Reassembling protein complexes after controlled disassembly by top-down mass spectrometry in native mode
The combined use of electrospray ionization run in so-called "native mode" with top-down mass spectrometry (nTDMS) is enhancing both structural biology and discovery proteomics by providing three levels of information in a single experiment: the intact mass of a protein or complex, the masses of its subunits and non-covalent cofactors, and fragment ion masses from direct dissociation of subunits that capture the primary sequence and combinations of diverse post-translational modifications (PTMs). While intact mass data are readily deconvoluted using well-known software options, the analysis of fragmentation data that result from a tandem MS experiment - essential for proteoform characterization - is not yet standardized. In this tutorial, we offer a decision-tree for the analysis of nTDMS experiments on protein complexes and diverse bioassemblies. We include an overview of strategies to navigate this type of analysis, provide example data sets, and highlight software for the hypothesis-driven interrogation of fragment ions for localization of PTMs, metals, and cofactors on native proteoforms. Throughout we have emphasized the key features (deconvolution, search mode, validation, other) that the reader can consider when deciding upon their specific experimental and data processing design using both open-access and commercial software.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2021 |
|---|---|
| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:465 |
|---|---|
| Enthalten in: |
International journal of mass spectrometry - 465(2021) vom: 13. Juli |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Schachner, Luis F [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
|---|
| Anmerkungen: |
Date Revised 21.09.2023 published: Print-Electronic Citation Status PubMed-not-MEDLINE |
|---|
| doi: |
10.1016/j.ijms.2021.116591 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM330811274 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM330811274 | ||
| 003 | DE-627 | ||
| 005 | 20231225212105.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231225s2021 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1016/j.ijms.2021.116591 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1102.xml |
| 035 | |a (DE-627)NLM330811274 | ||
| 035 | |a (NLM)34539228 | ||
| 035 | |a (PII)116591 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Schachner, Luis F |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Reassembling protein complexes after controlled disassembly by top-down mass spectrometry in native mode |
| 264 | 1 | |c 2021 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Revised 21.09.2023 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status PubMed-not-MEDLINE | ||
| 520 | |a The combined use of electrospray ionization run in so-called "native mode" with top-down mass spectrometry (nTDMS) is enhancing both structural biology and discovery proteomics by providing three levels of information in a single experiment: the intact mass of a protein or complex, the masses of its subunits and non-covalent cofactors, and fragment ion masses from direct dissociation of subunits that capture the primary sequence and combinations of diverse post-translational modifications (PTMs). While intact mass data are readily deconvoluted using well-known software options, the analysis of fragmentation data that result from a tandem MS experiment - essential for proteoform characterization - is not yet standardized. In this tutorial, we offer a decision-tree for the analysis of nTDMS experiments on protein complexes and diverse bioassemblies. We include an overview of strategies to navigate this type of analysis, provide example data sets, and highlight software for the hypothesis-driven interrogation of fragment ions for localization of PTMs, metals, and cofactors on native proteoforms. Throughout we have emphasized the key features (deconvolution, search mode, validation, other) that the reader can consider when deciding upon their specific experimental and data processing design using both open-access and commercial software | ||
| 650 | 4 | |a Journal Article | |
| 700 | 1 | |a Tran, Denise P |e verfasserin |4 aut | |
| 700 | 1 | |a Lee, Alexander |e verfasserin |4 aut | |
| 700 | 1 | |a McGee, John P |e verfasserin |4 aut | |
| 700 | 1 | |a Jooss, Kevin |e verfasserin |4 aut | |
| 700 | 1 | |a Durbin, Kenneth |e verfasserin |4 aut | |
| 700 | 1 | |a Seckler, Henrique Dos Santos |e verfasserin |4 aut | |
| 700 | 1 | |a Adams, Lauren |e verfasserin |4 aut | |
| 700 | 1 | |a Cline, Erika |e verfasserin |4 aut | |
| 700 | 1 | |a Melani, Rafael |e verfasserin |4 aut | |
| 700 | 1 | |a Ives, Ashley N |e verfasserin |4 aut | |
| 700 | 1 | |a Des Soye, Benjamin |e verfasserin |4 aut | |
| 700 | 1 | |a Kelleher, Neil L |e verfasserin |4 aut | |
| 700 | 1 | |a Patrie, Steven M |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t International journal of mass spectrometry |d 2006 |g 465(2021) vom: 13. Juli |w (DE-627)NLM169010813 |x 1387-3806 |7 nnns |
| 773 | 1 | 8 | |g volume:465 |g year:2021 |g day:13 |g month:07 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1016/j.ijms.2021.116591 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 465 |j 2021 |b 13 |c 07 | ||