Dataset Information


Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap.

ABSTRACT: Peptide labeling with isobaric tags has become a popular technique in quantitative shotgun proteomics. Using two different samples viz. a protein mixture and HeLa extracts, we show that three commercially available isobaric tags differ with regard to peptide identification rates: The number of identified proteins and peptides was largest with iTRAQ 4-plex, followed by TMT 6-plex, and smallest with iTRAQ 8-plex. In all experiments, we employed a previously described method where two scans were acquired for each precursor on an LTQ Orbitrap: A CID scan under standard settings for identification, and a HCD scan for quantification. The observed differences in identification rates were similar when data was searched with either Mascot or Sequest. We consider these findings to be the result of a combination of several factors, most notably prominent ions in CID spectra as a consequence of loss of fragments of the label tag from precursor ions. These fragment ions cannot be explained by current search engines and were observed to have a negative impact on peptide scores.


PROVIDER: S-EPMC3093924 | BioStudies | 2010-01-01

REPOSITORIES: biostudies

Similar Datasets

2012-01-01 | S-EPMC3390908 | BioStudies
2020-01-01 | S-EPMC7306224 | BioStudies
1000-01-01 | S-EPMC4318621 | BioStudies
1000-01-01 | S-EPMC2938101 | BioStudies
1000-01-01 | S-EPMC2556025 | BioStudies
2017-01-01 | S-EPMC5479408 | BioStudies
2012-01-01 | S-EPMC3377673 | BioStudies
2015-01-01 | S-EPMC4837894 | BioStudies
1000-01-01 | S-EPMC3270567 | BioStudies
2012-01-01 | S-EPMC3715028 | BioStudies