Data-independent acquisition mass spectrometry (DIA-MS) for proteomic applications in oncology

Krásný, Lukáš; Huang, Paul H.

doi:10.1039/d0mo00072h

Cited by 136 publications

(121 citation statements)

References 92 publications

(130 reference statements)

Supporting

Mentioning

121

Contrasting

Order By: Relevance

“…Most proteomic studies have been analyzed using data-dependent acquisition (DDA) method where a selected number of peptides are sequentially selected for MS2 analysis. However, the stochastic precursor selection of DDA can lead to inconsistent detection of peptides and the corresponding proteins in the sample cohort, resulting in many missing values in the data ( Gillet et al, 2012 ; Krasny and Huang, 2021 ). In the present study, we have analyzed 148 skeletal muscle proteomes from men who cover all glucose tolerance phenotypes: NGT, IFG, IGT, as well as T2D, using a data-independent acquisition method, a sequential window acquisition of all theoretical mass spectra (SWATH-MS) proteomics technique ( Gillet et al, 2012 ; Krasny and Huang, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…However, the stochastic precursor selection of DDA can lead to inconsistent detection of peptides and the corresponding proteins in the sample cohort, resulting in many missing values in the data ( Gillet et al, 2012 ; Krasny and Huang, 2021 ). In the present study, we have analyzed 148 skeletal muscle proteomes from men who cover all glucose tolerance phenotypes: NGT, IFG, IGT, as well as T2D, using a data-independent acquisition method, a sequential window acquisition of all theoretical mass spectra (SWATH-MS) proteomics technique ( Gillet et al, 2012 ; Krasny and Huang, 2021 ). SWATH-MS is an emerging mass spectrometric method that offers a high degree of quantitative accuracy, proteomic coverage, reproducibility of proteome coverage, and sample throughput, as well as a low number of missing values.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Skeletal muscle proteomes reveal downregulation of mitochondrial proteins in transition from prediabetes into type 2 diabetes

et al. 2021

View full text Add to dashboard Cite

Summary Skeletal muscle insulin resistance is a central defect in the pathogenesis of type 2 diabetes (T2D). Here, we analyzed skeletal muscle proteome in 148 vastus lateralis muscle biopsies obtained from men covering all glucose tolerance phenotypes: normal, impaired fasting glucose (IFG), impaired glucose tolerance (IGT) and T2D. Skeletal muscle proteome was analyzed by a sequential window acquisition of all theoretical mass spectra (SWATH-MS) proteomics technique. Our data indicate a downregulation in several proteins involved in mitochondrial electron transport or respiratory chain complex assembly already in IFG and IGT muscles, with most profound decreases observed in T2D. Additional phosphoproteomic analysis reveals altered phosphorylation in several signaling pathways in IFG, IGT, and T2D muscles, including those regulating glucose metabolic processes, and the structure of muscle cells. These data reveal several alterations present in skeletal muscle already in prediabetes and highlight impaired mitochondrial energy metabolism in the trajectory from prediabetes into T2D.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Skeletal muscle proteomes reveal downregulation of mitochondrial proteins in transition from prediabetes into type 2 diabetes

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Aiming at the drug development, several groups have used proteomics approach to observe up- or down-regulated effects of proteins resulting from disease activity or side effects of the treatments [ 44 , 45 , 128 , 129 , 130 , 131 ]. Moreover, the quest for the identification of biological markers or biomarkers using venom that may help in the early detection of pathologies such as cancer, and the quest for products able to evaluate the metastatic potential and propose new forms of treatment to tumors, remains an important goal of research groups and pharmaceutical companies.…”

Section: Discussionmentioning

confidence: 99%

Bothrops Jararaca Snake Venom Modulates Key Cancer-Related Proteins in Breast Tumor Cell Lines

Kisaki

Arcos

Montoni

et al. 2021

Toxins

View full text Add to dashboard Cite

Cancer is characterized by the development of abnormal cells that divide in an uncontrolled way and may spread into other tissues where they may infiltrate and destroy normal body tissue. Several previous reports have described biochemical anti-tumorigenic properties of crude snake venom or its components, including their capability of inhibiting cell proliferation and promoting cell death. However, to the best of our knowledge, there is no work describing cancer cell proteomic changes following treatment with snake venoms. In this work we describe the quantitative changes in proteomics of MCF7 and MDA-MB-231 breast tumor cell lines following treatment with Bothrops jararaca snake venom, as well as the functional implications of the proteomic changes. Cell lines were treated with sub-toxic doses at either 0.63 μg/mL (low) or 2.5 μg/mL (high) of B. jararaca venom for 24 h, conditions that cause no cell death per se. Proteomics analysis was conducted on a nano-scale liquid chromatography coupled on-line with mass spectrometry (nLC-MS/MS). More than 1000 proteins were identified and evaluated from each cell line treated with either the low or high dose of the snake venom. Protein profiling upon venom treatment showed differential expression of several proteins related to cancer cell metabolism, immune response, and inflammation. Among the identified proteins we highlight histone H3, SNX3, HEL-S-156an, MTCH2, RPS, MCC2, IGF2BP1, and GSTM3. These data suggest that sub-toxic doses of B. jararaca venom have potential to modulate cancer-development related protein targets in cancer cells. This work illustrates a novel biochemical strategy to identify therapeutic targets against cancer cell growth and survival.

show abstract

“…In this study, we utilise sequential window acquisition of all theoretical fragment ion spectra (SWATH)-MS to undertake proteomic profiling of FFPE tissue specimens in a cohort of STS patients across four histological subtypes ( n = 36). SWATH-MS is a next-generation proteomics method that offers high reproducibility in protein identification across multiple samples [ 10 ]. Due to the stochastic nature of precursor ion selection for fragmentation in conventional proteomic approaches such as data-dependent acquisition (DDA) mass spectrometry, there are routinely many missing values in large-scale proteomic studies, resulting in a reduction in the reproducibility of protein identification and quantification.…”

Section: Introductionmentioning

confidence: 99%

Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry

Milighetti

Krásný

Lee

et al. 2021

Journal of Proteomics

Self Cite

View full text Add to dashboard Cite

Soft tissue sarcomas (STS) are a group of rare and heterogeneous cancers. While large-scale genomic and epigenomic profiling of STS have been undertaken, proteomic analysis has thus far been limited. Here we utilise sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) for proteomic profiling of formalin fixed paraffin embedded (FFPE) specimens from a cohort of STS patients ( n = 36) across four histological subtypes (leiomyosarcoma, synovial sarcoma, undifferentiated pleomorphic sarcoma and dedifferentiated liposarcoma). We quantified 2951 proteins across all cases and show that there is a significant enrichment of gene sets associated with smooth muscle contraction in leiomyosarcoma, RNA splicing regulation in synovial sarcoma and leukocyte activation in undifferentiated pleomorphic sarcoma. We further identified a subgroup of STS cases that have a distinct expression profile in a panel of proteins, with worse survival outcomes when compared to the rest of the cohort. Our study highlights the value of comprehensive proteomic characterisation as a means to identify histotype-specific STS profiles that describe key biological pathways of clinical and therapeutic relevance; as well as for discovering new prognostic biomarkers in this group of rare and difficult-to-treat diseases.

show abstract

Data-independent acquisition mass spectrometry (DIA-MS) for proteomic applications in oncology

Abstract: Data-independent acquisition mass spectrometry (DIA-MS) is a next generation proteomic methodology that generates permanent digital proteome maps offering highly reproducible retrospective analysis of cellular and tissue specimens.

Cited by 136 publications

References 92 publications

Skeletal muscle proteomes reveal downregulation of mitochondrial proteins in transition from prediabetes into type 2 diabetes

Skeletal muscle proteomes reveal downregulation of mitochondrial proteins in transition from prediabetes into type 2 diabetes

Bothrops Jararaca Snake Venom Modulates Key Cancer-Related Proteins in Breast Tumor Cell Lines

Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry

Contact Info

Product

Resources

About