Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiplexed Nanoparticle Protein Corona Enables Accurate and Precise Deep Plasma Proteomics

ABSTRACT: The Proteograph Product Suite, a multiplexed nanoparticle (NP) protein corona-based proteomics workflow, substantially improves the depth of detection of proteins by mass spectrometry (MS) by compressing the dynamic range of protein abundances. Here, we explore the quantitative performance of the Proteograph Product Suite and its applicability to large-scale studies. Using multi-species spike-in experiments, we investigated fold-change accuracy, linearity, precision and the lower limit of quantification (LLOQ) for the Proteograph Product Suite in conjunction with multiple MS instruments. We also manufactured four distinct lots of NPs (each capable of supporting over 100,000 assays) and evaluated batch to batch reproducibility.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Bos Taurus (bovine)

TISSUE(S): Blood Plasma

SUBMITTER: Ting Huang

LAB HEAD: Asim Siddiqui

PROVIDER: PXD066817 | Pride | 2025-10-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	EXP23048_2023ms0267aX10_A.raw.mzML	Mzml
	EXP23048_2023ms0267aX11_A.raw.mzML	Mzml
	EXP23048_2023ms0267aX12_A.raw.mzML	Mzml
	EXP23048_2023ms0267aX17_A.raw.mzML	Mzml
	EXP23048_2023ms0267aX18_A.raw.mzML	Mzml

Items per page:

1 - 5 of 190

Similar Datasets

Multiplexed Nanoparticle Protein Corona Enables Accurate and Precise Deep Plasma Proteomics

Project description:The Proteograph Product Suite, a multiplexed nanoparticle (NP) protein corona-based proteomics workflow, substantially improves the depth of detection of proteins by mass spectrometry (MS) by compressing the dynamic range of protein abundances. Here, we explore the quantitative performance of the Proteograph Product Suite and its applicability to large-scale studies. Using multi-species spike-in experiments, we investigated fold-change accuracy, linearity, precision and the lower limit of quantification (LLOQ) for the Proteograph Product Suite in conjunction with multiple MS instruments. We also manufactured four distinct lots of NPs (each capable of supporting over 100,000 assays) and evaluated batch to batch reproducibility.

2025-10-22 | PXD066700 | Pride

Multiplexed Nanoparticle Protein Corona Enables Accurate and Precise Deep Plasma Proteomics

2025-10-22 | PXD066813 | Pride

Multiplexed Nanoparticle Protein Corona Enables Accurate and Precise Deep Plasma Proteomics

2025-10-22 | PXD066851 | Pride

timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery (Loading curve dataset)

Project description:Mass spectrometry (MS) has emerged as a valuable tool for plasma proteome profiling and disease biomarker discovery. However, wide range of plasma protein concentrations along with technical and biological variabilities, continue to present significant challenges for deep and reproducible protein quantitation across large patient cohorts. Here we demonstrate the qualitative and quantitative performance gain of the timsTOF HT over the timsTOF Pro 2 mass spectrometer in the analysis of neat (unfractionated) and Proteograph™ (PG)-processed plasma across a wide range of peptide loading masses and liquid chromatography (LC) gradients. We observed up to a 76% increase in total plasma peptide precursors identified and a >2-fold boost in quantifiable plasma peptide precursors (CV<20%) with timsTOF HT compared to timsTOF Pro 2. In an exploratory study of 20 late-stage cancer and 20 control sampleswe observed a ~50% increase in total and statistically significant plasma peptide precursors (q<0.05) with timsTOF HT compared to Pro 2. Our data demonstrated the superior performance of timsTOF HT in identifying and quantifying differences between biologically diverse samples, which can improve disease biomarker discovery in large cohort studies. Moreover, researchers can leverage datasets from this study to optimize their LCMS workflows for plasma protein profiling and biomarker discovery. See the details in a paper, entitled "timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery".

2024-01-16 | PXD047854 | Pride

timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery (Cancer cohort dataset)

2024-01-16 | PXD047839 | Pride

Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping

Project description:Proteogenomics studies generate hypotheses on protein function and provide genetic evidence for drug target prioritization. Most previous work has been conducted using affinity-based proteomics approaches. These technological face challenges, such as uncertainty regarding target identity, non-specific binding, and handling of variants that affect epitope affinity binding. Mass spectrometry (MS)-based proteomics can overcome some of these challenges. Here we report a pQTL study using the Proteograph™ Product Suite workflow (Seer, Inc.) where we quantify over 18,000 unique peptides from nearly 3,000 proteins in more than 320 blood samples from a multi-ethnic cohort in a bottom-up, peptide-centric, MS-based proteomics approach. We identify 184 protein-altering variants (PAVs) in 137 genes that are significantly associated with their corresponding variant peptides, confirming target specificity of co-associated affinity binders, identifying putatively causal cis-encoded proteins and providing experimental evidence for their presence in blood, including proteins that may be inaccessible to affinity-based proteomics.

2023-12-19 | PXD042852 | Pride

A proteogenomics study using the Seer Proteograph platform

Project description:In recent years, the development of molecular clocks has provided avenues for estimation of biological age. Traditionally, methylation-based epigenetic clocks have been the focus of age predictor developments, however individual proteomics, transcriptomics, and ATAC-Seq have provided avenues for other omic based clocks. However, the current limitation is the development of multi-omic clocks which are able to capture multiple facets of the central dogma to develop composite epigenetic clocks. To this end, the current project incorporates proteomic data from a pool of 2,000 samples which were incorporated into the development of a multi-omic informed epigenetic predictor. Here, we utilized the Seer ProteographTM platform to prepare protein reads from plasma samples collected from a pool of individuals collected from the Mass General Brigham's (MGB) Biobank, and then quantified using LC-MS, and analyzed using the software available from Seer. Additional QA/QC and normalization was conducted using in-house analytical scripts.

2025-09-29 | PXD048709 | Pride

Human Bone Marrow Interstitial Fluid Plasma Cell Dyscrasias LC-MSMS

Project description:Bone Marrow Interstital Fluid from 120 patients with various plasma cell dyscrasias were assessed using Seer's Proteograph XT platform and an LC-MS system. For each sample, two MS injections were performed, one for each nanoparticle incubation used in the Proteograph XT.

2025-10-21 | PXD059339 | Pride

Comparison of deep plasma proteome enrichment methods

Project description:Plasma is a complex biological fluid containing extracellular vesicles (EVs), residual platelets, and soluble proteins, all of which can serve as biomarkers for pathological conditions. While conventional plasma proteomics typically identifies hundreds of proteins, recent enrichment strategies have expanded coverage to thousands. It is not clear yet whether these methods enrich preferentially different classes of protein and whether they allow for reliable quantification Here, we compared three common advanced proteomic workflows—Seer Proteograph (nanoparticle-based), MagNET (SCX magnetic beads), and ENRICHplus (PreOmics)—as well as EV enrichment obtained by centrifugation. We aimed to explore the content in soluble proteins, EV cargo, and platelet-derived proteins in platelet-poor plasma (PPP) from healthy donors after the enrichments. Samples were analyzed using timsTOF platforms and quantified with DIA-NN in library-free mode. Functional insights were obtained using Over-Representation Analysis (ORA), Human Protein Atlas annotations, and EV-specific markers. Quantification was evaluated comparing each method to neat plasma using protein coefficient of variation and point-biserial correlation. We quantified an average of ~4500 proteins with EV centrifugation, ~4000 with Seer, ~2800 with ENRICHplus, ~2300 with MagNET, and ~900 with neat plasma. Each method enriched distinct protein signatures: EV markers such as CD81 were predominantly detected in EV preparations; lipoproteins were enriched in ENRICHplus; cytokine and hormone signaling pathways were most evident in Seer. Platelet protein intensity was directly correlated with total protein identifications but did not compromise quantification of low-abundance proteins. Across 50 healthy individuals, Proteograph consistently demonstrated reproducible enrichment and depletion patterns, with notable exceptions for proteins such as FCN3, F11, and FCGBP.

2025-10-17 | PXD063673 | Pride

Impact of Sample Preparation Strategies on The Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics

Project description:Serum proteomics plays a crucial role in biomarker discovery and disease research, yet the selection of an optimal sample preparation method remains challenging. Evaluating the accuracy of protein quantitation is of major importance and a vital part of a benchmarking study in proteomics, since clinical studies are based on the differential expression of certain proteins that can be used as biomarkers or be indicative for a pathological state. In this study, we performed a direct comparison of 6 widely used serum proteomic sample preparation workflows: In-gel digestion (IGD), Single-Pot Solid-Phase-enhanced Sample Preparation (SP3), Top 14 Abundant Protein Depletion (Top 14), Isopropanol/Trichloroacetic Acid (IPA/TCA) precipitation, PreOmics ENRICH-iST (PreOmics), and Seer Proteograph XT (Seer). Seer and PreOmics demonstrated superior quantitative accuracy especially for proteins with low abundance in serum while Seer enrichment approach provided the highest number of protein identifications (> 2000) as measured by an Orbitrap Exploris 480. All methods had median CVs close to or below 20%. This comparative analysis provides a comprehensive resource for selecting the most appropriate serum sample preparation strategy based on specific experimental needs, facilitating human serum proteomic profiling for biomedical research.

2025-09-15 | PXD062785 | Pride

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