HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples

Alex, J.; Gelfand, Craig A.; Haywood, Bruce C.; Warunek, David; Yi, Jizu; Schuchard, Mark D.; Mehigh, Richard J.; Cockrill, Steven L.; Scott, Graham; Tammen, Harald; Schulz‐Knappe, Peter; Speicher, David W.; Vitzthum, Frank; Haab, Brian B.; Siest, Gérard; Chan, Daniel W.

doi:10.1002/9783527609482.ch3

Cited by 100 publications

(151 citation statements)

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“…These observations suggest that CTAD could reduce artifacts associated with platelet activation. However, it has been reported that the optimal method for preparing plasma depends also on the subsequent technical analysis to be performed [24]. On the other hand, cysteinyl modification using specific oxidation by hydroxyethyl disulfide improves the appearance of protein spots for an acidic pH gradient ranging from 4 to 7 although this modification was initially developed to ameliorate protein migration in alkaline pH ranges [19].…”

Section: Discussionmentioning

confidence: 99%

Proteomic Analysis of Human Plasma Proteins by Two-Dimensional Gel Electrophoresis and by Antibody Arrays Following Depletion of High-Abundance Proteins

Desrosiers

Beaulieu

Buchanan

et al. 2007

Cell Biochem Biophys

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Detecting proteins that are present at lower levels in human plasma, for the identification of potential disease biomarkers, is complicated by a few highly abundant proteins. One promising strategy is the removal of these abundant proteins interfering with the analysis of plasma content by proteomic techniques. This study compared three affinity-based methods to remove the most abundant proteins in human plasma. Two of them, based on antibodies, which depletes the six or the 12 most abundant proteins, demonstrated the highest efficiency in enriching less abundant plasma proteins. Comparison of two anticoagulant treatments for plasma preparation, EDTA and CTAD, showed that this treatment influenced the patterns of lower-abundance proteins visible on 2-dimensional (2-D) gels. Several staining procedures including two fluorescent dyes, Sypro Ruby and Deep Purple, were also compared with a very sensitive silver staining method for the visualization of lower-abundance proteins on 2-D gels. Furthermore, treatments of lower-abundance plasma proteins with hydroxyethyl disulfide enhanced protein sharpness and resolution. The purpose of all these systematic comparisons was to select the most reliable methods in different steps of plasma preparation and handling as well as in analysis of proteins by 2-D gels to obtain highly reproducible patterns of lower-abundance plasma proteins. Importantly, the lower-abundance plasma proteins enriched by these optimized conditions were further analyzed by antibody microarrays allowing the identification of 61 proteins using 350 antibodies directed against signalling proteins suggesting that this proteomic strategy is a valuable approach for detecting potential plasma biomarkers.

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Section: Discussionmentioning

confidence: 99%

Proteomic Analysis of Human Plasma Proteins by Two-Dimensional Gel Electrophoresis and by Antibody Arrays Following Depletion of High-Abundance Proteins

Desrosiers

Beaulieu

Buchanan

et al. 2007

Cell Biochem Biophys

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“…The level of serological markers for cancer is usually very low. Therefore, adequate protein enrichment techniques should be employed before mass spectrometric analysis is conducted [18,19]. Current methods are also characterized by drawbacks.…”

Section: Introductionmentioning

confidence: 99%

iTRAQ-based quantitative analysis of cancer-derived secretory proteome reveals TPM2 as a potential diagnostic biomarker of colorectal cancer

Xiao

Shao

et al. 2016

Front. Med.

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Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. We aimed to find novel molecules as potential biomarkers for the early diagnosis of CRC. A serum-free conditioned medium was successfully collected from three pairs of CRC tissue and adjacent normal tissue. iTRAQ-based quantitative proteomic analysis was applied to compare the differences in secretome between primary CRC mucosa and adjacent normal mucosa. A total of 145 kinds of proteins were identified. Of these proteins, 29 were significantly different between CRC and normal tissue. Tropomyosin 2 β (TPM2) exhibited the most significant differences; as such, this protein was selected for further validation. Quantitative real-time PCR indicated that the mRNA expression of TPM2 significantly decreased in the CRC tissue compared with the paired adjacent normal tissue. Immunohistochemical analysis also confirmed that TPM2 was barely detected at protein levels in the CRC tissue. In summary, this study revealed potential molecules for future biomarker applications and provided an efficient approach for the differential analysis of cancer-associated secretome. TPM2 may be valuable for the early diagnosis of CRC.

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“…Although there is no unique or 'optimal' SOP when it comes to plasma processing, it is important to adhere to a single protocol for samples within the same study. Our recommendations are general guidelines falling within those reported by the Human Proteome Organization (HUPO) [16] and the Early Detection Research Network (EDRN) [17] with some modifications and include: processing of blood within 30 min of collection, centrifugation at room temperature to avoid platelet activation, preparation of small volume aliquots to avoid the effect of freeze and thaw cycles and immediate freezing after processing. We have also recommended the use of data sheets to record information such as the time when the sample was collected, time of processing, lot number of blood collection tubes, volume of blood in tube, presence of hemolysis, processing protocol used and any deviations to the SOP.…”

Section: Blood Samples For Researchmentioning

confidence: 99%

Making personalized medicine a reality: the challenges of a modern translational research biopsy-driven program in an academic setting: the Segal Cancer Center experience

et al. 2011

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The success of personalized medicine in the oncology clinic is very dependent on the results from a translational research effort to identify individual and host molecular biomarkers to enable proper selection of anticancer therapy. For this to happen, it is necessary to obtain timely access to high-quality biological samples of both host and tumor tissues and biological fluids. At the Segal Cancer Center, we have initiated several prospective sample collections based on research-driven breast biopsies in different contexts, including primary and metastatic breast lesions in patients receiving specific treatments. We here describe some of the challenges involved in such a translational research program and our experience in setting up biopsy-driven research protocols, highlighting the human aspects of conducting these complex enterprises.

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HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples

Cited by 100 publications

References 0 publications

Proteomic Analysis of Human Plasma Proteins by Two-Dimensional Gel Electrophoresis and by Antibody Arrays Following Depletion of High-Abundance Proteins

Proteomic Analysis of Human Plasma Proteins by Two-Dimensional Gel Electrophoresis and by Antibody Arrays Following Depletion of High-Abundance Proteins

iTRAQ-based quantitative analysis of cancer-derived secretory proteome reveals TPM2 as a potential diagnostic biomarker of colorectal cancer

Making personalized medicine a reality: the challenges of a modern translational research biopsy-driven program in an academic setting: the Segal Cancer Center experience

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