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Analysis of the Chlamydomonas proteome with UPS1 spike-in

ABSTRACT: Benchmarking dataset for the objective evaluation of quantitative and statistical workflows.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Chlamydomonas Reinhardtii

SUBMITTER: Evan McConnell

LAB HEAD: Leslie M. Hicks

PROVIDER: PXD009694 | Pride | 2020-10-20

REPOSITORIES: Pride

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Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics.

Berg Philip P McConnell Evan W EW Hicks Leslie M LM Popescu Sorina C SC Popescu George V GV

BMC bioinformatics 20190314 Suppl 2

<h4>Background</h4>Several methods to handle data generated from bottom-up proteomics via liquid chromatography-mass spectrometry, particularly for peptide-centric quantification dealing with post-translational modification (PTM) analysis like reversible cysteine oxidation are evaluated. The paper proposes a pipeline based on the R programming language to analyze PTMs from peptide-centric label-free quantitative proteomics data.<h4>Results</h4>Our methodology includes variance stabilization, nor ...[more]

PMID: 30871482

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