Dataset Information

Median Based Absolute Quantification using Fully Unlabelled Generic Internal Standard

ABSTRACT: By reporting molar abundances of proteins, absolute quantification determines their stoichiometry in complexes, pathways or networks and also relates them to abundances of non-protein biomolecules. Typically, absolute quantification relies either on protein- specific isotopically labelled peptide standards or on a semi-empirical calibration against the average abundance of peptides chosen from arbitrary selected standard proteins. Here we developed a generic protein standard FUGIS (Fully unlabelled Generic Internal Standard) that requires no isotopic labelling, synthesis of standards or external calibration and is applicable to proteins of any organismal origin. FUGIS is co-digested with analysed proteins and enables their absolute quantification in the same LC-MS/MS run. By using FUGIS, median based absolute quantification (MBAQ) workflow provides similar quantification accuracy compared to isotopically-labelled peptide standards and outperforms methods based on external calibration or selection of best ionized reporter peptides (Top3 quantification) with a median quantification error less than 15%

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human) Caenorhabditis Elegans

SUBMITTER: Bharath Kumar Raghuraman

LAB HEAD: Andrej Shevchenko

PROVIDER: PXD026886 | Pride | 2021-11-30

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20190711_pIBAQ_pIBAQ_lightscrambled_heavy_1M_1000ul_GS01_23ul_Dionex_120min_01.raw	Raw
	20190711_pIBAQ_pIBAQ_lightscrambled_heavy_1M_1000ul_GS01_23ul_Dionex_120min_02.raw	Raw
	20190711_pIBAQ_pIBAQ_lightscrambled_heavy_1M_1000ul_GS02_23ul_Dionex_120min_01.raw	Raw
	20190711_pIBAQ_pIBAQ_lightscrambled_heavy_1M_1000ul_GS02_23ul_Dionex_120min_02.raw	Raw
	20190711_pIBAQ_pIBAQ_lightscrambled_heavy_1M_1000ul_GS03_23ul_Dionex_120min_01.raw	Raw

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Publications

Median-Based Absolute Quantification of Proteins Using Fully Unlabeled Generic Internal Standard (FUGIS).

Raghuraman Bharath Kumar BK Bogdanova Aliona A Moon HongKee H Rzagalinski Ignacy I Geertsma Eric R ER Hersemann Lena L Shevchenko Andrej A

Journal of proteome research 20211122 1

By reporting the molar abundance of proteins, absolute quantification determines their stoichiometry in complexes, pathways, or networks. Typically, absolute quantification relies either on protein-specific isotopically labeled peptide standards or on a semiempirical calibration against the average abundance of peptides chosen from arbitrarily selected proteins. In contrast, a generic protein standard FUGIS (fully unlabeled generic internal standard) requires no isotopic labeling, chemical synth ...[more]

PMID: 34807614

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