Analysis of Mass Spectrometry Profiles of the Serum Proteome

Coombes, Kevin R.

doi:10.1373/clinchem.2004.040832

Cited by 28 publications

(15 citation statements)

References 28 publications

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“…The latter study rigorously examined the circumstances necessary for generation of reproducible and complex spectra, including laser conditions and matrix composition. Equally important is the development and evaluation of the optimal methods of data analysis, including new bioinformatic and biostatistical methods, each with their own specific attributes and drawbacks (49 ). Mass spectrometric profiling is a promising method of marker discovery, but well-designed studies are critical to allow proper interpretation of the clinical utility of the results and identification of key variables.…”

Section: Discussionmentioning

confidence: 99%

Influences of Blood Sample Processing on Low–Molecular-Weight Proteome Identified by Surface-Enhanced Laser Desorption/Ionization Mass Spectrometry

et al. 2005

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Background: Profiling approaches in proteomics, such as surface-enhanced laser desorption/ionization (SELDI) mass spectrometry, are used in disease marker discovery. The aim of this study was to investigate the potential influence of selected preanalytical factors on the results obtained. Methods: Plasma samples anticoagulated with EDTA, citrate, or heparin, and serum samples from healthy volunteers were profiled by SELDI on CM10, immobilized metal affinity capture (IMAC) array with copper, and H50 chip surfaces. Using linear mixed-effects models, we examined the influence of elapsed time between venipuncture and sample separation (immediate to 24 h) and the type of serum tube used (Greiner Vacuette activator, gel serum separator, or plain tubes). We analyzed purified platelets, as well as platelet-poor and platelet-rich plasma samples treated with calcium and/or thrombin to determine the platelet contribution, directly or via the clotting process, to the profiles generated. We then used cluster analysis to identify samples with similar peak profiles. Results: Different plasma types and sera could be distinguished on the basis of cluster analyses of their spectral profiles. Elapsed time between venipuncture and separation of plasma and serum from blood samples altered the profiles obtained, particularly for serum

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Section: Discussionmentioning

confidence: 99%

Influences of Blood Sample Processing on Low–Molecular-Weight Proteome Identified by Surface-Enhanced Laser Desorption/Ionization Mass Spectrometry

et al. 2005

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“…This approach was simple, available, and not invasive compared with other diagnostic approaches. Biases from sample collection, MALDI‐TOF/TOF MS performance, agents used, and the operator could influence the reproducibility . To minimize these influences, we standardized the collection and fractionation protocol, and optimized parameters of MALDI‐TOF/TOF MS .…”

Section: Discussionmentioning

confidence: 99%

“…Biases from sample collection, MALDI-TOF/TOF MS performance, agents used, and the operator could influence the reproducibility. 26,27 To minimize these influences, we standardized the collection and fractionation protocol, and optimized parameters of MALDI-TOF/TOF MS. [28][29][30] Distribution of age and gender between HCC and LC group were taken into account as we collected the patient serum samples. Strikingly, the MALDI-TOF/TOF MS peptide profiling technology needed no knowledge of the amino acid sequence of the peaks or their biological functions for class prediction.…”

Section: Discussionmentioning

confidence: 99%

Serum peptide pattern that differentially diagnoses hepatitis B virus‐related hepatocellular carcinoma from liver cirrhosis

Wang

Cao

Song

et al. 2014

J of Gastro and Hepatol

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“…This in turns leads to the rather low-resolution pattern that represents only a minority of proteins and peptides in the serum. Other limitations for SELDI protein profiling are due to variability such as in instrumental laser desorption energy level and ProteinChip array quality and in sample collection, processing, and storage (32, 49–53). These changes resulted in reproducible changes in serum proteome, and can sometimes overshadow the biological changes in the serum samples (32).…”

Section: Methodsmentioning

confidence: 99%

High Throughput Profiling of Serum Phosphoproteins/Peptides Using the SELDI-TOF-MS Platform

Jayachandran

Roth

2011

Methods in Molecular Biology

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Protein phosphorylation is a dynamic post-translational modification that plays a critical role in the regulation of a wide spectrum of biological events and cellular functions including signal transduction, gene expression, cell proliferation, and apoptosis. Determination of the sites and magnitudes of protein phosphorylation has been an essential step in the analysis of the control of many biological systems. A high throughput analysis of phosphorylation of proteins would provide a simple, logical, and useful tool for a functional dissection and prediction of biological functions and signaling pathways in association with these important molecular events. We have developed a functional proteomics technique using the ProteinChip array-based SELDI-TOF-MS analysis for high throughput profiling of phosphoproteins/phosphopeptides in human serum for the early detection and diagnosis as well as for the molecular staging of human cancer. The methodology and experimental approach consists of five steps: (1) generation of a total peptide pool of serum proteins by a global trypsin digestion; (2) rapid isolation of phosphopeptides from the total serum peptide pool by an affinity selection, purification, and enrichment using a novel automated micro-bioprocessing system with phospho-antibody-conjugated paramagnetic beads and a hybrid magnet plate; (3) high throughput phosphopeptide analysis on ProteinChip arrays by automated SELDI-TOF-MS; and (4) bioinformatics and statistical methods for data analysis. This method with appropriate modifications may be equally applicable to serine-, threonine- and tyrosine-phosphorylated proteins and for selectively isolating, profiling, and identifying phosphopeptides present in a highly complex phosphor-peptide mixture prepared from various human specimens such as cells, tissue samples, and serum and other body fluids.

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Analysis of Mass Spectrometry Profiles of the Serum Proteome

Cited by 28 publications

References 28 publications

Influences of Blood Sample Processing on Low–Molecular-Weight Proteome Identified by Surface-Enhanced Laser Desorption/Ionization Mass Spectrometry

Influences of Blood Sample Processing on Low–Molecular-Weight Proteome Identified by Surface-Enhanced Laser Desorption/Ionization Mass Spectrometry

Serum peptide pattern that differentially diagnoses hepatitis B virus‐related hepatocellular carcinoma from liver cirrhosis

High Throughput Profiling of Serum Phosphoproteins/Peptides Using the SELDI-TOF-MS Platform

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