SWATH‐MS as a tool for biomarker discovery: From basic research to clinical applications

SI Anjo, C Santa, B Manadas - Proteomics, 2017 - Wiley Online Library
In the era of quantitative proteomics, where mass spectrometry plays a pivotal role, in
particular associated with the use of data‐independent acquisition, it is time to perform an …

High-throughput proteomic sample preparation using pressure cycling technology

X Cai, Z Xue, C Wu, R Sun, L Qian, L Yue, W Ge, X Yi… - Nature …, 2022 - nature.com
High-throughput lysis and proteolytic digestion of biopsy-level tissue specimens is a major
bottleneck for clinical proteomics. Here we describe a detailed protocol of pressure cycling …

Evaluation of FASP, SP3, and iST protocols for proteomic sample preparation in the low microgram range

M Sielaff, J Kuharev, T Bohn, J Hahlbrock… - Journal of proteome …, 2017 - ACS Publications
Efficient and reproducible sample preparation is a prerequisite for any robust and sensitive
quantitative bottom-up proteomics workflow. Here, we performed an independent …

High‐throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification

Y Zhu, T Weiss, Q Zhang, R Sun, B Wang… - Molecular …, 2019 - Wiley Online Library
Formalin‐fixed, paraffin‐embedded (FFPE), biobanked tissue samples offer an invaluable
resource for clinical and biomarker research. Here, we developed a pressure cycling …

Artificial intelligence defines protein-based classification of thyroid nodules

Y Sun, S Selvarajan, Z Zang, W Liu, Y Zhu, H Zhang… - Cell discovery, 2022 - nature.com
Determination of malignancy in thyroid nodules remains a major diagnostic challenge. Here
we report the feasibility and clinical utility of develo** an AI-defined protein-based …

Accelerated lysis and proteolytic digestion of biopsy-level fresh-frozen and FFPE tissue samples using pressure cycling technology

H Gao, F Zhang, S Liang, Q Zhang, M Lyu… - Journal of proteome …, 2020 - ACS Publications
Pressure cycling technology (PCT)-assisted tissue lysis and digestion have facilitated
reproducible and high-throughput proteomic studies of both fresh-frozen (FF) and formalin …

Quantitative proteome landscape of the NCI-60 cancer cell lines

T Guo, A Luna, VN Rajapakse, CC Koh, Z Wu, W Liu… - Iscience, 2019 - cell.com
Here we describe a proteomic data resource for the NCI-60 cell lines generated by pressure
cycling technology and SWATH mass spectrometry. We developed the DIA-expert software …

Proteome analysis of tissues by mass spectrometry

I Dapic, L Baljeu‐Neuman, N Uwugiaren… - Mass spectrometry …, 2019 - Wiley Online Library
Tissues and biofluids are important sources of information used for the detection of diseases
and decisions on patient therapies. There are several accepted methods for preservation of …

Spatial proteomics for understanding the tissue microenvironment

Y Mao, X Wang, P Huang, R Tian - Analyst, 2021 - pubs.rsc.org
The human body comprises rich populations of cells, which are arranged into tissues and
organs with diverse functionalities. These cells exhibit a broad spectrum of phenotypes and …

Determination of coenzyme A and acetyl-coenzyme A in biological samples using HPLC with UV detection

YI Shurubor, M D'Aurelio, J Clark-Matott, EP Isakova… - Molecules, 2017 - mdpi.com
Coenzyme A (CoA) and acetyl-coenzyme A (acetyl-CoA) play essential roles in cell energy
metabolism. Dysregulation of the biosynthesis and functioning of both compounds may …