Dataset Information

Whole blood peptide assay stability by MRM-MS

ABSTRACT: Here, we investigate how delays in plasma processing affect peptide-centric “bottom-up” proteomics, using multiple reaction monitoring mass spectrometry (MRM-MS). We used validated Tier 2-level assays for proteotypic peptide surrogates of 270 human proteins to analyze plasma generated from whole blood that has been kept at room temperature from 0-40 hours before plasma generation. Moreover, we evaluated whether different plasma thawing conditions had an impact on the MRM-based plasma protein measurements.

ORGANISM(S): Homo Sapiens

SUBMITTER: Claudia Gaither

PROVIDER: PXD027957 | panorama | Thu Aug 18 00:00:00 BST 2022

REPOSITORIES: PanoramaPublic

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Publications

Multiple Reaction Monitoring-Mass Spectrometry Enables Robust Quantitation of Plasma Proteins Regardless of Whole Blood Processing Delays That May Occur in the Clinic.

Gaither Claudia C Popp Robert R Zahedi René P RP Borchers Christoph H CH

Molecular & cellular proteomics : MCP 20220217 5

Plasma is an important biofluid for clinical research and diagnostics. In the clinic, unpredictable delays-from minutes to hours-between blood collection and plasma generation are often unavoidable. These delays can potentially lead to protein degradation and modification and might considerably affect intact protein measurement methods such as sandwich enzyme-linked immunosorbent assays that bind proteins on two epitopes to increase specificity, thus requiring largely intact protein structures. ...[more]

PMID: 35182769

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Project description:Purpose: We generated extensive transcriptional and proteomic profiles from a Her2-driven mouse model of breast cancer that closely recapitulates human breast cancer. This report makes these data publicly available in raw and processed forms, as a resource to the community. Importantly, we previously made biospecimens from this same mouse model freely available through a sample repository, so researchers can obtain samples to test biological hypotheses without the need of breeding animals and collecting biospecimens. Experimental design: Twelve datasets are available, encompassing 841 LC-MS/MS experiments (plasma and tissues) and 255 microarray analyses of multiple tissues (thymus, spleen, liver, blood cells, and breast). Cases and controls were rigorously paired to avoid bias. Results: In total, 18,880 unique peptides were identified (PeptideProphet peptide error rate â¤1%), with 3884 and 1659 non-redundant protein groups identified in plasma and tissue datasets, respectively. Sixty-one of these protein groups overlapped between cancer plasma and cancer tissue. Conclusions and clinical relevance: These data are of use for advancing our understanding of cancer biology, for software and quality control tool development, investigations of analytical variation in MS/MS data, and selection of proteotypic peptides for MRM-MS. The availability of these datasets will contribute positively to clinical proteomics. Affymetrix GeneChip Mouse Genome 430 2.0 microarrays were used to profile whole tissues from 5 different tissue types of 25 tumor-bearing and 25 control mice of the Her2/Neu breast cancer mouse model. The 5 tissues tested were from breast, liver, spleen, blood cell, and thymus. The tumor-bearing mice were bitransgenic for MMTV-rtTA/TetO-NeuNT, and the control mice were transgenic for TetO-NeuNT only. The control mice were age- and cage-matched to the tumor-bearing mice. All samples were lysed and total RNA isolated and amplified prior to hybridization.

Dataset Information

Whole blood peptide assay stability by MRM-MS

Publications

Multiple Reaction Monitoring-Mass Spectrometry Enables Robust Quantitation of Plasma Proteins Regardless of Whole Blood Processing Delays That May Occur in the Clinic.

Similar Datasets

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