Proteomics

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MaxLFQ label-free quantification algorithm benchmark datasets

ABSTRACT: We developed a set of algorithms for label-free quantification, termed MaxLFQ, embedded into MaxQuant. This contains two datasets to benchmark MaxLFQ: The proteome benchmark dataset consists of of HeLa and E. coli lysates mixed at defined ratios. The dynamic range benchmark dataset consists of UPS1/UPS2 standards (Sigma) spiked into E. coli lysates and quantified against each other.

INSTRUMENT(S): LTQ Orbitrap, Q Exactive

ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606)

SUBMITTER: None Listed 

PROVIDER: MSV000081831 | MassIVE | Tue Dec 19 14:33:00 GMT 2017

SECONDARY ACCESSION(S): PXD000279

REPOSITORIES: MassIVE

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Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ.

Cox Jürgen J   Hein Marco Y MY   Luber Christian A CA   Paron Igor I   Nagaraj Nagarjuna N   Mann Matthias M  

Molecular & cellular proteomics : MCP 20140617 9

Protein quantification without isotopic labels has been a long-standing interest in the proteomics field. However, accurate and robust proteome-wide quantification with label-free approaches remains a challenge. We developed a new intensity determination and normalization procedure called MaxLFQ that is fully compatible with any peptide or protein separation prior to LC-MS analysis. Protein abundance profiles are assembled using the maximum possible information from MS signals, given that the pr  ...[more]

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