Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry

Müller, Friedrich; Kolbowski, Lars; Bernhardt, Oliver M.; Reiter, Lukas; Rappsilber, Juri

doi:10.1074/mcp.tir118.001276

Cited by 41 publications

(46 citation statements)

References 71 publications

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“…Commonly, cross-linked proteins are electrophoretically pre-purified from organic contaminants and aggregates while using SDS gel electrophoresis, followed by the extrusion of peptides from the gel band after proteolysis in the same gel band. A study has been reported that focused on QCLMS [ 113 ], in order to investigate the protein structural conformations in solution used with in-gel digestion protocols ( Figure 5 ). The digestion of photoactivated cross-linked proteins was performed after SDS pre-separation and concentration in polyacrylamide gel.…”

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

“…The digestion of photoactivated cross-linked proteins was performed after SDS pre-separation and concentration in polyacrylamide gel. Müller et al claimed that they were able to detect 414 unique residue pairs, out of which 292 (70%) were quantifiable across triplicate analyses with a coefficient of variation (CV) of 10% [ 113 ]. In addition, several other studies suggested the use of ‘in-gel’ digestion in their cross-linking proteomics experiments ( Figure 5 ) [ 114 , 115 , 116 , 117 , 118 ].…”

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

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Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)

et al. 2021

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The fundamentals of how protein–protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein–protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.

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Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)

et al. 2021

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“…38 The estimate of the number of expected cross-linked peptides for XL-BSA was obtained by simulating potential cross-linked peptides using the JWalk approach, and considering only peptides of length 6 or less. 40,41 Compared to the 4.5 fmol reference amount of linear BSA, without accounting for ionization differences between linear and XL peptides, the estimated XL-BSA on-column amounts were determined as about 8 amol and between 0.06 and 99 amol using the Hi [3] method the probabilistic method, respectively. A more detailed evaluation of the method and biological application are beyond the scope of the current study.…”

Section: Quantitative Analysis Of Xl-bsamentioning

confidence: 99%

“…[12][13][14][15] This need for isotope labels has been a requirement largely due to the reliance on DDA acquisition modes for analysis of cross-linked peptides. Although in its infancy, some exploration has been carried out into quantitation of cross-linked peptides without the use of isotopic labels and using alternative acquisition modes, suggesting compatibility with XL-MS. 16,17 This research expands the field of quantitative XL-MS to include an increased variety of acquisition modes and removes the requirement for labels.…”

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confidence: 99%

Evaluation of Acquisition Modes for the Quantitative Analysis of Cross-Linked Peptides by Targeted and Untargeted Mass Spectrometry

Britt

Cragnolini²,

Khatun³

et al. 2020

Preprint

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<div> <div> <p>Cross-linking mass spectrometry (XL-MS) is a structural biology technique that can provide insights into the structure and interactions of proteins and their complexes, especially those that cannot be easily assessed by other methods. Quantitative XL-MS has the potential to probe the structural and temporal dynamics of protein complexes; however, it requires further development. Until recently, quantitative XL-MS has largely relied upon isotopic labeling and data dependent acquisition (DDA) methods, limiting the number of biological samples that can be studied in a single experiment. Here, the acquisition modes available on an ion mobility (IM) enabled QToF mass spectrometer are evaluated for the quantitation of cross-linked peptides, eliminating the need for isotopic labels and thus expanding the number of comparable studies that can be conducted in parallel. Workflows were optimized using metabolite and peptide standards analyzed in biological matrices, facilitating modelling of the data and addressing linearity issues, which allow for significant increases in dynamic range. Evaluation of the DDA acquisition method commonly used in XL-MS studies indicated consistency issues between technical replicates and reduced performance in quantitative metrics. On the contrary, data independent acquisition (DIA) and parallel reaction monitoring (PRM) modes proved more robust for analyte quantitation. Mobility enabled modes exhibited an improvement in sensitivity due to the added dimension of separation, and a simultaneous reduction in dynamic range, which was largely recovered by correction methods. Hi[3] and probabilistic quantitation methods were successfully applied to the DIA data, determining the molar amounts of cross-linked peptides relative to their linear counterparts.</p></div></div>

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“…Accuracy and reproducibility of QCLMS analysis can be improved by data-independent acquisition (DIA) [18]. DIA is an acquisition method that combines high throughput of DDA with the sensitivity of targeted acquisition methods (selected, parallel or multiple reaction monitoring; SRM, PRM, MRM) [19][20][21].…”

Section: Introductionmentioning

confidence: 99%

A protocol for studying structural dynamics of proteins by quantitative crosslinking mass spectrometry and data-independent acquisition

Müller

Rappsilber

2020

Journal of Proteomics

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ACN -acetonitrile AGC -automatic gain control ANOVA -analysis of variance BS 3 -bis[sulfosuccinimidyl] suberate CL -crosslinking CLMS -crosslinking/mass spectrometry CV -coefficient of variation DDA -data-dependent acquisition DIA -data-independent acquisition DTT -dithiothreitol HCD -high energy collision dissociation HSA -human serum albumin IAA -2-iodoacetamide LC-MS -liquid chromatography-mass spectrometry LFQ -label-free quantitation PRM -parallel reaction monitoring PSM -peptide spectrum matches QCLMS -quantitative crosslinking/mass spectrometry SCX -strong cation exchange chromatography SRM/MRM -selected reaction monitoring/multiple reaction monitoring URPs -unique residue pairs

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Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry

Cited by 41 publications

References 71 publications

Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)

Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)

Evaluation of Acquisition Modes for the Quantitative Analysis of Cross-Linked Peptides by Targeted and Untargeted Mass Spectrometry

A protocol for studying structural dynamics of proteins by quantitative crosslinking mass spectrometry and data-independent acquisition

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