A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.
Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5172568?pdf=render |
| _version_ | 1818249151122505728 |
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| author | Juan D Chavez Jimmy K Eng Devin K Schweppe Michelle Cilia Keith Rivera Xuefei Zhong Xia Wu Terrence Allen Moshe Khurgel Akhilesh Kumar Athanasios Lampropoulos Mårten Larsson Shuvadeep Maity Yaroslav Morozov Wimal Pathmasiri Mathew Perez-Neut Coriness Pineyro-Ruiz Elizabeth Polina Stephanie Post Mark Rider Dorota Tokmina-Roszyk Katherine Tyson Debora Vieira Parrine Sant'Ana James E Bruce |
| author_facet | Juan D Chavez Jimmy K Eng Devin K Schweppe Michelle Cilia Keith Rivera Xuefei Zhong Xia Wu Terrence Allen Moshe Khurgel Akhilesh Kumar Athanasios Lampropoulos Mårten Larsson Shuvadeep Maity Yaroslav Morozov Wimal Pathmasiri Mathew Perez-Neut Coriness Pineyro-Ruiz Elizabeth Polina Stephanie Post Mark Rider Dorota Tokmina-Roszyk Katherine Tyson Debora Vieira Parrine Sant'Ana James E Bruce |
| author_sort | Juan D Chavez |
| collection | DOAJ |
| description | Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions. |
| first_indexed | 2024-12-12T15:31:56Z |
| format | Article |
| id | doaj.art-3ba39bd136884daab38534c011a3f079 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-12T15:31:56Z |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-3ba39bd136884daab38534c011a3f0792022-12-22T00:20:06ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-011112e016754710.1371/journal.pone.0167547A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.Juan D ChavezJimmy K EngDevin K SchweppeMichelle CiliaKeith RiveraXuefei ZhongXia WuTerrence AllenMoshe KhurgelAkhilesh KumarAthanasios LampropoulosMårten LarssonShuvadeep MaityYaroslav MorozovWimal PathmasiriMathew Perez-NeutCoriness Pineyro-RuizElizabeth PolinaStephanie PostMark RiderDorota Tokmina-RoszykKatherine TysonDebora Vieira Parrine Sant'AnaJames E BruceChemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions.http://europepmc.org/articles/PMC5172568?pdf=render |
| spellingShingle | Juan D Chavez Jimmy K Eng Devin K Schweppe Michelle Cilia Keith Rivera Xuefei Zhong Xia Wu Terrence Allen Moshe Khurgel Akhilesh Kumar Athanasios Lampropoulos Mårten Larsson Shuvadeep Maity Yaroslav Morozov Wimal Pathmasiri Mathew Perez-Neut Coriness Pineyro-Ruiz Elizabeth Polina Stephanie Post Mark Rider Dorota Tokmina-Roszyk Katherine Tyson Debora Vieira Parrine Sant'Ana James E Bruce A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. PLoS ONE |
| title | A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. |
| title_full | A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. |
| title_fullStr | A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. |
| title_full_unstemmed | A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. |
| title_short | A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. |
| title_sort | general method for targeted quantitative cross linking mass spectrometry |
| url | http://europepmc.org/articles/PMC5172568?pdf=render |
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