with a >90% relapse-free rate, and the other one showing ≥1 hyperactive kinase and being associated with an up to 9.5-fold higher relapse risk. Each kinase pattern encompasses different mutational patterns, simplifying mutation-based taxonomy. Drug regimens designed based on these 6 kinases show promising antitumour activity in TNBC cell lines and patient-derived xenografts. In summary, the present study elucidates phosphosites and kinases implicated in TNBC and suggests a target-based clinical classification system for TNBC. Triple-negative breast cancer (TNBC) lacks prognostic and predictive markers. Here, the authors use phosphoproteomics to define kinases with distinct activity profiles in TNBC, demonstrating their prognostic value as well as their utility for simplifying TNBC classification and designing drug regimens.
Collapse
Affiliation(s)
- Ivana Zagorac
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain
| | - Sara Fernandez-Gaitero
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain
| | - Renske Penning
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Maria J Bueno
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain
| | - Silvana Mouron
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain
| | - Luis Manso
- Medical Oncology, Hospital 12 de Octubre, Madrid, 28029, Spain
| | - Manuel M Morente
- Biobank, CNIO - Spanish National Cancer Research Center, Madrid, 28029, Spain
| | - Soledad Alonso
- Pathology Department, Hospital Universitario de Guadalajara, Guadalajara, 19002, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, VHIO - Vall d'Hebron Institute of Oncology, Barcelona, 08035, Spain
| | - Javier Muñoz
- Proteomics Unit, CNIO - Spanish National Cancer Research Center, Madrid, 28029, Spain
| | - Gonzalo Gómez-López
- Bioinformatics Unit, CNIO - Spanish National Cancer Research Center, Madrid, 28029, Spain
| | | | - Veronica Jimenez-Renard
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain
| | - Albert Gris-Oliver
- Experimental Therapeutics Group, VHIO - Vall d'Hebron Institute of Oncology, Barcelona, 08035, Spain
| | - Fatima Al-Shahrour
- Bioinformatics Unit, CNIO - Spanish National Cancer Research Center, Madrid, 28029, Spain
| | - Elena Piñeiro-Yañez
- Bioinformatics Unit, CNIO - Spanish National Cancer Research Center, Madrid, 28029, Spain
| | | | - Juan V Apala
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain
| | - Amalia Moreno-Torres
- Pathology Department, Hospital Universitario de Fuenlabrada, Fuenlabrada, 28942, Spain
| | - Ramon Colomer
- Medical Oncology, Hospital La Princesa, Madrid, 28006, Spain
| | - Ana Dopazo
- Genomics Unit, CNIC - Spanish National Center for Cardiovascular Research, Madrid, 28029, Spain
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Miguel Quintela-Fandino
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain. .,Medical Oncology, Hospital Universitario Fuenlabrada, Madrid, 28942, Spain. .,Medical Oncology, Hospital Universitario Quirón, Madrid, 28223, Spain.
| |
Collapse
|
16
|
Wu Y, Chen J, Liu Z, Wang F. Identification of pyridoxal phosphate-modified proteins using mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:195-200. [PMID: 29164709 DOI: 10.1002/rcm.8030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Pyridoxal 5'-phosphate (PLP) cooperates with a variety of enzymes in all organisms for many important biological processes. The development of mass spectrometry-based methodology for high-throughput modification analyses could provide an alternative way for PLP identification. The present study aims to identify PLP modification. METHODS More PLP site-determining information was obtained by introducing multistage activation (MSA)-assisted collision-induced dissociation (CID). We then utilized immobilized metal ion affinity chromatography (IMAC) with Ti4+ to enrich the PLP peptides. In addition, alkaline phosphatase (ALP) was used to remove the phosphoryl group and further confirm the PLP modification site. RESULTS MSA was able to greatly enhance the identification and localization of PLP modification. We applied this strategy to analyze PLP-modified proteins in Escherichia coli samples and accurately determine PLP site K270 in tryptophanase. CONCLUSIONS MSA-assisted CID was used to provide better identification of PLP-modified peptides. Furthermore, tryptophanase with PLP modification at K270 in E. coli was identified with Ti4+ -IMAC enrichment followed by ALP treatment. This method provides a promising alternative for investigating biological functions of PLP-modified proteins.
Collapse
Affiliation(s)
- Yue Wu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, Liaoning, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, Liaoning, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, Liaoning, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, Liaoning, PR China
| |
Collapse
|
17
|
Potel CM, Lin MH, Heck AJR, Lemeer S. Defeating Major Contaminants in Fe 3+- Immobilized Metal Ion Affinity Chromatography (IMAC) Phosphopeptide Enrichment. Mol Cell Proteomics 2018; 17:1028-1034. [PMID: 29449344 DOI: 10.1074/mcp.tir117.000518] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/15/2018] [Indexed: 11/06/2022] Open
Abstract
Here we demonstrate that biomolecular contaminants, such as nucleic acid molecules, can seriously interfere with immobilized metal ion affinity chromatography (IMAC)-based phosphopeptide enrichments. We address and largely solve this issue, developing a robust protocol implementing methanol/chloroform protein precipitation and enzymatic digestion using benzonase, which degrades all forms of DNA and RNA, before IMAC-column loading. This simple procedure resulted in a drastic increase of enrichment sensitivity, enabling the identification of around 17,000 unique phosphopeptides and 12,500 unambiguously localized phosphosites in human cell-lines from a single LC-MS/MS run, constituting a 50% increase when compared with the standard protocol. The improved protocol was also applied to bacterial samples, increasing the number of identified bacterial phosphopeptides even more strikingly, by a factor 10, when compared with the standard protocol. For E. coli we detected around 1300 unambiguously localized phosphosites per LC-MS/MS run. The preparation of these ultra-pure phosphopeptide samples only requires marginal extra costs and sample preparation time and should thus be adoptable by every laboratory active in the field of phosphoproteomics.
Collapse
Affiliation(s)
- Clement M Potel
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Miao-Hsia Lin
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Simone Lemeer
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
18
|
Wang H, Zhong J, Xiao K, Tian Z. Enrichment of intact phosphoproteins using immobilized titanium(IV) affinity chromatography microspheres. SEPARATION SCIENCE PLUS 2018. [DOI: 10.1002/sscp.201700008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hao Wang
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability; Tongji University; China
| | - Jinqiang Zhong
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability; Tongji University; China
| | - Kaijie Xiao
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability; Tongji University; China
| | - Zhixin Tian
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability; Tongji University; China
| |
Collapse
|
19
|
Yao Y, Dong J, Dong M, Liu F, Wang Y, Mao J, Ye M, Zou H. An immobilized titanium (IV) ion affinity chromatography adsorbent for solid phase extraction of phosphopeptides for phosphoproteome analysis. J Chromatogr A 2017; 1498:22-28. [DOI: 10.1016/j.chroma.2017.03.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
|
20
|
Schummer A, Fischer S, Oeljeklaus S, Warscheid B. Study of Peroxisomal Protein Phosphorylation by Functional Proteomics. Methods Mol Biol 2017; 1595:267-289. [PMID: 28409471 DOI: 10.1007/978-1-4939-6937-1_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Reversible protein phosphorylation is a frequently occurring posttranslational modification mediated by protein kinases and phosphatases that plays an essential role in the regulation of a large number of cellular processes. Evidence is accumulating that protein phosphorylation is also an important mechanism governing processes associated with peroxisome biology. For an improved and detailed understanding of these processes and their regulation it is therefore crucial to study phosphorylation of peroxisome-associated proteins and to determine the phosphorylated amino acid(s). To place peroxisome-related processes into a larger, cellular context, it is further required to identify the kinases and phosphatases catalyzing phosphorylation and dephosphorylation events in peroxisomal proteins. We here provide a strategy for the targeted analysis of peroxisomal phosphoproteins of Saccharomyces cerevisiae combining affinity purification of epitope-tagged peroxisomal proteins with Phos-tag SDS-PAGE and high-resolution mass spectrometry (MS) for the identification and precise localization of in vivo phosphosites. Furthermore, we describe a protocol for an MS-based in vitro kinase assay using recombinant peroxisomal proteins and a selected kinase facilitating the site-resolved analysis of kinase-substrate relationships.
Collapse
Affiliation(s)
- Andreas Schummer
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Sven Fischer
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany.
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
| |
Collapse
|
21
|
Borisova ME, Wagner SA, Beli P. Mass Spectrometry-Based Proteomics for Quantifying DNA Damage-Induced Phosphorylation. Methods Mol Biol 2017; 1599:215-227. [PMID: 28477122 DOI: 10.1007/978-1-4939-6955-5_16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein phosphorylation plays central regulatory roles in DNA damage repair and signaling. Protein kinases of the phosphatidylinositol 3-kinase-related kinase family ATM, ATR, and DNA-PKcs mediate phosphorylation of hundreds of substrates after DNA damage and thereby orchestrate the cellular response to DNA damage. Protein phosphorylation can be studied using antibodies that specifically recognize phosphorylated protein species; however, this approach is limited by existing antibodies and does not permit unbiased discovery of phosphorylation sites or analyzing phosphorylation sites in a high-throughput manner. Mass spectrometry (MS)-based proteomics has emerged as a powerful method for identification of phosphorylation sites on individual proteins and proteome-wide. To identify phosphorylation sites, proteins are digested into peptides and phosphopeptides are enriched using titanium dioxide (TiO2)-based chromatography followed by the identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Quantitative proteomics approaches, such as stable isotope labeling with amino acids in cell culture (SILAC), enable relative quantification of phosphopeptide abundance in different conditions. Here, we describe a streamlined protocol for enrichment of phosphopeptides using TiO2-based chromatography, and outline the application of quantitative phosphoproteomics for the identification of DNA damage-induced phosphorylation and substrates of kinases functioning after DNA damage.
Collapse
Affiliation(s)
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
| |
Collapse
|
22
|
Ruprecht B, Koch H, Domasinska P, Frejno M, Kuster B, Lemeer S. Optimized Enrichment of Phosphoproteomes by Fe-IMAC Column Chromatography. Methods Mol Biol 2017; 1550:47-60. [PMID: 28188522 DOI: 10.1007/978-1-4939-6747-6_5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Phosphorylation is among the most important post-translational modifications of proteins and has numerous regulatory functions across all domains of life. However, phosphorylation is often substoichiometric, requiring selective and sensitive methods to enrich phosphorylated peptides from complex cellular digests. Various methods have been devised for this purpose and we have recently described a Fe-IMAC HPLC column chromatography setup which is capable of comprehensive, reproducible, and selective enrichment of phosphopeptides out of complex peptide mixtures. In contrast to other formats such as StageTips or batch incubations using TiO2 or Ti-IMAC beads, Fe-IMAC HPLC columns do not suffer from issues regarding incomplete phosphopeptide binding or elution and enrichment efficiency scales linearly with the amount of starting material. Here, we provide a step-by-step protocol for the entire phosphopeptide enrichment procedure including sample preparation (lysis, digestion, desalting), Fe-IMAC column chromatography (column setup, operation, charging), measurement by LC-MS/MS (nHPLC gradient, MS parameters) and data analysis (MaxQuant). To increase throughput, we have optimized several key steps such as the gradient time of the Fe-IMAC separation (15 min per enrichment), the number of consecutive enrichments possible between two chargings (>20) and the column recharging itself (<1 h). We show that the application of this protocol enables the selective (>90 %) identification of more than 10,000 unique phosphopeptides from 1 mg of HeLa digest within 2 h of measurement time (Q Exactive Plus).
Collapse
Affiliation(s)
- Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany
- Center for Integrated Protein Science Munich (CIPSM), Freising, Germany
| | - Heiner Koch
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Petra Domasinska
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Faculty of Chemical Technology, Department of Biological and Biochemical Sciences, University of Pardubice, Pardubice, Czech Republic
| | - Martin Frejno
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany
- Department of Oncology, University of Oxford, Oxford, UK
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany.
- Center for Integrated Protein Science Munich (CIPSM), Freising, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Biomolecular Mass Spectrometry Center, Technische Universität München, Freising, Germany.
| | - Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany
- Center for Integrated Protein Science Munich (CIPSM), Freising, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
23
|
Robinson MR, Brodbelt JS. Integrating Weak Anion Exchange and Ultraviolet Photodissociation Mass Spectrometry with Strategic Modulation of Peptide Basicity for the Enrichment of Sulfopeptides. Anal Chem 2016; 88:11037-11045. [PMID: 27768275 DOI: 10.1021/acs.analchem.6b02899] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Tyrosine sulfation is an important post-translational modification but remains difficult to detect in biological samples owing to its low stoichiometric abundance and the lack of effective enrichment methods. In the present study, weak anion exchange (WAX) is evaluated for the enrichment of sulfopeptides that have been modified via carbamylation to convert all primary amines to less basic carbamates. The decrease in basicity enhanced the binding of carbamylated sulfopeptides to WAX resin relative to nonsulfated peptides. Upon elution and electrospray ionization in the negative mode, ultraviolet photodissociation (UVPD) was applied for peptide sequencing. Application of the method to a tryptic digest of bovine coagulation factor V resulted in identification of sulfation on tyrosine 1513.
Collapse
Affiliation(s)
- Michelle R Robinson
- Department of Chemistry, The University of Texas , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas , Austin, Texas 78712, United States
| |
Collapse
|
24
|
Tyanova S, Temu T, Cox J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc 2016; 11:2301-2319. [PMID: 27809316 DOI: 10.1038/nprot.2016.136] [Citation(s) in RCA: 2659] [Impact Index Per Article: 332.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
MaxQuant is one of the most frequently used platforms for mass-spectrometry (MS)-based proteomics data analysis. Since its first release in 2008, it has grown substantially in functionality and can be used in conjunction with more MS platforms. Here we present an updated protocol covering the most important basic computational workflows, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques. This protocol presents a complete description of the parameters used in MaxQuant, as well as of the configuration options of its integrated search engine, Andromeda. This protocol update describes an adaptation of an existing protocol that substantially modifies the technique. Important concepts of shotgun proteomics and their implementation in MaxQuant are briefly reviewed, including different quantification strategies and the control of false-discovery rates (FDRs), as well as the analysis of post-translational modifications (PTMs). The MaxQuant output tables, which contain information about quantification of proteins and PTMs, are explained in detail. Furthermore, we provide a short version of the workflow that is applicable to data sets with simple and standard experimental designs. The MaxQuant algorithms are efficiently parallelized on multiple processors and scale well from desktop computers to servers with many cores. The software is written in C# and is freely available at http://www.maxquant.org.
Collapse
Affiliation(s)
- Stefka Tyanova
- Computational Systems Biochemistry, Max-Planck Institute for Biochemistry, Martinsried, Germany
| | - Tikira Temu
- Computational Systems Biochemistry, Max-Planck Institute for Biochemistry, Martinsried, Germany
| | - Juergen Cox
- Computational Systems Biochemistry, Max-Planck Institute for Biochemistry, Martinsried, Germany
| |
Collapse
|
25
|
Jiang L, Huang T, Feng S, Wang J. Zirconium(IV) functionalized magnetic nanocomposites for extraction of organophosphorus pesticides from environmental water samples. J Chromatogr A 2016; 1456:49-57. [DOI: 10.1016/j.chroma.2016.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/30/2016] [Accepted: 06/02/2016] [Indexed: 11/17/2022]
|
26
|
von Stechow L, Francavilla C, Olsen JV. Recent findings and technological advances in phosphoproteomics for cells and tissues. Expert Rev Proteomics 2016; 12:469-87. [PMID: 26400465 PMCID: PMC4819829 DOI: 10.1586/14789450.2015.1078730] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Site-specific phosphorylation is a fast and reversible covalent post-translational modification that is tightly regulated in cells. The cellular machinery of enzymes that write, erase and read these modifications (kinases, phosphatases and phospho-binding proteins) is frequently deregulated in different diseases, including cancer. Large-scale studies of phosphoproteins – termed phosphoproteomics – strongly rely on the use of high-performance mass spectrometric instrumentation. This powerful technology has been applied to study a great number of phosphorylation-based phenotypes. Nevertheless, many technical and biological challenges have to be overcome to identify biologically relevant phosphorylation sites in cells and tissues. This review describes different technological strategies to identify and quantify phosphorylation sites with high accuracy, without significant loss of analysis speed and reproducibility in tissues and cells. Moreover, computational tools for analysis, integration and biological interpretation of phosphorylation events are discussed.
Collapse
Affiliation(s)
- Louise von Stechow
- a Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Chiara Francavilla
- a Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | | |
Collapse
|
27
|
Batalha IL, Zhou H, Lilley K, Lowe CR, Roque ACA. Mimicking nature: Phosphopeptide enrichment using combinatorial libraries of affinity ligands. J Chromatogr A 2016; 1457:76-87. [PMID: 27345211 DOI: 10.1016/j.chroma.2016.06.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 12/11/2022]
Abstract
Phosphorylation is a reversible post-translational modification of proteins that controls a plethora of cellular processes and triggers specific physiological responses, for which there is a need to develop tools to characterize phosphorylated targets efficiently. Here, a combinatorial library of triazine-based synthetic ligands comprising 64 small molecules has been rationally designed, synthesized and screened for the enrichment of phosphorylated peptides. The lead candidate (coined A8A3), composed of histidine and phenylalanine mimetic components, showed high binding capacity and selectivity for binding mono- and multi-phosphorylated peptides at pH 3. Ligand A8A3 was coupled onto both cross-linked agarose and magnetic nanoparticles, presenting higher binding capacities (100-fold higher) when immobilized on the magnetic support. The magnetic adsorbent was further screened against a tryptic digest of two phosphorylated proteins (α- and β-caseins) and one non-phosphorylated protein (bovine serum albumin, BSA). The MALDI-TOF mass spectra of the eluted peptides allowed the identification of nine phosphopeptides, comprising both mono- and multi-phosphorylated peptides.
Collapse
Affiliation(s)
- Iris L Batalha
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Houjiang Zhou
- Cambridge Centre for Proteomics, Cambridge, CB2 1QR, UK
| | | | - Christopher R Lowe
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, CB2 1QT, Cambridge, UK
| | - Ana C A Roque
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| |
Collapse
|
28
|
Ruprecht B, Roesli C, Lemeer S, Kuster B. MALDI-TOF and nESI Orbitrap MS/MS identify orthogonal parts of the phosphoproteome. Proteomics 2016; 16:1447-56. [PMID: 26990019 DOI: 10.1002/pmic.201500523] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/02/2016] [Accepted: 03/11/2016] [Indexed: 01/01/2023]
Abstract
Phosphorylation is a reversible posttranslational protein modification which plays a pivotal role in intracellular signaling. Despite extensive efforts, phosphorylation site mapping of proteomes is still incomplete motivating the exploration of alternative methods that complement existing workflows. In this study, we compared tandem mass spectrometry (MS/MS) on matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) and nano-electrospray ionization (nESI) Orbitrap instruments with respect to their ability to identify phosphopeptides from complex proteome digests. Phosphopeptides were enriched from tryptic digests of cell lines using Fe-IMAC column chromatography and subjected to LC-MS/MS analysis. We found that the two analytical workflows exhibited considerable orthogonality. For instance, MALDI-TOF MS/MS favored the identification of phosphopeptides encompassing clear motif signatures for acidic residue directed kinases. The extent of orthogonality of the two LC-MS/MS systems was comparable to that of using alternative proteases such as Asp-N, Arg-C, chymotrypsin, Glu-C and Lys-C on just one LC-MS/MS instrument. Notably, MALDI-TOF MS/MS identified an unexpectedly high number and percentage of phosphotyrosine sites (∼20% of all sites), possibly as a direct consequence of more efficient ionization. The data clearly show that LC-MALDI MS/MS can be a useful complement to LC-nESI MS/MS for phosphoproteome mapping and particularly so for acidic and phosphotyrosine containing peptides.
Collapse
Affiliation(s)
- Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany.,Center for Protein Science Munich (CIPSM), Freising, Germany
| | - Christoph Roesli
- HI-STEM - Heidelberg, Institute for Stem Cell Technology and Experimental Medicine gemeinnützige GmbH, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany.,Center for Protein Science Munich (CIPSM), Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany.,Center for Protein Science Munich (CIPSM), Freising, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Bavarian Biomolecular Mass Spectrometry Center, Technische Universität München, Freising, Germany
| |
Collapse
|
29
|
de Keijzer J, Mulder A, de Beer J, de Ru AH, van Veelen PA, van Soolingen D. Mechanisms of Phenotypic Rifampicin Tolerance in Mycobacterium tuberculosis Beijing Genotype Strain B0/W148 Revealed by Proteomics. J Proteome Res 2016; 15:1194-204. [PMID: 26930559 DOI: 10.1021/acs.jproteome.5b01073] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The "successful" Russian clone B0/W148 of Mycobacterium tuberculosis Beijing is well-known for its capacity to develop antibiotic resistance. During treatment, resistant mutants can occur that have inheritable resistance to specific antibiotics. Next to mutations, M. tuberculosis has several mechanisms that increase their tolerance to a variety of antibiotics. Insights in the phenotypic mechanisms that contribute to drug tolerance will increase our understanding of how antibiotic resistance develops in M. tuberculosis. In this study, we examined the (phospho)proteome dynamics in M. tuberculosis Beijing strain B0/W148 when exposed to a high dose of rifampicin; one of the most potent first-line antibiotics. A total of 2,534 proteins and 191 phosphorylation sites were identified, and revealed the differential regulation of DosR regulon proteins, which are necessary for the development of a dormant phenotype that is less susceptible to antibiotics. By examining independent phenotypic markers of dormancy, we show that persisters of in vitro rifampicin exposure entered a metabolically hypoactive state, which yields rifampicin and other antibiotics largely ineffective. These new insights in the role of protein regulation and post-translational modifications during the initial phase of rifampicin treatment reveal a shortcoming in the antituberculosis regimen that is administered to 8-9 million individuals annually.
Collapse
Affiliation(s)
- Jeroen de Keijzer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC) , Leiden 2300 RC, The Netherlands
| | - Arnout Mulder
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM) , Bilthoven 3720 BA, The Netherlands
| | - Jessica de Beer
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM) , Bilthoven 3720 BA, The Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC) , Leiden 2300 RC, The Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC) , Leiden 2300 RC, The Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM) , Bilthoven 3720 BA, The Netherlands.,Departments of Pulmonary Diseases and Medical Microbiology, Radboud University Medical Center , Nijmegen 6500 HB, The Netherlands
| |
Collapse
|
30
|
Ding L, Yang R, Yang G, Cao J, Li P, Zhou Y. Identification of putative phosphoproteins in wheat spikes induced by Fusarium graminearum. PLANTA 2016; 243:719-31. [PMID: 26669597 PMCID: PMC4757628 DOI: 10.1007/s00425-015-2441-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/03/2015] [Indexed: 05/10/2023]
Abstract
Phosphorylation and dephosphorylation events were initiated in wheat scab resistance. The putative FHB-responsive phosphoproteins are mainly involved in three functional groups and contain at least one tyrosine, serine, or threonine phosphorylation site. Fusarium head blight (FHB), caused by Fusarium graminearum, is a severe disease in wheat. Protein phosphorylation plays an important role in plant-pathogen interactions, however, a global analysis of protein phosphorylation in response to FHB infection remains to be explored. To study the effect of FHB on the phosphorylation state of wheat proteins, proteins extracted from spikes of a resistant wheat cultivar after 6 h of inoculation with F. graminearum or sterile H2O were separated by two-dimensional gel electrophoresis, and then the immunodetection of putative phosphoproteins was conducted by Western blotting using specific anti-phosphotyrosine antibody, anti-phosphothreonine antibody and anti-phosphoserine antibody. A total of 35 phosphorylated signals was detected and protein identities of 28 spots were determined. Functional categorization showed that the putative FHB-responsive phosphoproteins were mainly involved in defense/stress response, signal transduction, and metabolism. The phosphorylation status of proteins associated with signaling pathways mediated by salicylic acid, calcium ions, small GTPase, as well as with detoxification, reactive oxygen species scavenging, antimicrobial compound synthesis, and cell wall fortification was regulated in wheat spikes in response to F. graminearum infection. The present study reveals dynamics of wheat phosphoproteome in response to F. graminearum infection and suggests an important role of protein Ser/Thr/Tyr phosphorylation in fundamental mechanisms of wheat scab resistance.
Collapse
Affiliation(s)
- Lina Ding
- College of Life Sciences, Jiangsu University, Zhenjiang, 212013, China.
| | - Ruiying Yang
- Laboratory Middle School, Juancheng, 274600, Shandong, China
| | - Guoxing Yang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Cao
- College of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Peng Li
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Yang Zhou
- College of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| |
Collapse
|
31
|
Zhai R, Tian F, Xue R, Jiao F, Hao F, Zhang Y, Qian X. Metal ion-immobilized magnetic nanoparticles for global enrichment and identification of phosphopeptides by mass spectrometry. RSC Adv 2016. [DOI: 10.1039/c5ra22006h] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Highly selective and sensitive enrichment for global phosphopeptides by novel magnetic nanoparticles Fe3O4@TCPP-DOTA-Ms.
Collapse
Affiliation(s)
- Rui Zhai
- College of Life Science and Bio-Engineering
- Beijing University of Technology
- Beijing 100022
- China
- State Key Laboratory of Proteomics
| | - Fang Tian
- State Key Laboratory of Proteomics
- Beijing Proteome Research Center, Beijing
- Institute of Radiation Medicine
- Beijing 102206
- China
| | - Ruiqing Xue
- State Key Laboratory of Proteomics
- Beijing Proteome Research Center, Beijing
- Institute of Radiation Medicine
- Beijing 102206
- China
| | - Fenglong Jiao
- State Key Laboratory of Proteomics
- Beijing Proteome Research Center, Beijing
- Institute of Radiation Medicine
- Beijing 102206
- China
| | - Feiran Hao
- State Key Laboratory of Proteomics
- Beijing Proteome Research Center, Beijing
- Institute of Radiation Medicine
- Beijing 102206
- China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics
- Beijing Proteome Research Center, Beijing
- Institute of Radiation Medicine
- Beijing 102206
- China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics
- Beijing Proteome Research Center, Beijing
- Institute of Radiation Medicine
- Beijing 102206
- China
| |
Collapse
|
32
|
Fast and easy phosphopeptide fractionation by combinatorial ERLIC-SCX solid-phase extraction for in-depth phosphoproteome analysis. Nat Protoc 2015; 11:37-45. [DOI: 10.1038/nprot.2015.134] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
33
|
Raaijmakers LM, Giansanti P, Possik PA, Mueller J, Peeper DS, Heck AJR, Altelaar AFM. PhosphoPath: Visualization of Phosphosite-centric Dynamics in Temporal Molecular Networks. J Proteome Res 2015; 14:4332-41. [DOI: 10.1021/acs.jproteome.5b00529] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Linsey M. Raaijmakers
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Piero Giansanti
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Patricia A. Possik
- Division
of Molecular Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Judith Mueller
- Division
of Molecular Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Daniel S. Peeper
- Division
of Molecular Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - A. F. Maarten Altelaar
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
34
|
Herring LE, Grant KG, Blackburn K, Haugh JM, Goshe MB. Development of a tandem affinity phosphoproteomic method with motif selectivity and its application in analysis of signal transduction networks. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 988:166-74. [PMID: 25777480 PMCID: PMC4489695 DOI: 10.1016/j.jchromb.2015.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/02/2015] [Accepted: 02/07/2015] [Indexed: 11/26/2022]
Abstract
Phosphorylation is an important post-translational modification that is involved in regulating many signaling pathways. Of particular interest are the growth factor mediated Ras and phosphoinositide 3-kinase (PI3K) signaling pathways which, if misregulated, can contribute to the progression of cancer. Phosphoproteomic methods have been developed to study regulation of signaling pathways; however, due to the low stoichiometry of phosphorylation, understanding these pathways is still a challenge. In this study, we have developed a multi-dimensional method incorporating electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) with tandem IMAC/TiO2 enrichment for subsequent phosphopeptide identification by LC/MS/MS. We applied this method to PDGF-stimulated NIH 3T3 cells to provide over 11,000 unique phosphopeptide identifications. Upon motif analysis, IMAC was found to enrich for basophilic kinase substrates while the subsequent TiO2 step enriched for acidophilic kinase substrates, suggesting that both enrichment methods are necessary to capture the full complement of kinase substrates. Biological functions that were over-represented at each PDGF stimulation time point, together with the phosphorylation dynamics of several phosphopeptides containing known kinase phosphorylation sites, illustrate the feasibility of this approach in quantitative phosphoproteomic studies.
Collapse
Affiliation(s)
- Laura E Herring
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, United States
| | - Kyle G Grant
- Gene Therapy Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-73522, United States
| | - Kevin Blackburn
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, United States
| | - Jason M Haugh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, United States
| | - Michael B Goshe
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, United States.
| |
Collapse
|
35
|
Doll S, Burlingame AL. Mass spectrometry-based detection and assignment of protein posttranslational modifications. ACS Chem Biol 2015; 10:63-71. [PMID: 25541750 PMCID: PMC4301092 DOI: 10.1021/cb500904b] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Recent
advances in mass spectrometry (MS)-based proteomics allow
the identification and quantitation of thousands of posttranslational
modification (PTM) sites in a single experiment. This follows from
the development of more effective class enrichment strategies, new
high performance instrumentation and bioinformatic algorithms with
rigorous scoring strategies. More widespread use of these combined
capabilities have led to a vast expansion in our knowledge of the
complexity of biological processes mediated by PTMs. The classes most
actively pursued include phosphorylation, ubiquitination, O-GlcNAcylation,
methylation, and acetylation. Very recently succinylation, SUMOylation,
and citrullination have emerged. Among the some 260 000 PTM
sites that have been identified in the human proteome thus far, only
a few have been assigned to key regulatory and/or other biological
roles. Here, we provide an update of MS-based PTM analyses, with a
focus on current enrichment strategies coupled with revolutionary
advances in high performance MS. Furthermore, we discuss examples
of the discovery of recently described biological roles of PTMs and
address the challenges of defining site-specific functions.
Collapse
Affiliation(s)
- Sophia Doll
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, United States
- Department
of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Alma L. Burlingame
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, United States
| |
Collapse
|
36
|
Iliuk AB, Arrington JV, Tao WA. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis 2014; 35:3430-40. [PMID: 24890697 PMCID: PMC4250476 DOI: 10.1002/elps.201400153] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022]
Abstract
Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine.
Collapse
Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Weiguo Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
37
|
Ruprecht B, Koch H, Medard G, Mundt M, Kuster B, Lemeer S. Comprehensive and reproducible phosphopeptide enrichment using iron immobilized metal ion affinity chromatography (Fe-IMAC) columns. Mol Cell Proteomics 2014; 14:205-15. [PMID: 25394399 DOI: 10.1074/mcp.m114.043109] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Advances in phosphopeptide enrichment methods enable the identification of thousands of phosphopeptides from complex samples. Current offline enrichment approaches using TiO(2), Ti, and Fe immobilized metal ion affinity chromatography (IMAC) material in batch or microtip format are widely used, but they suffer from irreproducibility and compromised selectivity. To address these shortcomings, we revisited the merits of performing phosphopeptide enrichment in an HPLC column format. We found that Fe-IMAC columns enabled the selective, comprehensive, and reproducible enrichment of phosphopeptides out of complex lysates. Column enrichment did not suffer from bead-to-sample ratio issues and scaled linearly from 100 μg to 5 mg of digest. Direct measurements on an Orbitrap Velos mass spectrometer identified >7500 unique phosphopeptides with 90% selectivity and good quantitative reproducibility (median cv of 15%). The number of unique phosphopeptides could be increased to more than 14,000 when the IMAC eluate was subjected to a subsequent hydrophilic strong anion exchange separation. Fe-IMAC columns outperformed Ti-IMAC and TiO(2) in batch or tip mode in terms of phosphopeptide identification and intensity. Permutation enrichments of flow-throughs showed that all materials largely bound the same phosphopeptide species, independent of physicochemical characteristics. However, binding capacity and elution efficiency did profoundly differ among the enrichment materials and formats. As a result, the often quoted orthogonality of the materials has to be called into question. Our results strongly suggest that insufficient capacity, inefficient elution, and the stochastic nature of data-dependent acquisition in mass spectrometry are the causes of the experimentally observed complementarity. The Fe-IMAC enrichment workflow using an HPLC format developed here enables rapid and comprehensive phosphoproteome analysis that can be applied to a wide range of biological systems.
Collapse
Affiliation(s)
- Benjamin Ruprecht
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany, ¶ Center for Integrated Protein Science Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Heiner Koch
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Guillaume Medard
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Max Mundt
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Bernhard Kuster
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany, ¶ Center for Integrated Protein Science Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Simone Lemeer
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany, ¶ Center for Integrated Protein Science Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| |
Collapse
|
38
|
Tape C, Worboys JD, Sinclair J, Gourlay R, Vogt J, McMahon KM, Trost M, Lauffenburger DA, Lamont DJ, Jørgensen C. Reproducible automated phosphopeptide enrichment using magnetic TiO2 and Ti-IMAC. Anal Chem 2014; 86:10296-302. [PMID: 25233145 PMCID: PMC4206527 DOI: 10.1021/ac5025842] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 09/18/2014] [Indexed: 12/28/2022]
Abstract
Reproducible, comprehensive phosphopeptide enrichment is essential for studying phosphorylation-regulated processes. Here, we describe the application of hyper-porous magnetic TiO2 and Ti-IMAC microspheres for uniform automated phosphopeptide enrichment. Combining magnetic microspheres with a magnetic particle-handling robot enables rapid (45 min), reproducible (r2 ≥ 0.80) and high-fidelity (>90% purity) phosphopeptide purification in a 96-well format. Automated phosphopeptide enrichment demonstrates reproducible synthetic phosphopeptide recovery across 2 orders of magnitude, "well-to-well" quantitative reproducibility indistinguishable to internal SILAC standards, and robust "plate-to-plate" reproducibility across 5 days of independent enrichments. As a result, automated phosphopeptide enrichment enables statistical analysis of label-free phosphoproteomic samples in a high-throughput manner. This technique uses commercially available, off-the-shelf components and can be easily adopted by any laboratory interested in phosphoproteomic analysis. We provide a free downloadable automated phosphopeptide enrichment program to facilitate uniform interlaboratory collaboration and exchange of phosphoproteomic data sets.
Collapse
Affiliation(s)
- Christopher
J. Tape
- The
Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jonathan D. Worboys
- The
Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
| | - John Sinclair
- The
Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
| | - Robert Gourlay
- FingerPrints
Proteomics Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Janis Vogt
- FingerPrints
Proteomics Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Kelly M. McMahon
- Cancer
Research UK Manchester Institute, The University
of Manchester, Wilmslow
Road, Manchester M20 4BX, United Kingdom
| | - Matthias Trost
- FingerPrints
Proteomics Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Douglas A. Lauffenburger
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Douglas J. Lamont
- FingerPrints
Proteomics Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Claus Jørgensen
- The
Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
- Cancer
Research UK Manchester Institute, The University
of Manchester, Wilmslow
Road, Manchester M20 4BX, United Kingdom
| |
Collapse
|
39
|
Sharma K, D'Souza RCJ, Tyanova S, Schaab C, Wiśniewski JR, Cox J, Mann M. Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. Cell Rep 2014; 8:1583-94. [PMID: 25159151 DOI: 10.1016/j.celrep.2014.07.036] [Citation(s) in RCA: 706] [Impact Index Per Article: 70.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 05/30/2014] [Accepted: 07/22/2014] [Indexed: 11/17/2022] Open
Abstract
Regulatory protein phosphorylation controls normal and pathophysiological signaling in eukaryotic cells. Despite great advances in mass-spectrometry-based proteomics, the extent, localization, and site-specific stoichiometry of this posttranslational modification (PTM) are unknown. Here, we develop a stringent experimental and computational workflow, capable of mapping more than 50,000 distinct phosphorylated peptides in a single human cancer cell line. We detected more than three-quarters of cellular proteins as phosphoproteins and determined very high stoichiometries in mitosis or growth factor signaling by label-free quantitation. The proportion of phospho-Tyr drastically decreases as coverage of the phosphoproteome increases, whereas Ser/Thr sites saturate only for technical reasons. Tyrosine phosphorylation is maintained at especially low stoichiometric levels in the absence of specific signaling events. Unexpectedly, it is enriched on higher-abundance proteins, and this correlates with the substrate KM values of tyrosine kinases. Our data suggest that P-Tyr should be considered a functionally separate PTM of eukaryotic proteomes.
Collapse
Affiliation(s)
- Kirti Sharma
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Rochelle C J D'Souza
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Stefka Tyanova
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christoph Schaab
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Jacek R Wiśniewski
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| |
Collapse
|
40
|
Matheron L, van den Toorn H, Heck AJR, Mohammed S. Characterization of Biases in Phosphopeptide Enrichment by Ti4+-Immobilized Metal Affinity Chromatography and TiO2 Using a Massive Synthetic Library and Human Cell Digests. Anal Chem 2014; 86:8312-20. [DOI: 10.1021/ac501803z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Lucrece Matheron
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences and The
Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Henk van den Toorn
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences and The
Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences and The
Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences and The
Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, OX1 3TA, Oxford, United Kingdom
- Department
of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, United Kingdom
| |
Collapse
|
41
|
de Graaf EL, Kaplon J, Zhou H, Heck AJR, Peeper DS, Altelaar AFM. Phosphoproteome dynamics in onset and maintenance of oncogene-induced senescence. Mol Cell Proteomics 2014; 13:2089-100. [PMID: 24961811 DOI: 10.1074/mcp.m113.035436] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression of the BRAF(V600E) oncoprotein is known to cause benign lesions, such as melanocytic nevi (moles). Despite the oncogenic function of mutant BRAF, these lesions are arrested by a cell-autonomous mechanism called oncogene-induced senescence. Infrequently, nevi can progress to malignant melanoma, through mechanisms that are incompletely understood. To gain more insight into this vital tumor-suppression mechanism, we performed a mass-spectrometry-based screening of the proteome and phosphoproteome in cycling and senescent cells and in cells with abrogated senescence. Proteome analysis of senescent cells revealed the up-regulation of established senescence biomarkers, including specific cytokines, but also several proteins not previously associated with senescence, including extracellular matrix-interacting. Using both general and targeted phosphopeptide enrichment by Ti(4+)-IMAC and phosphotyrosine antibody enrichment, we identified over 15,000 phosphorylation sites. Among the regulated phosphorylation sites we encountered components of the interleukin, BRAF/MAPK, and CDK-retinoblastoma pathways and several other factors. The extensive proteome and phosphoproteome dataset of BRAF(V600E)-expressing senescent cells provides molecular clues as to how oncogene-induced senescence is initiated, maintained, or evaded, serving as a comprehensive proteomic basis for functional validation.
Collapse
Affiliation(s)
- Erik L de Graaf
- From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands; ¶Center for Biomedical Genetics, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Joanna Kaplon
- ‖Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Houjiang Zhou
- From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands; ¶Center for Biomedical Genetics, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Daniel S Peeper
- ‖Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - A F Maarten Altelaar
- From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| |
Collapse
|
42
|
Iesmantavicius V, Weinert BT, Choudhary C. Convergence of ubiquitylation and phosphorylation signaling in rapamycin-treated yeast cells. Mol Cell Proteomics 2014; 13:1979-92. [PMID: 24961812 PMCID: PMC4125731 DOI: 10.1074/mcp.o113.035683] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The target of rapamycin (TOR) kinase senses the availability of nutrients and coordinates cellular growth and proliferation with nutrient abundance. Inhibition of TOR mimics nutrient starvation and leads to the reorganization of many cellular processes, including autophagy, protein translation, and vesicle trafficking. TOR regulates cellular physiology by modulating phosphorylation and ubiquitylation signaling networks; however, the global scope of such regulation is not fully known. Here, we used a mass-spectrometry-based proteomics approach for the parallel quantification of ubiquitylation, phosphorylation, and proteome changes in rapamycin-treated yeast cells. Our data constitute a detailed proteomic analysis of rapamycin-treated yeast with 3590 proteins, 8961 phosphorylation sites, and 2299 di-Gly modified lysines (putative ubiquitylation sites) quantified. The phosphoproteome was extensively modulated by rapamycin treatment, with more than 900 up-regulated sites one hour after rapamycin treatment. Dynamically regulated phosphoproteins were involved in diverse cellular processes, prominently including transcription, membrane organization, vesicle-mediated transport, and autophagy. Several hundred ubiquitylation sites were increased after rapamycin treatment, and about half as many decreased in abundance. We found that proteome, phosphorylation, and ubiquitylation changes converged on the Rsp5-ubiquitin ligase, Rsp5 adaptor proteins, and Rsp5 targets. Putative Rsp5 targets were biased for increased ubiquitylation, suggesting activation of Rsp5 by rapamycin. Rsp5 adaptor proteins, which recruit target proteins for Rsp5-dependent ubiquitylation, were biased for increased phosphorylation. Furthermore, we found that permeases and transporters, which are often ubiquitylated by Rsp5, were biased for reduced ubiquitylation and reduced protein abundance. The convergence of multiple proteome-level changes on the Rsp5 system indicates a key role of this pathway in the response to rapamycin treatment. Collectively, these data reveal new insights into the global proteome dynamics in response to rapamycin treatment and provide a first detailed view of the co-regulation of phosphorylation- and ubiquitylation-dependent signaling networks by this compound.
Collapse
Affiliation(s)
- Vytautas Iesmantavicius
- From the ‡Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Brian T Weinert
- From the ‡Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Chunaram Choudhary
- From the ‡Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| |
Collapse
|
43
|
de Graaf EL, Giansanti P, Altelaar AFM, Heck AJR. Single-step enrichment by Ti4+-IMAC and label-free quantitation enables in-depth monitoring of phosphorylation dynamics with high reproducibility and temporal resolution. Mol Cell Proteomics 2014; 13:2426-34. [PMID: 24850871 DOI: 10.1074/mcp.o113.036608] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Quantitative phosphoproteomics workflows traditionally involve additional sample labeling and fractionation steps for accurate and in-depth analysis. Here we report a high-throughput, straightforward, and comprehensive label-free phosphoproteomics approach using the highly selective, reproducible, and sensitive Ti(4+)-IMAC phosphopeptide enrichment method. We demonstrate the applicability of this approach by monitoring the phosphoproteome dynamics of Jurkat T cells stimulated by prostaglandin E2 (PGE2) over six different time points, measuring in total 108 snapshots of the phosphoproteome. In total, we quantitatively monitored 12,799 unique phosphosites over all time points with very high quantitative reproducibility (average r > 0.9 over 100 measurements and a median cv < 0.2). PGE2 is known to increase cellular cAMP levels, thereby activating PKA. The in-depth analysis revealed temporal regulation of a wide variety of phosphosites associated not only with PKA, but also with a variety of other classes of kinases. Following PGE2 stimulation, several pathways became only transiently activated, revealing that in-depth dynamic profiling requires techniques with high temporal resolution. Moreover, the large publicly available dataset provides a valuable resource for downstream PGE2 signaling dynamics in T cells, and cAMP-mediated signaling in particular. More generally, our method enables in-depth, quantitative, high-throughput phosphoproteome screening on any system, requiring very little sample, sample preparation, and analysis time.
Collapse
Affiliation(s)
- Erik L de Graaf
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Piero Giansanti
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - A F Maarten Altelaar
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
44
|
Mann K, Edsinger E. The Lottia gigantea shell matrix proteome: re-analysis including MaxQuant iBAQ quantitation and phosphoproteome analysis. Proteome Sci 2014; 12:28. [PMID: 25018669 PMCID: PMC4094399 DOI: 10.1186/1477-5956-12-28] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/01/2014] [Indexed: 12/29/2022] Open
Abstract
Background Although the importance of proteins of the biomineral organic matrix and their posttranslational modifications for biomineralization is generally recognized, the number of published matrix proteomes is still small. This is mostly due to the lack of comprehensive sequence databases, usually derived from genomic sequencing projects. However, in-depth mass spectrometry-based proteomic analysis, which critically depends on high-quality sequence databases, is a very fast tool to identify candidates for functional biomineral matrix proteins and their posttranslational modifications. Identification of such candidate proteins is facilitated by at least approximate quantitation of the identified proteins, because the most abundant ones may also be the most interesting candidates for further functional analysis. Results Re-quantification of previously identified Lottia shell matrix proteins using the intensity-based absolute quantification (iBAQ) method as implemented in the MaxQuant identification and quantitation software showed that only 57 of the 382 accepted identifications constituted 98% of the total identified matrix proteome. This group of proteins did not contain obvious intracellular proteins, such as cytoskeletal components or ribosomal proteins, invariably identified as minor components of high-throughput biomineral matrix proteomes. Fourteen of these major proteins were phosphorylated to a variable extent. All together we identified 52 phospho sites in 20 of the 382 accepted proteins with high confidence. Conclusions We show that iBAQ quantitation may be a useful tool to narrow down the group of functional biomineral matrix protein candidates for further research in cell biology, genetics or materials research. Knowledge of posttranslational modifications in these major proteins could be a valuable addition to previously published proteomes. This is true especially for phosphorylation, because this modification was already shown to modify mineralization processes in some instances.
Collapse
Affiliation(s)
- Karlheinz Mann
- Max-Planck-Institut für Biochemie, Abteilung Proteomics und Signaltransduktion, Am Klopferspitz 18, Martinsried D-82152, Germany
| | - Eric Edsinger
- Rokhsar Department, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA ; Present address: Brenner Unit, Okinawa institute of Science and Technology, 1919-0 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| |
Collapse
|
45
|
Francavilla C, Hekmat O, Blagoev B, Olsen JV. SILAC-based temporal phosphoproteomics. Methods Mol Biol 2014; 1188:125-48. [PMID: 25059609 DOI: 10.1007/978-1-4939-1142-4_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent years, thanks to advances in Mass Spectrometry (MS)-based quantitative proteomics, studies on signaling pathways have moved from a detailed description of individual components to system-wide analysis of entire signaling cascades, also providing spatio-temporal views of intracellular pathways. Quantitative proteomics that combines stable isotope labeling by amino acid in cell culture (SILAC) with enrichment strategies for post-translational modification-bearing peptides and high-performance tandem mass spectrometry represents a powerful and unbiased approach to monitor dynamic signaling events. Here we provide an optimized SILAC-based proteomic workflow to analyze temporal changes in phosphoproteomes, which involve a generic three step enrichment protocol for phosphopeptides. SILAC-labeled peptides from digested whole cell lysates are as a first step enriched for phosphorylated tyrosines by immunoaffinity and then further enriched for phosphorylated serine/threonine peptides by strong cation exchange in combination with titanium dioxide-beads chromatography. Analysis of enriched peptides on Orbitrap-based MS results in comprehensive and accurate reconstruction of temporal changes of signaling networks.
Collapse
Affiliation(s)
- Chiara Francavilla
- Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | | | | | | |
Collapse
|
46
|
Wakabayashi M, Yoshihara H, Masuda T, Tsukahara M, Sugiyama N, Ishihama Y. Phosphoproteome Analysis of Formalin-Fixed and Paraffin-Embedded Tissue Sections Mounted on Microscope Slides. J Proteome Res 2013; 13:915-24. [DOI: 10.1021/pr400960r] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Masaki Wakabayashi
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroki Yoshihara
- Institute
for Advanced Biosciences, Keio University, Daihoji, Tsuruoka, Yamagata 997-0017, Japan
| | - Takeshi Masuda
- Institute
for Advanced Biosciences, Keio University, Daihoji, Tsuruoka, Yamagata 997-0017, Japan
| | - Mai Tsukahara
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Institute
for Advanced Biosciences, Keio University, Daihoji, Tsuruoka, Yamagata 997-0017, Japan
| | - Yasushi Ishihama
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Institute
for Advanced Biosciences, Keio University, Daihoji, Tsuruoka, Yamagata 997-0017, Japan
| |
Collapse
|
47
|
Tsai CF, Hsu CC, Hung JN, Wang YT, Choong WK, Zeng MY, Lin PY, Hong RW, Sung TY, Chen YJ. Sequential Phosphoproteomic Enrichment through Complementary Metal-Directed Immobilized Metal Ion Affinity Chromatography. Anal Chem 2013; 86:685-93. [DOI: 10.1021/ac4031175] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Chia-Feng Tsai
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Jo-Nan Hung
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yi-Ting Wang
- Chemical Biology and Molecular Biophysics
Program, Taiwan International Graduate Program, Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical
Sciences, National Taiwan University, Taipei, Taiwan
| | - Wai-Kok Choong
- Institute
of Information Science, Academia Sinica, Taipei, Taiwan
| | - Ming-Yao Zeng
- Institute
of Chemistry and Biochemistry, National Chung Cheng University, Chia-yi
County, Taiwan
| | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ruo-Wei Hong
- Institute
of Chemistry and Biochemistry, National Chung Cheng University, Chia-yi
County, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, Taipei, Taiwan
| | - Yu-Ju Chen
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics
Program, Taiwan International Graduate Program, Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
48
|
Mayne J, Starr AE, Ning Z, Chen R, Chiang CK, Figeys D. Fine Tuning of Proteomic Technologies to Improve Biological Findings: Advancements in 2011–2013. Anal Chem 2013; 86:176-95. [DOI: 10.1021/ac403551f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Janice Mayne
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Zhibin Ning
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Rui Chen
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Cheng-Kang Chiang
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Daniel Figeys
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| |
Collapse
|
49
|
Olsen JV, Mann M. Status of large-scale analysis of post-translational modifications by mass spectrometry. Mol Cell Proteomics 2013; 12:3444-52. [PMID: 24187339 PMCID: PMC3861698 DOI: 10.1074/mcp.o113.034181] [Citation(s) in RCA: 419] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cellular function can be controlled through the gene expression program, but often protein post-translational modifications (PTMs) provide a more precise and elegant mechanism. Key functional roles of specific modification events—for instance, during the cell cycle—have been known for decades, but only in the past 10 years has mass-spectrometry-(MS)-based proteomics begun to reveal the true extent of the PTM universe. In this overview for the special PTM issue of Molecular and Cellular Proteomics, we take stock of where MS-based proteomics stands in the large-scale analysis of protein modifications. For many PTMs, including phosphorylation, ubiquitination, glycosylation, and acetylation, tens of thousands of sites can now be confidently identified and localized in the sequence of the protein. The quantification of PTM levels between different cellular states is likewise established, with label-free methods showing particular promise. It is also becoming possible to determine the absolute occupancy or stoichiometry of PTM sites on a large scale. Powerful software for the bioinformatic analysis of thousands of PTM sites has been developed. However, a complete inventory of sites has not been established for any PTM, and this situation will persist into the foreseeable future. Furthermore, although PTM coverage by MS-based methods is impressive, it still needs to be improved, especially in tissues and in clinically relevant systems. The central challenge for the field is to develop streamlined methods for determining biological functions for the myriad of modifications now known to exist.
Collapse
Affiliation(s)
- Jesper V Olsen
- Department of Proteomics, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | | |
Collapse
|
50
|
Peng M, Scholten A, Heck AJR, van Breukelen B. Identification of enriched PTM crosstalk motifs from large-scale experimental data sets. J Proteome Res 2013; 13:249-59. [PMID: 24087892 DOI: 10.1021/pr4005579] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Post-translational modifications (PTMs) play an important role in the regulation of protein function. Mass spectrometry based proteomics experiments nowadays identify tens of thousands of PTMs in a single experiment. A wealth of data has therefore become publically available. Evidently the biological function of each PTM is the key question to be addressed; however, such analyses focus primarily on single PTM events. This ignores the fact that PTMs may act in concert in the regulation of protein function, a process termed PTM crosstalk. Relatively little is known on the frequency and functional relevance of crosstalk between PTM sites. In a bioinformatics approach, we extracted PTMs occurring in proximity in the protein sequence from publically available databases. These PTMs and their flanking sequences were subjected to stringent motif searches, including a scoring for evolutionary conservation. Our unprejudiced approach was able to detect a respectable set of motifs, of which about half were described previously. Among these we could add many new proteins harboring these motifs. We extracted also several novel motifs, which through their widespread appearance and high conservation may pinpoint at previously nonannotated concerted PTM actions. By employing network analyses on these proteins, we propose putative functional roles for these novel motifs with two PTM sites in close proximity.
Collapse
Affiliation(s)
- Mao Peng
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | | | | |
Collapse
|