scholarly journals Prostate cancer serum biomarker discovery through proteomic analysis of alpha-2 macroglobulin protein complexes

2008 ◽  
Vol 2 (9) ◽  
pp. 1223-1233 ◽  
Author(s):  
Earle F. Burgess ◽  
Amy-Joan L. Ham ◽  
David L. Tabb ◽  
Dean Billheimer ◽  
Bruce J. Roth ◽  
...  
2005 ◽  
Vol 173 (4S) ◽  
pp. 383-383
Author(s):  
C. Nicole White ◽  
Zhen Zhang ◽  
Derek Chappell ◽  
Jason M. Rosenzweig ◽  
Lori J. Sokoll ◽  
...  

2005 ◽  
Vol 173 (4S) ◽  
pp. 383-383
Author(s):  
Rainer Kuefer ◽  
Matthias D. Hofer ◽  
Christoph Zorn ◽  
Bjoern G. Volkmer ◽  
Juergen E. Gschwend ◽  
...  

2002 ◽  
Vol 3 (3) ◽  
pp. 221-225

In recent months a bumper crop of genomes has been completed, including the fission yeast (Schizosaccharomyces pombe) and rice (Oryza sativa). Two large-scale studies ofSaccharomyces cerevisiaeprotein complexes provided a picture of the eukaryotic proteome as a network of complexes. Amongst the other stories of interest was a demonstration that proteomic analysis of blood samples can be used to detect ovarian cancer, perhaps even as early as stage I.


PROTEOMICS ◽  
2007 ◽  
Vol 7 (16) ◽  
pp. 2688-2697 ◽  
Author(s):  
Ming Zhou ◽  
Timothy D. Veenstra

PRILOZI ◽  
2015 ◽  
Vol 36 (1) ◽  
pp. 5-36 ◽  
Author(s):  
Katarina Davalieva ◽  
Momir Polenakovic

Abstract Prostate cancer (PCa) is the second most frequently diagnosed malignancy in men worldwide. The introduction of prostate specific antigen (PSA) has greatly increased the number of men diagnosed with PCa but at the same time, as a result of the low specificity, led to overdiagnosis, resulting to unnecessary biopsies and high medical cost treatments. The primary goal in PCa research today is to find a biomarker or biomarker set for clear and effecttive diagnosis of PCa as well as for distinction between aggressive and indolent cancers. Different proteomic technologies such as 2-D PAGE, 2-D DIGE, MALDI MS profiling, shotgun proteomics with label-based (ICAT, iTRAQ) and label-free (SWATH) quantification, MudPIT, CE-MS have been applied to the study of PCa in the past 15 years. Various biological samples, including tumor tissue, serum, plasma, urine, seminal plasma, prostatic secretions and prostatic-derived exosomes were analyzed with the aim of identifying diagnostic and prognostic biomarkers and developing a deeper understanding of the disease at the molecular level. This review is focused on the overall analysis of expression proteomics studies in the PCa field investigating all types of human samples in the search for diagnostics biomarkers. Emphasis is given on proteomics platforms used in biomarker discovery and characterization, explored sources for PCa biomarkers, proposed candidate biomarkers by comparative proteomics studies and the possible future clinical application of those candidate biomarkers in PCa screening and diagnosis. In addition, we review the specificity of the putative markers and existing challenges in the proteomics research of PCa.


2019 ◽  
Author(s):  
Rui Sun ◽  
Christie Hunter ◽  
Chen Chen ◽  
Weigang Ge ◽  
Nick Morrice ◽  
...  

ABSTRACTWe report and evaluated a microflow, single-shot, short gradient SWATH MS method intended to accelerate the discovery and verification of protein biomarkers in clinical specimens. The method uses 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 204 of FFPE prostate tissue samples from 58 prostate cancer patients and 10 prostatic hyperplasia patients. Altogether we identified 27,976 proteotypic peptides and 4,043 SwissProt proteins from these 204 samples. Compared to a reference SWATH method with 2-hour gradient the accelerated method consumed only 27% instrument time, quantified 80% proteins and showed reduced batch effects. 3,800 proteins were quantified by both methods in two different instruments with relatively high consistency (r = 0.77). 75 proteins detected by the accelerated method with differential abundance between clinical groups were selected for further validation. A shortlist of 134 selected peptide precursors from the 75 proteins were analyzed using MRM-HR, exhibiting high quantitative consistency with the 15-min SWATH method (r = 0.89) in the same sample set. We further verified the capacity of these 75 proteins in separating benign and malignant tissues (AUC = 0.99) in an independent prostate cancer cohort (n=154).Overall our data show that the single-shot short gradient microflow-LC SWATH MS method achieved about 4-fold acceleration of data acquisition with reduced batch effect and a moderate level of protein attrition compared to a standard SWATH acquisition method. Finally, the results showed comparable ability to separate clinical groups.


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