Track topics on Twitter Track topics that are important to you
We reported and evaluated a microflow, single-shot, short gradient SWATH MS method intended to accelerate the discovery and verification of protein biomarkers in preclassified clinical specimens. The method uses a 15 min gradient microflow-LC peptide separation, an optimized SWATH MS window configuration, and OpenSWATH software for data analysis. We applied the method to a cohort containing 204 FFPE tissue samples from 58 prostate cancer patients and 10 benign prostatic hyperplasia patients. Altogether we identified 27,975 proteotypic peptides and 4037 SwissProt proteins from these 204 samples. Compared to a reference SWATH method with a 2 h gradient, we found 3800 proteins were quantified by the two methods on two different instruments with relatively high consistency ( = 0.77). The accelerated method consumed only 17% instrument time, while quantifying 80% of proteins compared to the 2 h gradient SWATH. Although the missing value rate increased by 20%, batch effects reduced by 21%. 75 deregulated proteins measured by the accelerated method were selected for further validation. A shortlist of 134 selected peptide precursors from the 75 proteins were analyzed using MRM-HR, and the results exhibited high quantitative consistency with the 15 min SWATH method ( = 0.89) in the same sample set. We further verified the applicability of these 75 proteins in separating benign and malignant tissues (AUC = 0.99) in an independent prostate cancer cohort ( = 154). Altogether, the results showed that the 15 min gradient microflow SWATH accelerated large-scale data acquisition by 6 times, reduced batch effect by 21%, introduced 20% more missing values, and exhibited comparable ability to separate disease groups.
This article was published in the following journal.
Name: Journal of proteome research
Formalin-fixed, paraffin-embedded (FFPE), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here we developed a pressure cycling technology (PCT)-SWATH mass sp...
Massive formalin-fixed, paraffin-embedded (FFPE) tissue archives exist worldwide, representing an invaluable resource for clinical proteomics research. However, current protocols for FFPE proteomics l...
In the context of mRNA biomarker profiling, formalin fixed paraffin embedded (FFPE) samples represent an interesting source for retrospective analysis. However, the implementation in routine analysis ...
Next-generation sequencing (NGS) analyses on DNA derived from archived Formalin-Fixed Paraffin-Embedded (FFPE) clinical material can provide a powerful tool in oncology research and clinical diagnosti...
Formalin-fixed, paraffin-embedded (FFPE) preservation is the preferred method to archive clinical tissue biopsy samples for histopathological diagnosis. As advances in clinical molecular pathology con...
RATIONALE: Studying samples of tissue from patients with cancer in the laboratory may help doctors identify and learn more about changes that occur in DNA and identify biomarkers related t...
The purpose of the study is to better understand the function of asthma and COPD, and response to therapy. There are two Phases to this study broken into two arms. In Phase I, our propose ...
RATIONALE: Studying the proteins expressed in samples of tumor tissue from patients with cancer may help doctors identify and learn more about biomarkers related to cancer. It may also hel...
This is a prospective, Single time point, discovery study intending to identify biomarkers that can differentiate endometriosis from other underlying reasons for pelvic pain. Patients unde...
1. Develop a Next-Generation Sequencing (NGS) workflow for mutation profiling of formalin-fixed paraffin-embedded (FFPE) tissue and cell-free DNA (cfDNA) specimens. 2. Calculate th...
A small cytosolic fatty-acid binding protein that forms a lipid-binding beta-barrel structure and is expressed by CARDIOMYOCYTES and at lower levels in brain tissue. It is released into plasma immediately following cardiac injury and may therefore serve as a useful biomarker for the early detection of MYOCARDIAL INFARCTION.
A serine threonine kinase that controls a wide range of growth-related cellular processes. The protein is referred to as the target of RAPAMYCIN due to the discovery that TACROLIMUS (commonly known as rapamycin) forms an inhibitory complex with TACROLIMUS BINDING PROTEIN 1A that blocks the action of its enzymatic activity.
The use of needles usually larger than 14-gauge to remove tissue samples large enough to retain cellular architecture for pathology examination.
Clonal hematopoetic disorder caused by an acquired genetic defect in PLURIPOTENT STEM CELLS. It starts in MYELOID CELLS of the bone marrow, invades the blood and then other organs. The condition progresses from a stable, more indolent, chronic phase (LEUKEMIA, MYELOID, CHRONIC PHASE) lasting up to 7 years, to an advanced phase composed of an accelerated phase (LEUKEMIA, MYELOID, ACCELERATED PHASE) and BLAST CRISIS.
The simultaneous analysis of multiple samples of TISSUES or CELLS from BIOPSY or in vitro culture that have been arranged in an array format on slides or microchips.
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...
Multiple Sclerosis MS
Multiple sclerosis (MS) is the most common disabling neurological condition affecting 100,000 young adults in the UK. The condition results from autoimmune damage to myelin, causing interference in nerve signaling. Symptoms experienced depend on the pa...