Proteomics

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Quantitative proteogenomic characterization of inflamed murine colon tissue using an integrated discovery, verification, and validation proteogenomic workflow

ABSTRACT: Rag2-/-Il10-/- mice were subjected to infection by Helicobacter hepaticus and allowed to develop long-term infections. Proximal colon tissue was then harvested from the mice for analysis. RNA was isolated from the samples and submitted for transcriptomic analysis; this data was then used to create a custom RNA-based FASTA database. Protein isolated from the proximal colon samples were digested and analyzed via bottom-up mass spectrometry. The custom FASTA database was then used for proteogenomic analysis of the raw mass spectrometry data in the Galaxy for proteomics (Galaxy-P) platform.

INSTRUMENT(S): Orbitrap Fusion, Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Colon

DISEASE(S): Colon Cancer,Inflammatory Bowel Disease

SUBMITTER: Andrew Rajczewski  

LAB HEAD: Timothy J Griffin

PROVIDER: PXD028407 | Pride | 2022-05-19

REPOSITORIES: Pride

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5632_con_1_DDA.raw Raw
5632_con_1_PRM.raw Raw
5633_con_2_DDA.raw Raw
5633_con_2_PRM.raw Raw
5634_con_3_DDA.raw Raw
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Publications

Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow.

Rajczewski Andrew T AT   Han Qiyuan Q   Mehta Subina S   Kumar Praveen P   Jagtap Pratik D PD   Knutson Charles G CG   Fox James G JG   Tretyakova Natalia Y NY   Griffin Timothy J TJ  

Proteomes 20220414 2

Chronic inflammation of the colon causes genomic and/or transcriptomic events, which can lead to expression of non-canonical protein sequences contributing to oncogenesis. To better understand these mechanisms, <i>Rag2</i><sup>-/-</sup><i>Il10</i><sup>-/-</sup> mice were infected with <i>Helicobacter hepaticus</i> to induce chronic inflammation of the cecum and the colon. Transcriptomic data from harvested proximal colon samples were used to generate a customized FASTA database containing non-ca  ...[more]

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