Guide Serum/Plasma Proteomics: Methods and Protocols

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Further developments in informatic analyses, software developments, and computational tools are providing insights into large data sets, open-source data along with large-scale application of bioinformatics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

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SWATH Mass Spectrometry for Proteomics of Non-Depleted Plasma | Springer Nature Experiments

Quantitative protein analysis by mass spectrometry. Methods Mol Biol. Deep profiling of proteome and phosphoproteome by isobaric labeling, extensive liquid chromatography, and mass spectrometry. Methods Enzymol. Systematic optimization of long gradient chromatography mass spectrometry for deep analysis of brain proteome. JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy. Semiquantitative proteomic analysis of rat forebrain postsynaptic density fractions by mass spectrometry. J Biol Chem. Exponentially modified protein abundance index emPAI for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein.

Mass spectrometry for proteomics - part one

Ihaka R, Gentleman R. R: a language for data analysis and graphics. Journal of Computational and Graphical Statistics. Nucleic Acids Res. Architecture of the human interactome defines protein communities and disease networks. A scored human protein-protein interaction network to catalyze genomic interpretation. The ProteomeXchange consortium in supporting the cultural change in proteomics public data deposition. Plasma proteome database as a resource for proteomics research: update. Clinical proteomics in neurodegenerative diseases.

Proteomics Clin Appl.

LC-MS/MS Proteomic Analysis of Dried Blood Spots: A Comparison with Whole Blood

J Neurosci. Neurochem Res. Gene expression changes by amyloid beta peptide-stimulated human postmortem brain microglia identify activation of multiple inflammatory processes. J Leukoc Biol.

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Biochim Biophys Acta. PGC-1 coactivators: inducible regulators of energy metabolism in health and disease. J Clin Invest. PGC-1alpha expression decreases in the Alzheimer disease brain as a function of dementia. Arch Neurol. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. The human plasma proteome draft of building on the human plasma peptideatlas from mass spectrometry and complementary assays. Plasma proteome profiling to assess human health and disease. Cell Syst. Quantitative variability of plasma proteins in a human twin population. Download references.

All authors read and approved the final manuscript. The authors thank all other lab and facility members for helpful discussion, and Brian K. Erickson and Steven P.

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  5. The MS analysis was performed in the Center for Proteomics and Metabolomics; and the peptide synthesis was carried out in the Hartwell Center, both at St. Reviewer account details: Username: reviewer ebi. All the participants have given the written informed consent. This research was approved by the Institutional Review Committee. All experiments were performed in accordance with the relevant guidelines and regulations. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

    Correspondence to Junmin Peng. Reprints and Permissions.

    Human Serum and Plasma Proteomics

    Search all BMC articles Search. Abstract Background Blood-based protein measurement is a routine practice for detecting biomarkers in human disease. Protein digestion and TMT labeling The digestion and labeling were performed based on an optimized protocol [ 32 , 33 ].

    Identification and quantification of proteins by JUMP software suite The bioinformatics processing of identification was carried out with our recently developed JUMP search engine, which combines the advantage of pattern- and tag-dependent scoring to improve sensitivity and specificity [ 35 ]. Calculation of abundance index of identified proteins by PSMs The absolute protein abundance index of serum proteome was calculated based on previously reported methods [ 37 , 38 ], using the total number of PSMs matched to a particular protein, normalized by theoretically detectable peptides from the protein.

    Evaluation of sample variations and principal component analysis The measurement variation was analyzed according to intra- and inter-group replicates. Differential expression DE analysis, pathway enrichment and protein—protein interaction PPI analysis DE analysis was determined by student t test in the following steps: i calculating p values and applying a threshold of 0.

    Results and discussion Multiplexed quantitative analysis of undepleted human serum proteome A flowchart of the experiment is presented in Fig. Full size image. Conclusions We identified proteins and demonstrated high proteome coverage, sensitivity and reproducibility, as well as multiplexed targeted assays.

    Serum/Plasma Proteomics

    References 1. Article Google Scholar 4. Article Google Scholar 5. Google Scholar Article Google Scholar PubMed Google Scholar Acknowledgements The authors thank all other lab and facility members for helpful discussion, and Brian K. Completing interests The authors declare that they have no competing interests.

    Consent for publication The authors declare that they have no competing interests. Ethics approval and consent to participate All the participants have given the written informed consent. Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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    Summary of human cases used in this study. Table S2. The two methods achieve complimentary goals in the field of blood research and pave the way for future translation of next-generation proteomics technologies into clinical practice. Cysteine oxidation. Antibody Data Search Beta. Authors: Julie A.

    Reisz 1 ,. Katelyn M. Chessler 1 ,. Monika Dzieciatkowska 1 ,. Kirk C. Hansen 1. Julie A.