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Kaulich PT, Jeong K, Kohlbacher O, Tholey A. Influence of different sample preparation approaches on proteoform identification by top-down proteomics. Nat Methods 2024:10.1038/s41592-024-02481-6. [PMID: 39438734 DOI: 10.1038/s41592-024-02481-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 09/23/2024] [Indexed: 10/25/2024]
Abstract
Top-down proteomics using mass spectrometry facilitates the identification of intact proteoforms, that is, all molecular forms of proteins. Multiple past advances have lead to the development of numerous sample preparation workflows. Here we systematically investigated the influence of different sample preparation steps on proteoform and protein identifications, including cell lysis, reduction and alkylation, proteoform enrichment, purification and fractionation. We found that all steps in sample preparation influence the subset of proteoforms identified (for example, their number, confidence, physicochemical properties and artificially generated modifications). The various sample preparation strategies resulted in complementary identifications, substantially increasing the proteome coverage. Overall, we identified 13,975 proteoforms from 2,720 proteins of human Caco-2 cells. The results presented can serve as suggestions for designing and adapting top-down proteomics sample preparation strategies to particular research questions. Moreover, we expect that the sampling bias and modifications identified at the intact protein level will also be useful in improving bottom-up proteomics approaches.
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Affiliation(s)
- Philipp T Kaulich
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Kyowon Jeong
- Applied Bioinformatics, Computer Science Department, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Computer Science Department, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
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Song M, Zhang Y, Zhu W, Zhou W, Li X, Yang A, Tong P, Wu Z, Chen H. Mass Spectrometry Analysis on the Breakage of Allergens in High-Molecular-Mass Polymer of Roasted Peanuts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3142-3149. [PMID: 38299554 DOI: 10.1021/acs.jafc.3c07007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Peanut allergy is a prevalent and concerning food allergy. Roasting can introduce structural changes to peanut allergens, affecting their allergenicity, but the structure on the primary structure is unclear. Here, the breakage sites were identified by mass spectrometry and software tools, and structural changes were simulated by molecular dynamics and displayed by PyMOL software. Results revealed that the appearance frequencies of L, Q, F, and E were high at the N-terminal of the breakage site, while S and E were dominant at the C-terminal. In the conformational structure, breakage sites were found close to disulfide bonds and the Cupin domains of Ara h 1 and Ara h 3. The breakage of allergens destroyed linear epitopes and might change the conformation of epitopes, which could influence peanuts' potential allergenicity.
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Affiliation(s)
- Min Song
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330031, China
- College of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Ying Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330031, China
- College of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Weichao Zhu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330031, China
- College of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Wenlong Zhou
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330031, China
- College of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Xin Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330031, China
- College of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Anshu Yang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330031, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China
| | - Ping Tong
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330031, China
- College of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Zhihua Wu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330031, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China
| | - Hongbing Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330031, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China
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Kaulich PT, Cassidy L, Tholey A. Identification of proteoforms by top-down proteomics using two-dimensional low/low pH reversed-phase liquid chromatography-mass spectrometry. Proteomics 2024; 24:e2200542. [PMID: 36815320 DOI: 10.1002/pmic.202200542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/24/2023]
Abstract
In top-down (TD) proteomics, efficient proteoform separation is crucial to reduce the sample complexity and increase the depth of the analysis. Here, we developed a two-dimensional low pH/low pH reversed-phase liquid chromatography separation scheme for TD proteomics. The first dimension for offline fractionation was performed using a polymeric reversed-phase (PLRP-S) column with trifluoroacetic acid as ion-pairing reagent. The second dimension, a C4 nanocolumn with formic acid as ion-pairing reagent, was coupled online with a high-field asymmetric ion mobility spectrometry (FAIMS) Orbitrap Tribrid mass spectrometer. For both dimensions several parameters were optimized, such as the adaption of the LC gradients in the second dimension according to the elution time (i.e., fraction number) in the first dimension. Avoidance of elevated temperatures and prolonged exposure to acidic conditions minimized cleavage of acid labile aspartate-proline peptide bonds. Furthermore, a concatenation strategy was developed to reduce the total measurement time. We compared our low/low pH with a previously published high pH (C4, ammonium formate)/low pH strategy and found that both separation strategies led to complementary proteoform identifications, mainly below 20 kDa, with a higher number of proteoforms identified by the low/low pH separation. With the optimized separation scheme, more than 4900 proteoforms from 1250 protein groups were identified in Caco-2 cells.
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Affiliation(s)
- Philipp T Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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Cassidy L, Kaulich PT, Tholey A. Proteoforms expand the world of microproteins and short open reading frame-encoded peptides. iScience 2023; 26:106069. [PMID: 36818287 PMCID: PMC9929600 DOI: 10.1016/j.isci.2023.106069] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Microproteins and short open reading frame-encoded peptides (SEPs) can, like all proteins, carry numerous posttranslational modifications. Together with posttranscriptional processes, this leads to a high number of possible distinct protein molecules, the proteoforms, out of a limited number of genes. The identification, quantification, and molecular characterization of proteoforms possess special challenges to established, mainly bottom-up proteomics (BUP) based analytical approaches. While BUP methods are powerful, proteins have to be inferred rather than directly identified, which hampers the detection of proteoforms. An alternative approach is top-down proteomics (TDP) which allows to identify intact proteoforms. This perspective article provides a brief overview of modified microproteins and SEPs, introduces the proteoform terminology, and compares present BUP and TDP workflows highlighting their major advantages and caveats. Necessary future developments in TDP to fully accentuate its potential for proteoform-centric analytics of microproteins and SEPs will be discussed.
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Affiliation(s)
- Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Philipp T. Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany,Corresponding author
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