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Proteomic identification of monoclonal antibodies from rabbit serum and analysis of FDR using differential cysteine labeling

ABSTRACT: Proteomic analysis of serum antibodies is challenging due to the non-germline origin of immunoglobulin (Ig) sequences and the complexity of Ig primary structure, with regions of hypervariable sequence interspersed within highly conserved framework sections resulting in an unusually high frequency of peptide-spectrum mis-identification using standard reference database search methods. Using a strategy of differential cysteine labeling with two alkylating reagents, we examined peptide-spectrum matches and decoy-based error modeling for the interpretation of antibody-derived mass spectral data.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Oryctolagus Cuniculus (rabbit)

TISSUE(S): Blood Serum

SUBMITTER: Daniel Boutz

LAB HEAD: Edward Marcotte

PROVIDER: PXD000916 | Pride | 2014-04-24

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	CCH1_1a_IodoEtOH.raw	Raw
	CCH1_1a_IodoEtOH_ConJ.mgf	Mgf
	CCH1_1a_IodoEtOH_ConJ.pep.xml	Pepxml
	CCH1_1a_IodoEtOH_ShuffleDB.mgf	Mgf
	CCH1_1a_IodoEtOH_ShuffleDB.pep.xml	Pepxml

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Publications

Proteomic identification of monoclonal antibodies from serum.

Boutz Daniel R DR Horton Andrew P AP Wine Yariv Y Lavinder Jason J JJ Georgiou George G Marcotte Edward M EM

Analytical chemistry 20140501 10

Characterizing the in vivo dynamics of the polyclonal antibody repertoire in serum, such as that which might arise in response to stimulation with an antigen, is difficult due to the presence of many highly similar immunoglobulin proteins, each specified by distinct B lymphocytes. These challenges have precluded the use of conventional mass spectrometry for antibody identification based on peptide mass spectral matches to a genomic reference database. Recently, progress has been made using botto ...[more]

PMID: 24684310

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RAG1/2 induces double-stranded DNA breaks at non-Ig loci in the proximity of single sequence repeats in developing B cells

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Global FDR control across multiple RNAseq experiments.

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