Format

Send to

Choose Destination
See comment in PubMed Commons below
Anal Chem. 2011 Nov 15;83(22):8403-10. doi: 10.1021/ac2017053. Epub 2011 Oct 27.

SILACtor: software to enable dynamic SILAC studies.

Author information

1
Department of Genome Sciences, University of Washington, Seattle, Washington 98109-4717, United States.

Abstract

Stable isotope labeling by amino acids in cell culture (SILAC) is a versatile tool in proteomics that has been used to explore protein turnover on a large scale. However, these studies pose a significant undertaking that can be greatly simplified through the use of computational tools that automate the data analysis. While SILAC technology has enjoyed rapid adoption through the availability of several software tools, algorithms do not exist for the automated analysis of protein turnover data generated using SILAC technology. Presented here is a software tool, SILACtor, designed to trace and compare SILAC-labeled peptides across multiple time points. SILACtor is used to profile protein turnover rates for more than 500 HeLa cell proteins using a SILAC label-chase approach. Additionally, SILACtor contains a method for the automated generation of accurate mass and retention time inclusion lists that target peptides of interest showing fast or slow turnover rates relative to the other peptides observed in the samples. SILACtor enables improved protein turnover studies using SILAC technology and also provides a framework for features extensible to comparative SILAC analyses and targeted methods.

PMID:
21954881
PMCID:
PMC3255570
DOI:
10.1021/ac2017053
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for American Chemical Society Icon for PubMed Central
    Loading ...
    Support Center