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Ogata K, Takagi S, Sugiyama N, Ishihama Y. Motif-Targeting Phosphoproteome Analysis of Cancer Cells for Profiling Kinase Inhibitors. Cancers (Basel) 2022; 15:cancers15010078. [PMID: 36612075 PMCID: PMC9817674 DOI: 10.3390/cancers15010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
We present a motif-targeting phosphoproteome analysis workflow utilizing in vitro kinase reaction to enrich a subset of peptides with specific primary sequence motifs. Phosphopeptides are enriched and dephosphorylated with alkaline phosphatase, followed by in vitro kinase reaction to phosphorylate substrate peptides with specific primary-sequence motifs. These phosphopeptides are enriched again, TMT-labeled, dephosphorylated to enhance MS-detectability, and analyzed by LC/MS/MS. We applied this approach to inhibitor-treated cancer cells, and successfully profiled the inhibitory spectra of multiple kinase inhibitors. We anticipate this approach will be applicable to target specific subsets of the phosphoproteome using the wide variety of available recombinant protein kinases.
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Danko K, Lukasheva E, Zhukov VA, Zgoda V, Frolov A. Detergent-Assisted Protein Digestion-On the Way to Avoid the Key Bottleneck of Shotgun Bottom-Up Proteomics. Int J Mol Sci 2022; 23:13903. [PMID: 36430380 PMCID: PMC9695859 DOI: 10.3390/ijms232213903] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 11/16/2022] Open
Abstract
Gel-free bottom-up shotgun proteomics is the principal methodological platform for the state-of-the-art proteome research. This methodology assumes quantitative isolation of the total protein fraction from a complex biological sample, its limited proteolysis with site-specific proteases, analysis of the resulted peptides with nanoscaled reversed-phase high-performance liquid chromatography-(tandem) mass spectrometry (nanoRP-HPLC-MS and MS/MS), protein identification by sequence database search and peptide-based quantitative analysis. The most critical steps of this workflow are protein reconstitution and digestion; therefore, detergents and chaotropic agents are strongly mandatory to ensure complete solubilization of complex protein isolates and to achieve accessibility of all protease cleavage sites. However, detergents are incompatible with both RP separation and electrospray ionization (ESI). Therefore, to make LC-MS analysis possible, several strategies were implemented in the shotgun proteomics workflow. These techniques rely either on enzymatic digestion in centrifugal filters with subsequent evacuation of the detergent, or employment of MS-compatible surfactants, which can be degraded upon the digestion. In this review we comprehensively address all currently available strategies for the detergent-assisted proteolysis in respect of their relative efficiency when applied to different biological matrices. We critically discuss the current progress and the further perspectives of these technologies in the context of its advances and gaps.
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Affiliation(s)
- Katerina Danko
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chaussee 3, Pushkin, 196608 St. Petersburg, Russia
| | - Viktor Zgoda
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Andrej Frolov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
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OGATA K, ISHIHAMA Y. Temperature Dependence of Retention Behavior of Phosphorylated Peptides in Ion-Pair Reversed-Phase Liquid Chromatography. CHROMATOGRAPHY 2022. [DOI: 10.15583/jpchrom.2022.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kosuke OGATA
- Graduate School of Pharmaceutical Sciences, Kyoto University
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Yamamoto K, Morikawa K, Shimizu H, Sano H, Kazoe Y, Kitamori T. Accelerated protein digestion and separation with picoliter volume utilizing nanofluidics. LAB ON A CHIP 2022; 22:1162-1170. [PMID: 35133382 DOI: 10.1039/d1lc00923k] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single cell analyses can provide critical biological insight into cellular heterogeneity. In particular, the proteome, which governs cell functions, is much more difficult to analyze because it is principally impossible to amplify proteins compared to nucleic acids. The most promising approach to single cell proteomics is based on the liquid chromatography mass spectrometry (LC-MS) platform. However, pretreatments before MS detection have two critical issues for single cell analysis: analyte loss as a result of adsorption and artifacts due to the duration of analysis. This is a serious problem because single cells have a limited number of protein molecules and a small volume. To solve these issues, we developed an integrated nanofluidic device to manipulate samples on a femtoliter to picoliter (fL-pL) scale to achieve high-throughput analysis via suppressing analyte loss. This device can perform tryptic digestion, chromatographic separation, and non-labeled detection with high consistency. In addition, we introduced an open/close valve by physical deformation of glass on a nanometer scale to independently modify the nanochannel surfaces and control sample aliquots. The injection system equipped with this valve achieved an injection volume of 1.0 ± 0.1 pL. By using this integrated device, we found that the chromatogram of bulk-digestion for 12 hours resembled that of 15 min-digestion in the nanochannel, which indicated that these conditions reached a similar state of digestion. Therefore, an integrated device for ultra-fast protein analysis was developed on a 1 pL scale for the first time.
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Affiliation(s)
- Koki Yamamoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
| | - Kyojiro Morikawa
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan.
| | - Hisashi Shimizu
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan.
| | - Hiroki Sano
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan.
| | - Yutaka Kazoe
- Department of System Design Engineering, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Kanagawa 223-8522, Japan
| | - Takehiko Kitamori
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan.
- Collaborative Research Organization for Micro and Nano Multifunctional Devices, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan
- Institute of Nanoengineering and Microsystems, Department of Power Mechanical Engineering, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan, Republic of China
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CoolTip: Low-Temperature Solid-Phase Extraction Microcolumn for Capturing Hydrophilic Peptides and Phosphopeptides. Mol Cell Proteomics 2021; 20:100170. [PMID: 34740827 PMCID: PMC8646264 DOI: 10.1016/j.mcpro.2021.100170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 10/06/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
Reversed-phase solid-phase extraction (SPE) techniques are commonly used for desalting samples before LC/MS/MS in shotgun proteomics. However, hydrophilic peptides are often lost during the desalting step under the standard SPE conditions. Here, we describe a simple protocol in which a stop-and-go extraction tip packed with a poly(styrene-divinylbenzene) copolymer disc is used at 4 °C during sample loading without any organic solvent. Using this method, which we designate as the CoolTip protocol, we identified 2.9-fold more tryptic peptides and 6.1-fold more tryptic phosphopeptides from HeLa lysates than the standard SPE protocol for hydrophilic peptides, with a mobile phase of less than 8% acetonitrile in LC/MS/MS. There was no decrease in the recovery of hydrophobic peptides. CoolTip also provided better quantitative reproducibility in LC/MS/MS analysis. We anticipate that this protocol will provide improved performance in many kinds of shotgun proteomics experiments. CoolTip, a StageTip with a poly(styrene-divinylbenzene) disc operated at 4 °C. Identification of more 6.1-fold hydrophilic phosphopeptides from HeLa lysates. No decrease in the recovery of hydrophobic peptides using the CoolTip protocol. Better reproducibility in quantitative LC/MS/MS analysis.
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YAMAMOTO S. <i>In Situ </i>Photopolymerization of Functionalized Polyacrylamide-Based Preconcentrators for Highly Sensitive Specific Detection of Various Analytes by Microchip Electrophoresis. CHROMATOGRAPHY 2021. [DOI: 10.15583/jpchrom.2020.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ogata K, Chang CH, Ishihama Y. Effect of Phosphorylation on the Collision Cross Sections of Peptide Ions in Ion Mobility Spectrometry. Mass Spectrom (Tokyo) 2021; 10:A0093. [PMID: 33552826 PMCID: PMC7843839 DOI: 10.5702/massspectrometry.a0093] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/09/2020] [Indexed: 11/23/2022] Open
Abstract
The insertion of ion mobility spectrometry (IMS) between LC and MS can improve peptide identification in both proteomics and phosphoproteomics by providing structural information that is complementary to LC and MS, because IMS separates ions on the basis of differences in their shapes and charge states. However, it is necessary to know how phosphate groups affect the peptide collision cross sections (CCS) in order to accurately predict phosphopeptide CCS values and to maximize the usefulness of IMS. In this work, we systematically characterized the CCS values of 4,433 pairs of mono-phosphopeptide and corresponding unphosphorylated peptide ions using trapped ion mobility spectrometry (TIMS). Nearly one-third of the mono-phosphopeptide ions evaluated here showed smaller CCS values than their unphosphorylated counterparts, even though phosphorylation results in a mass increase of 80 Da. Significant changes of CCS upon phosphorylation occurred mainly in structurally extended peptides with large numbers of basic groups, possibly reflecting intramolecular interactions between phosphate and basic groups.
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Affiliation(s)
- Kosuke Ogata
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606–8501, Japan
| | - Chih-Hsiang Chang
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606–8501, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606–8501, Japan
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