Proteomics

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ON THE ACCURACY, PRECISION AND STATISTICAL SIGNIFICANCE OF COMPRESSED RATIOS IN ISOBARIC LABELLING

ABSTRACT: Despite the outstanding advantages that isobaric labelling has to offer in quantitative proteomics, its precision and accuracy are undermined by ratio compression, which is consequence of the co-isolation of peptides within a selected isolation window. Here, using the two-proteomes approach we investigated the relationships between precision and accuracy on the statistical significance of peptide and protein ratios in three types of mass spectrometers.

INSTRUMENT(S): LTQ Orbitrap Velos, Bruker Daltonics maXis series, Q Exactive

ORGANISM(S): Homo Sapiens (human) Escherichia Coli

SUBMITTER: Ana Martinez  

LAB HEAD: Javier Muñoz Peralta

PROVIDER: PXD003640 | Pride | 2016-08-08

REPOSITORIES: Pride

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Dataset's files

Source:
Action DRS
201504241_AM_EC_IWFixed3.0_2-D1_01_3786-02.msf Msf
201504241_AM_EC_IWFixed3.0_2-D1_01_3786.mgf Mgf
20150424_AM_EC_IWFixed1.5_2-D1_01_3779-02.msf Msf
20150424_AM_EC_IWFixed1.5_2-D1_01_3779.mgf Mgf
20150424_AM_EC_IWFixed1.5_2-D1_01_3784-02.msf Msf
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Publications

On the Statistical Significance of Compressed Ratios in Isobaric Labeling: A Cross-Platform Comparison.

Martinez-Val Ana A   Garcia Fernando F   Ximénez-Embún Pilar P   Ibarz Nuria N   Zarzuela Eduardo E   Ruppen Isabel I   Mohammed Shabaz S   Munoz Javier J  

Journal of proteome research 20160804 9

Isobaric labeling is gaining popularity in proteomics due to its multiplexing capacity. However, copeptide fragmentation introduces a bias that undermines its accuracy. Several strategies have been shown to partially and, in some cases, completely solve this issue. However, it is still not clear how ratio compression affects the ability to identify a protein's change of abundance as statistically significant. Here, by using the "two proteomes" approach (E. coli lysates with fixed 2.5 ratios in t  ...[more]

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