Discovery of potential protein biomarkers of lung adenocarcinoma in bronchoalveolar lavage fluid by SWATH MS data-independent acquisition and targeted data extraction

Ortea, Ignacio; Rodríguez‐Ariza, Antonio; Chicano-Gálvez, Eduardo; Vacas, M.S. Arenas; Gámez, Bernabé Jurado

doi:10.1016/j.jprot.2016.02.010

Cited by 77 publications

(65 citation statements)

References 34 publications

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“…In addition to investigating biomarkers from biopsies, proteins from BALF hold great potential as lung cancer biomarkers due to new mildly invasive endoscopy-based collection techniques. Ortea et al analyzed BALF from patients with lung adenocarcinoma using SWATH [65], and 44 proteins showed a higher than 3.75 fold-change relative to controls. In another study, the rapid label-free quantitative capabilities of uDIA were demonstrated for investigations of oral cancer biomarker proteins using conditioned media from cultured squamous cancer cell lines.…”

Section: Application Of Dia/swath Workflows To Clinically Relevantmentioning

confidence: 99%

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

Meyer

Schilling

2017

Expert Review of Proteomics

130

105

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Introduction While selected/multiple-reaction monitoring (SRM or MRM) is considered the gold standard for quantitative protein measurement, emerging data-independent acquisition (DIA) using high-resolution scans have opened a new dimension of high-throughput, comprehensive quantitative proteomics. These newer methodologies are particularly well suited for discovery of biomarker candidates from human disease samples, and for investigating and understanding human disease pathways. Areas covered This article reviews the current state of targeted and untargeted DIA mass spectrometry-based proteomic workflows, including SRM, parallel-reaction monitoring (PRM) and untargeted DIA (e.g., SWATH). Corresponding bioinformatics strategies, as well as application in biological and clinical studies are presented. Expert commentary Nascent application of highly-multiplexed untargeted DIA, such as SWATH, for accurate protein quantification from clinically relevant and disease-related samples shows great potential to comprehensively investigate biomarker candidates and understand disease.

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Section: Application Of Dia/swath Workflows To Clinically Relevantmentioning

confidence: 99%

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

Meyer

Schilling

2017

Expert Review of Proteomics

130

105

View full text Add to dashboard Cite

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“…Moreover, integrated biomarker discovery from multiple sample types including lung cancer tissues, cell lines and conditioned medium has established to construct a biomarker model (TFPI, MDK, OPN, MMP2, TIMP1, CEA, CYFRA 21–1, SCC) which enables to classify lung cancer patients from high risk smokers [8]. A recent clinical research of the bronchoalveolar lavage fluid (BALF) proteomic analysis by combining a simple pre-treatment and a sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) DIA MS approach provided useful resources for the discovery of potential biomarkers for lung disease [45]. BALF is usually discarded after using a portion of the fluid for standard pathological procedure, but Ortea et al used BALF as source for proteomic analysis and identified sensitive biomarkers by targeted proteomics DIA.…”

Section: Biomarkers In Lung Cancermentioning

confidence: 99%

Quantitative proteomics in lung cancer

Cheung

Juan

2017

J Biomed Sci

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Lung cancer is the most common cause of cancer-related death worldwide, less than 7% of patients survive 10 years following diagnosis across all stages of lung cancer. Late stage of diagnosis and lack of effective and personalized medicine reflect the need for a better understanding of the mechanisms that underlie lung cancer progression. Quantitative proteomics provides the relative different protein abundance in normal and cancer patients which offers the information for molecular interactions, signaling pathways, and biomarker identification. Here we introduce both theoretical and practical applications in the use of quantitative proteomics approaches, with principles of current technologies and methodologies including gel-based, label free, stable isotope labeling as well as targeted proteomics. Predictive markers of drug resistance, candidate biomarkers for diagnosis, and prognostic markers in lung cancer have also been discovered and analyzed by quantitative proteomic analysis. Moreover, construction of protein networks enables to provide an opportunity to interpret disease pathway and improve our understanding in cancer therapeutic strategies, allowing the discovery of molecular markers and new therapeutic targets for lung cancer.

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“…SWATH has been justified to be valuable in a few cancer types for biomarker discovery, such as prostate cancer22, colorectal cancer23, gastric cancer24, and lung cancer25. However, its application in the NPC field is very limited.…”

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confidence: 99%

SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma

Luo

Mok

Lin

et al. 2017

Sci Rep

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Nasopharyngeal carcinoma (NPC) is a serious threat to public health, and the biomarker discovery is of urgent needs. The data-independent mode (DIA) based sequential window acquisition of all theoretical fragment-ion spectra (SWATH) mass spectrometry (MS) has been proved to be precise in protein quantitation and efficient for cancer biomarker researches. In this study, we performed the first SWATH-MS analysis comparing the NPC and normal tissues. Spike-in stable isotope labeling by amino acids in cell culture (super-SILAC) MS was used as a shotgun reference. We identified and quantified 1414 proteins across all SWATH-MS analyses. We found that SWATH-MS had a unique feature to preferentially detect proteins with smaller molecular weights than either super-SILAC MS or human proteome background. With SWATH-MS, 29 significant differentially express proteins (DEPs) were identified. Among them, carbonic anhydrase 2 (CA2) was selected for further validation per novelty, MS quality and other supporting rationale. With the tissue microarray analysis, we found that CA2 had an AUC of 0.94 in differentiating NPC from normal tissue samples. In conclusion, SWATH-MS has unique features in proteome analysis, and it leads to the identification of CA2 as a potentially new diagnostic biomarker for NPC.

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Discovery of potential protein biomarkers of lung adenocarcinoma in bronchoalveolar lavage fluid by SWATH MS data-independent acquisition and targeted data extraction

Cited by 77 publications

References 34 publications

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

Quantitative proteomics in lung cancer

SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma

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