Proteoforms expand the world of microproteins and short open reading frame-encoded peptides
Summary: 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 numbe...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-02-01
|
| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004223001463 |
| _version_ | 1797903346652151808 |
|---|---|
| author | Liam Cassidy Philipp T. Kaulich Andreas Tholey |
| author_facet | Liam Cassidy Philipp T. Kaulich Andreas Tholey |
| author_sort | Liam Cassidy |
| collection | DOAJ |
| description | Summary: 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. |
| first_indexed | 2024-04-10T09:31:26Z |
| format | Article |
| id | doaj.art-ddc7ab6abe1d433cbc769867b435ddc3 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-04-10T09:31:26Z |
| publishDate | 2023-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-ddc7ab6abe1d433cbc769867b435ddc32023-02-19T04:27:08ZengElsevieriScience2589-00422023-02-01262106069Proteoforms expand the world of microproteins and short open reading frame-encoded peptidesLiam Cassidy0Philipp T. Kaulich1Andreas Tholey2Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, GermanySystematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, GermanySystematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany; Corresponding authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S2589004223001463BiochemistryMolecular biologyMolecular mechanism of gene regulationProteomics |
| spellingShingle | Liam Cassidy Philipp T. Kaulich Andreas Tholey Proteoforms expand the world of microproteins and short open reading frame-encoded peptides iScience Biochemistry Molecular biology Molecular mechanism of gene regulation Proteomics |
| title | Proteoforms expand the world of microproteins and short open reading frame-encoded peptides |
| title_full | Proteoforms expand the world of microproteins and short open reading frame-encoded peptides |
| title_fullStr | Proteoforms expand the world of microproteins and short open reading frame-encoded peptides |
| title_full_unstemmed | Proteoforms expand the world of microproteins and short open reading frame-encoded peptides |
| title_short | Proteoforms expand the world of microproteins and short open reading frame-encoded peptides |
| title_sort | proteoforms expand the world of microproteins and short open reading frame encoded peptides |
| topic | Biochemistry Molecular biology Molecular mechanism of gene regulation Proteomics |
| url | http://www.sciencedirect.com/science/article/pii/S2589004223001463 |
| work_keys_str_mv | AT liamcassidy proteoformsexpandtheworldofmicroproteinsandshortopenreadingframeencodedpeptides AT philipptkaulich proteoformsexpandtheworldofmicroproteinsandshortopenreadingframeencodedpeptides AT andreastholey proteoformsexpandtheworldofmicroproteinsandshortopenreadingframeencodedpeptides |