Great Gains in Mass Spectrometry Data Interpretation

Slavov, Nikolai

doi:10.1021/acs.jproteome.3c00099

Cited by 2 publications

(2 citation statements)

References 9 publications

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“…DO-MS should enable broader adoption of cutting-edge methods, such as DIA and plexDIA methods for driving biological research. 55…”

Section: Discussionmentioning

confidence: 99%

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS

Wallmann,

Leduc,

Slavov

2023

J. Proteome Res.

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Mass spectrometry (MS) enables specific and accurate quantification of proteins with ever-increasing throughput and sensitivity. Maximizing this potential of MS requires optimizing data acquisition parameters and performing efficient quality control for large datasets. To facilitate these objectives for dataindependent acquisition (DIA), we developed a second version of our framework for data-driven optimization of MS methods (DO-MS). The DO-MS app v2.0 (do-ms.slavovlab.net) allows one to optimize and evaluate results from both label-free and multiplexed DIA (plexDIA) and supports optimizations particularly relevant to single-cell proteomics. We demonstrate multiple use cases, including optimization of duty cycle methods, peptide separation, number of survey scans per duty cycle, and quality control of single-cell plexDIA data. DO-MS allows for interactive data display and generation of extensive reports, including publication of quality figures that can be easily shared. The source code is available at github.com/SlavovLab/DO-MS.

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“…DO-MS should enable broader adoption of cutting-edge methods, such as DIA and plexDIA methods for driving biological research. 55…”

Section: Discussionmentioning

confidence: 99%

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS

Wallmann,

Leduc,

Slavov

2023

J. Proteome Res.

Self Cite

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“…Extensive reviews on instrumentation used in proteomics are available elsewhere (Gillet et al, 2016;Zhao, Xue, et al, 2023) and this section focuses on recent advancements which can better clarify metaproteomics datasets. Two new technologies have distinguished themselves in the (meta)proteomics literature: field asymmetric ion mobility spectrometry (FAIMS) and parallel accumulation-serial fragmentation (PASEF).…”

Section: Instrumentationmentioning

confidence: 99%

Critical steps in an environmental metaproteomics workflow

Nebauer,

Pearson,

Neilan

2024

Environmental Microbiology

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Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non‐expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high‐quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single‐organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.

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Great Gains in Mass Spectrometry Data Interpretation

Cited by 2 publications

References 9 publications

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS

Critical steps in an environmental metaproteomics workflow

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