Harmonizing structural mass spectrometry analyses in the mass spec studio

Ziemianowicz, Daniel S.; Sarpe, Vladimir; Crowder, David A.; Pells, Troy J.; Raval, Shaunak; Hepburn, Morgan; Rafiei, Atefeh; Schriemer, David C.

doi:10.1016/j.jprot.2020.103844

Cited by 7 publications

(7 citation statements)

References 85 publications

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“…To initiate protein structure modeling exercises with structural mass spectrometry data, we created IMProv in the Mass Spec Studio ( 63 ). The Studio contains apps for both XL-MS (CRIMP) and HX-MS (HX-PIPE and HX-DEAL), which were used to process data for the modeling runs described below.…”

Section: Resultsmentioning

confidence: 99%

IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics

Ziemianowicz

Saltzberg

Pells

et al. 2021

Molecular & Cellular Proteomics

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Proteomics methodology has expanded to include protein structural analysis, primarily through cross-linking mass spectrometry (XL-MS) and hydrogen–deuterium exchange mass spectrometry (HX-MS). However, while the structural proteomics community has effective tools for primary data analysis, there is a need for structure modeling pipelines that are accessible to the proteomics specialist. Integrative structural biology requires the aggregation of multiple distinct types of data to generate models that satisfy all inputs. Here, we describe IMProv, an app in the Mass Spec Studio that combines XL-MS data with other structural data, such as cryo-EM densities and crystallographic structures, for integrative structure modeling on high-performance computing platforms. The resource provides an easily deployed bundle that includes the open-source Integrative Modeling Platform program (IMP) and its dependencies. IMProv also provides functionality to adjust cross-link distance restraints according to the underlying dynamics of cross-linked sites, as characterized by HX-MS. A dynamics-driven conditioning of restraint values can improve structure modeling precision, as illustrated by an integrative structure of the five-membered Polycomb Repressive Complex 2. IMProv is extensible to additional types of data.

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Section: Resultsmentioning

confidence: 99%

IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics

Ziemianowicz

Saltzberg

Pells

et al. 2021

Molecular & Cellular Proteomics

Self Cite

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“…A conceptual integrative or hybrid modeling workflow, which outlines main steps of the structure determination process, was proposed . A number of computer program solutions for integrative structural modeling, such as MS Studio and Integrative Modeling Platform (IMP) have been developed. , The approach can be further generalized beyond protein structure determination to the level of organelles and whole cells.…”

Section: Combination Of Multiple Approaches For the Elucidation Of Pr...mentioning

confidence: 99%

“…99 A number of computer program solutions for integrative structural modeling, such as MS Studio and Integrative Modeling Platform (IMP) have been developed. 100,101 The approach can be further generalized beyond protein structure determination to the level of organelles and whole cells.…”

Section: Combination Of Multiple Approaches For the Elucidation Of Pr...mentioning

confidence: 99%

Protein Chemistry Combined with Mass Spectrometry for Protein Structure Determination

Petrotchenko

Borchers

2021

Chem. Rev.

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The advent of soft-ionization mass spectrometry for biomolecules has opened up new possibilities for the structural analysis of proteins. Combining protein chemistry methods with modern mass spectrometry has led to the emergence of the distinct field of structural proteomics. Multiple protein chemistry approaches, such as surface modification, limited proteolysis, hydrogen–deuterium exchange, and cross-linking, provide diverse and often orthogonal structural information on the protein systems studied. Combining experimental data from these various structural proteomics techniques provides a more comprehensive examination of the protein structure and increases confidence in the ultimate findings. Here, we review various types of experimental data from structural proteomics approaches with an emphasis on the use of multiple complementary mass spectrometric approaches to provide experimental constraints for the solving of protein structures.

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“…Structural mass spectrometry (MS) , has emerged as a powerful tool to gather information ranging from primary protein sequence to post-translational modifications and can even provide three-dimensional (3D) information on proteins and protein complexes. Unfortunately, a collection of different approaches is often needed to provide the different structural information, presenting a major challenge in high-throughput structural MS experimentation.…”

Section: Introductionmentioning

confidence: 99%

Online Cross-Linking of Peptides and Proteins during Contained-Electrospray Ionization Mass Spectrometry

2022

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Recent advancements in mass spectrometry (MS) now enable all levels of protein structures to be characterized, including primary protein sequence, post-translational modifications, and three-dimensional protein conformations. However, protein conformational studies by MS require the use of many separate techniques that are performed independently of each other. Herein, we described a contained-electrospray (ES) experiment that has potential to integrate peptide/protein cross-linking with the general MS workflow. In our experiment, cross-linking of protein/peptide occurs simultaneously with ionization after analytes, and cross-linkers are sprayed from two separate ES emitters. The online cross-linking process occurring in the charged microdroplet environment was optimized using trilysine peptide and bis(sulfosuccinimidyl)suberate cross-linker. We detected the electrostatic complex between analyte and cross-linker, the mono-linked intermediate, and the fully cross-linked product, allowing us to correctly predict the sequence of reaction events in the cross-linking process. Importantly, we observed that the terminal fully cross-linked product is composed of two distinct conformations. In one form, the product involved cross-linking between two ε-NH2 amines in lysine residues, while the other conformer was formed by a reaction between one ε-NH2 amine and the N-terminus. The experimental conditions for selecting one cross-linked species over others during the online ES ionization–MS analysis have been detailed. Appropriate parameters enabled the reaction between α-lactalbumin proteins and cross-linkers using a non-denaturing spray condition. These results establish a framework for a future development in high-throughput structural MS method, where all levels of protein information can be gathered in a single experiment.

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Harmonizing structural mass spectrometry analyses in the mass spec studio

Cited by 7 publications

References 85 publications

IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics

IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics

Protein Chemistry Combined with Mass Spectrometry for Protein Structure Determination

Online Cross-Linking of Peptides and Proteins during Contained-Electrospray Ionization Mass Spectrometry

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