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Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues

ABSTRACT: We developed 6,927 quantitative multiple reaction monitoring mass spectrometry (MRM-MS) assays that measure 2,187 unique proteins in 20 mouse organs and tissues to enable system-level analysis of protein expression in mice. Targets for assay development were selected by untargeted MS analysis, and corresponding stable isotope-labelled standards were synthesized in-house. Development experiments determined the lower limit of quantitation, linear range, and repeatability of each assay. Subsequently, the developed assays were formatted into panels tailored to each organ or tissue type and were used to measure normal protein concentrations in samples from three mouse strains; C57BL/6NCrl, NOD/SCID, and BALB/cAnNCrl. In total 5,149 measurements were obtained corresponding to 1,691 unique proteins, and results included sex- and strain-specific profiles in protein abundances. Collectively, these assays are the largest group of quantitative MRM-MS assays established and implemented in mice to date, and enable accurate quantitation of mouse proteins for molecular phenotyping. Furthermore, the measured concentration data provide important biological information for experimental design involving mouse models.

ORGANISM(S): Mus Musculus

SUBMITTER: Sarah Michaud

PROVIDER: PXD020930 | panorama | Thu Jan 04 00:00:00 GMT 2024

REPOSITORIES: PanoramaPublic

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Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues.

Michaud Sarah A SA Pětrošová Helena H Sinclair Nicholas J NJ Kinnear Andrea L AL Jackson Angela M AM McGuire Jamie C JC Hardie Darryl B DB Bhowmick Pallab P Ganguly Milan M Flenniken Ann M AM Nutter Lauryl M J LMJ McKerlie Colin C Smith Derek D Mohammed Yassene Y Schibli David D Sickmann Albert A Borchers Christoph H CH

Communications biology 20240102 1

Mouse is the mammalian model of choice to study human health and disease due to its size, ease of breeding and the natural occurrence of conditions mimicking human pathology. Here we design and validate multiple reaction monitoring mass spectrometry (MRM-MS) assays for quantitation of 2118 unique proteins in 20 murine tissues and organs. We provide open access to technical aspects of these assays to enable their implementation in other laboratories, and demonstrate their suitability for proteomi ...[more]

PMID: 38168632

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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.

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Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues

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Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues.

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