Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Additions to the Human Plasma Proteome via a Tandem MARS Depletion iTRAQ-Based Workflow.

ABSTRACT: Robust platforms for determining differentially expressed proteins in biomarker and discovery studies using human plasma are of great interest. While increased depth in proteome coverage is desirable, it is associated with costs of experimental time due to necessary sample fractionation. We evaluated a robust quantitative proteomics workflow for its ability (1) to provide increased depth in plasma proteome coverage and (2) to give statistical insight useful for establishing differentially expressed plasma proteins. The workflow involves dual-stage immunodepletion on a multiple affinity removal system (MARS) column, iTRAQ tagging, offline strong-cation exchange chromatography, and liquid chromatography tandem mass spectrometry (LC-MS/MS). Independent workflow experiments were performed in triplicate on four plasma samples tagged with iTRAQ 4-plex reagents. After stringent criteria were applied to database searched results, 689 proteins with at least two spectral counts (SC) were identified. Depth in proteome coverage was assessed by comparison to the 2010 Human Plasma Proteome Reference Database in which our studies reveal 399 additional proteins which have not been previously reported. Additionally, we report on the technical variation of this quantitative workflow which ranges from ±11 to 30%.

SUBMITTER: Cao Z

PROVIDER: S-EPMC3590782 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Proteomic analyses of human plasma: Venus versus Mars.

Project description:BackgroundPlasma is vital for the resuscitation of injured patients and to restore necessary procoagulants, especially Factors (F)II, FV, FVII, FX, and FXIII; however, female plasma has been implicated in the majority of transfusion-related acute lung injury (TRALI) cases and male-only plasma transfusion regimens have significantly decreased the incidence of TRALI. Little is known about the human plasma proteome, and no comparisons have been made between male and female plasma; therefore, we hypothesize that there are significant differences between plasma from male and female donors.Study design and methodsFive units of fresh-frozen plasma each were collected from nulliparous female donors and male donors, and the proteome was analyzed by depleting the 14 most common proteins by immunoaffinity columns followed by protein separation by one dimension gel electrophoresis, tryptic digestion of the proteins, analysis of the peptides by liquid chromatography-tandem mass spectrometry, and identification employing human protein sequence databases.ResultsFemale plasma versus male plasma contained pregnancy zone protein (419- to 580-fold), FV (twofold), α(1)-antitrypsin (twofold), β(2) -microglobulin (twofold), and Complement Factors H and C4B (1.5- to 2-fold) at significantly higher concentrations than males and males contained significant increases in Fc-binding protein (twofold), protein Z-dependent protease inhibitor (twofold), phosphatidylinositol glycan-specific phospholipase (fourfold), protein S-100 (threefold), and transgelin-2 (14-fold) versus females (p < 0.005). The increases in FV, α(1)-antitrypsin, and β(2)-microglobulin were confirmed by an activity assay or immunoblots.ConclusionWe conclude that there are proteomic differences between male and female plasma, which could be exploited to improve clinical outcomes in transfused patients.

| S-EPMC3235251 | biostudies-literature

Depletion of abundant plasma proteins for extracellular vesicle proteome characterization: benefits and pitfalls.

Project description:Blood extracellular vesicles (EVs) play essential roles in cell-cell communication and their molecular cargo is a promising source of disease biomarkers. However, proteomic characterization of plasma-derived EVs is challenged by the presence of highly abundant plasma proteins, which limits the detection of less abundant proteins, and by the low number of EVs in biological fluids. The aim of this study was to investigate if the removal of abundant plasma proteins prior to EV isolation could improve plasma-derived EV characterization by LC-MS/MS and expand the proteome coverage. Plasma depletion was performed using a single-use spin column and EVs were isolated from only 100 µL of non-depleted and depleted plasma by size exclusion chromatography. Afterwards, EVs were characterized by nanoparticle tracking analysis and mass spectrometry-based proteomics using a data-independent acquisition approach. Depleted plasma-derived EVs had higher particle concentrations and particle-to-protein ratios. Depletion did increase the protein coverage with a higher number of identifications in EVs from depleted plasma (474 proteins) than from non-depleted (386 proteins). However, EVs derived from non-depleted plasma carried a slightly higher number of common EV markers. Overall, our findings suggest that plasma depletion prior to EV isolation by size exclusion chromatography provides higher yield and protein coverage, but slightly lower identification of EV markers. This study also showed the possibility to characterize the proteome of EVs derived from small plasma volumes, encouraging the clinical feasibility of the discovery of EV biomarkers.

| S-EPMC10287573 | biostudies-literature

Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry.

Project description:There is significant interest in characterization of the human plasma proteome due to its potential for providing biomarkers applicable to clinical diagnosis and treatment and for gaining a better understanding of human diseases. We describe here a strategy for comparative proteome analyses of human plasma, which is applicable to biomarker identifications for various disease states. Multidimensional liquid chromatography-mass spectrometry (LC-MS/MS) has been applied to make comparative proteome analyses of plasma samples from an individual prior to and 9 h after lipopolysaccharide (LPS) administration. Peptide peak areas and the number of peptide identifications for each protein were used to evaluate the reproducibility of LC-MS/MS and to compare relative changes in protein concentration between the samples following LPS treatment. A total of 804 distinct plasma proteins (not including immunoglobulins) were confidently identified with 32 proteins observed to be significantly increased in concentration following LPS administration, including several known inflammatory response or acute-phase mediators such as C-reactive protein, serum amyloid A and A2, LPS-binding protein, LPS-responsive and beige-like anchor protein, hepatocyte growth factor activator, and von Willebrand factor, and thus, constituting potential biomarkers for inflammatory response.

| S-EPMC1781926 | biostudies-literature

Human Plasma Proteome During Normal Pregnancy

Project description:This study used SomaScan v 4.1 to profile>7000 proteins in maternal plasma and asses changes with gestational age and maternal characteristics. The study proposed models to estimate the expected protein abundance so that future datasets can be normalized agains these expected value to obtain Multiples of the Mean values.

2022-09-26 | GSE206454 | GEO

Genomic atlas of the human plasma proteome.

Project description:Although plasma proteins have important roles in biological processes and are the direct targets of many drugs, the genetic factors that control inter-individual variation in plasma protein levels are not well understood. Here we characterize the genetic architecture of the human plasma proteome in healthy blood donors from the INTERVAL study. We identify 1,927 genetic associations with 1,478 proteins, a fourfold increase on existing knowledge, including trans associations for 1,104 proteins. To understand the consequences of perturbations in plasma protein levels, we apply an integrated approach that links genetic variation with biological pathway, disease, and drug databases. We show that protein quantitative trait loci overlap with gene expression quantitative trait loci, as well as with disease-associated loci, and find evidence that protein biomarkers have causal roles in disease using Mendelian randomization analysis. By linking genetic factors to diseases via specific proteins, our analyses highlight potential therapeutic targets, opportunities for matching existing drugs with new disease indications, and potential safety concerns for drugs under development.

| S-EPMC6697541 | biostudies-literature

IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments.

Project description:Reproducibility has become a major concern in biomedical research. In proteomics, bioinformatic workflows can quickly consist of multiple software tools each with its own set of parameters. Their usage involves the definition of often hundreds of parameters as well as data operations to ensure tool interoperability. Hence, a manuscript's methods section is often insufficient to completely describe and reproduce a data analysis workflow. Here we present IsoProt: A complete and reproducible bioinformatic workflow deployed on a portable container environment to analyze data from isobarically labeled, quantitative proteomics experiments. The workflow uses only open source tools and provides a user-friendly and interactive browser interface to configure and execute the different operations. Once the workflow is executed, the results including the R code to perform statistical analyses can be downloaded as an HTML document providing a complete record of the performed analyses. IsoProt therefore represents a reproducible bioinformatics workflow that will yield identical results on any computer platform.

| S-EPMC6456869 | biostudies-literature

Human Plasma Proteome During Normal Pregnancy

Project description:Human Plasma Proteome During Normal Pregnancy

| PRJNA851013 | ENA

Additions to the "Martian Flora": new botanical records from the Mars Desert Research Station, Utah.

Project description:The Mars Desert Research Station (MDRS) is a Mars-simulation campus set in a Martian planetary analogue in southern Utah. Despite a long history of astrobiology research, collections-based taxonomic inventories of the macro-level biodiversity around the station are relatively new. This study serves to add to the initial vascular plant list published for the station in 2016, where 39 species were recorded for MDRS. Here we report 40 new species, two new taxa recorded only to genus and two species re-identified from our 2016 fieldwork, bringing the total number of taxa in the "Martian" flora to 79 species and two taxa recorded to genus.

| S-EPMC7447676 | biostudies-literature

Mutation patterns of amino acid tandem repeats in the human proteome.

Project description:BACKGROUND: Amino acid tandem repeats are found in nearly one-fifth of human proteins. Abnormal expansion of these regions is associated with several human disorders. To gain further insight into the mutational mechanisms that operate in this type of sequence, we have analyzed a large number of mutation variants derived from human expressed sequence tags (ESTs). RESULTS: We identified 137 polymorphic variants in 115 different amino acid tandem repeats. Of these, 77 contained amino acid substitutions and 60 contained gaps (expansions or contractions of the repeat unit). The analysis showed that at least about 21% of the repeats might be polymorphic in humans. We compared the mutations found in different types of amino acid repeats and in adjacent regions. Overall, repeats showed a five-fold increase in the number of gap mutations compared to adjacent regions, reflecting the action of slippage within the repetitive structures. Gap and substitution mutations were very differently distributed between different amino acid repeat types. Among repeats containing gap variants we identified several disease and candidate disease genes. CONCLUSION: This is the first report at a genome-wide scale of the types of mutations occurring in the amino acid repeat component of the human proteome. We show that the mutational dynamics of different amino acid repeat types are very diverse. We provide a list of loci with highly variable repeat structures, some of which may be potentially involved in disease.

| S-EPMC1557989 | biostudies-literature

Advances and Utility of the Human Plasma Proteome.

Project description:The study of proteins circulating in blood offers tremendous opportunities to diagnose, stratify, or possibly prevent diseases. With recent technological advances and the urgent need to understand the effects of COVID-19, the proteomic analysis of blood-derived serum and plasma has become even more important for studying human biology and pathophysiology. Here we provide views and perspectives about technological developments and possible clinical applications that use mass-spectrometry(MS)- or affinity-based methods. We discuss examples where plasma proteomics contributed valuable insights into SARS-CoV-2 infections, aging, and hemostasis and the opportunities offered by combining proteomics with genetic data. As a contribution to the Human Proteome Organization (HUPO) Human Plasma Proteome Project (HPPP), we present the Human Plasma PeptideAtlas build 2021-07 that comprises 4395 canonical and 1482 additional nonredundant human proteins detected in 240 MS-based experiments. In addition, we report the new Human Extracellular Vesicle PeptideAtlas 2021-06, which comprises five studies and 2757 canonical proteins detected in extracellular vesicles circulating in blood, of which 74% (2047) are in common with the plasma PeptideAtlas. Our overview summarizes the recent advances, impactful applications, and ongoing challenges for translating plasma proteomics into utility for precision medicine.

| S-EPMC9469506 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data