Dataset Information

Selection of reference peptides for absolute quantification of budding yeast proteome

ABSTRACT: Absolute quantification of proteome is one of the most important tasks in proteomic research. The aim in this analysis is selection of reference tryptic peptides used for stable isotope-labeled standard, based on their spectral peak intensities. Approximate abundance is also calculated by label-free quantitative method, in which identification frequency (counts of peptide spectral matchings) in each protein is normalized by observability of peptide ions to calculate relative copy number of proteins. For proteins with higher relative copy number, peptide ions that fulfill following criteria — 2- or 3-charge state, without methionine residues and well known post-translational modification sites — are selected as reference tryptic peptides.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

TISSUE(S): Cell Culture

SUBMITTER: Keiji Kito

LAB HEAD: Keiji Kito

PROVIDER: PXD003085 | Pride | 2016-10-06

REPOSITORIES: Pride

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Publications

A strategy for absolute proteome quantification with mass spectrometry by hierarchical use of peptide-concatenated standards.

Kito Keiji K Okada Mitsuhiro M Ishibashi Yuko Y Okada Satoshi S Ito Takashi T

Proteomics 20160428 10

The accurate and precise absolute abundance of proteins can be determined using mass spectrometry by spiking the sample with stable isotope-labeled standards. In this study, we developed a strategy of hierarchical use of peptide-concatenated standards (PCSs) to quantify more proteins over a wider dynamic range. Multiple primary PCSs were used for quantification of many target proteins. Unique "ID-tag peptides" were introduced into individual primary PCSs, allowing us to monitor the exact amounts ...[more]

PMID: 27030420

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			Action	DRS
	Scer_analysis1.RAW	Raw
	Scer_analysis1.mgf	Mgf
	Scer_analysis1.msf	Msf
	Scer_analysis1.pep.XML	Pepxml
	Scer_analysis1_ORF_PSM_list.xlsx	Xlsx