High-Throughput Proteomic Analysis of Fresh-Frozen Biopsy Tissue Samples Using Pressure Cycling Technology Coupled with SWATH Mass Spectrometry

2017 ◽  
pp. 279-287 ◽  
Author(s):  
Yi Zhu ◽  
Tiannan Guo
Keyword(s):  
Mass Spectrometry ◽  
High Throughput ◽  
Proteomic Analysis ◽  
Tissue Samples ◽  
Pressure Cycling ◽  
Biopsy Tissue ◽  
Fresh Frozen ◽  
Pressure Cycling Technology

Accelerated Lysis and Proteolytic Digestion of Biopsy-Level Fresh-Frozen and FFPE Tissue Samples Using Pressure Cycling Technology

2020 ◽  
Vol 19 (5) ◽  
pp. 1982-1990 ◽  
Author(s):  
Huanhuan Gao ◽  
Fangfei Zhang ◽  
Shuang Liang ◽  
Qiushi Zhang ◽  
Mengge Lyu ◽  
...  
Keyword(s):  
Ffpe Tissue ◽  
Proteolytic Digestion ◽  
Tissue Samples ◽  
Pressure Cycling ◽  
Fresh Frozen ◽  
Pressure Cycling Technology

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

2019 ◽  
Vol 13 (11) ◽  
pp. 2305-2328 ◽  
Author(s):  
Yi Zhu ◽  
Tobias Weiss ◽  
Qiushi Zhang ◽  
Rui Sun ◽  
Bo Wang ◽  
...  
Keyword(s):  
High Throughput ◽  
Proteomic Analysis ◽  
Ffpe Tissue ◽  
Tissue Samples

scholarly journals Serial in-solution digestion protocol for mass spectrometry-based glycomics and proteomics analysis

2020 ◽  
Vol 16 (4) ◽  
pp. 364-376 ◽  
Author(s):  
Manveen K. Sethi ◽  
Margaret Downs ◽  
Joseph Zaia
Keyword(s):  
Mass Spectrometry ◽  
High Throughput ◽  
Proteomic Analysis ◽  
Proteomics Analysis

A high-throughput & efficient protocol for mass spectrometry-based glycomic and proteomic analysis.

scholarly journals How Do We Define the Genomic Landscape?

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. SCI-13-SCI-13
Author(s):  
Sandeep S. Dave
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Conflicts Of Interest ◽  
Genomic Analysis ◽  
Future Directions ◽  
Tissue Samples ◽  
Genomic Landscape ◽  
Fresh Frozen ◽  
Definition Of ◽  
Formalin Fixed

High throughput sequencing is a revolutionary technology for the definition of the genomic features of tumors. This talk will provide a review of the relevant methodologies for non-experts in the field. The presentation will include a discussion of how high throughput sequencing is performed, its relative strengths and weaknesses, and how it is applicable to formalin-fixed and fresh/frozen tissue samples. The talk will also describe future directions in the genomic analysis of tumors. Disclosures No relevant conflicts of interest to declare.

scholarly journals Protein Classifier for Thyroid Nodules Learned from Rapidly Acquired Proteotypes

2020 ◽  
Author(s):  
Yaoting Sun ◽  
Sathiyamoorthy Selvarajan ◽  
Zelin Zang ◽  
Wei Liu ◽  
Yi Zhu ◽  
...  
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Thyroid Nodules ◽  
Thyroid Tissue ◽  
Tissue Samples ◽  
Pressure Cycling ◽  
Data Independent Acquisition ◽  
Artificial Neural ◽  
Pressure Cycling Technology ◽  
Sizeable Number

SUMMARYUp to 30% of thyroid nodules cannot be accurately classified as benign or malignant by cytopathology. Diagnostic accuracy can be improved by nucleic acid-based testing, yet a sizeable number of diagnostic thyroidectomies remains unavoidable. In order to develop a protein classifier for thyroid nodules, we analyzed the quantitative proteomes of 1,725 retrospective thyroid tissue samples from 578 patients using pressure-cycling technology and data-independent acquisition mass spectrometry. With artificial neural networks, a classifier of 14 proteins achieved over 93% accuracy in classifying malignant thyroid nodules. This classifier was validated in retrospective samples of 271 patients (91% accuracy), and prospective samples of 62 patients (88% accuracy) from four independent centers. These rapidly acquired proteotypes and artificial neural networks supported the establishment of an effective protein classifier for classifying thyroid nodules.

The use of formalin fixed wax embedded tissue for proteomic analysis: Table 1

2011 ◽  
Vol 64 (4) ◽  
pp. 297-302 ◽  
Author(s):  
Lynda D Ralton ◽  
Graeme I Murray
Keyword(s):  
Proteomic Analysis ◽  
Protein Separation ◽  
Biomarker Discovery ◽  
Outcome Data ◽  
Fresh Tissue ◽  
Tissue Samples ◽  
Highly Sensitive ◽  
Fresh Frozen ◽  
Proteomics Research ◽  
Formalin Fixed

The potential of proteomic approaches to elucidate disease pathogenesis and biomarker discovery is increasingly being recognised. These studies are usually based on the use of fresh tissue samples. Problems in obtaining and storing fresh frozen samples, especially either for the investigation of rare diseases or for the study of microscopic disease foci, have led to the investigation of the possible use of formalin fixed wax embedded tissue for proteomic biomarker detection Overcoming problems with protein cross-linking associated with formalin fixation of tissues, especially by using heat-mediated retrieval techniques combined with highly sensitive methods for protein separation and identification are now emerging, giving promise to the use of formalin fixed wax embedded tissues for proteomic analysis. Formalin fixed wax embedded tissues, together with their associated clinical and pathological information outcome may provide significant potential opportunities for proteomics research. Such studies of formalin fixed wax embedded tissue will allow access to already acquired clinical tissue samples which can be readily correlated with clinical, pathological and outcome data. It also provides access to rare types of tissue/diseases that would be either difficult to collect prospectively in a timely manner or are unlikely to be available as fresh samples. The purpose of this review is to provide an overview of the issues associated with the use of formalin fixed wax embedded tissues for proteomics.

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