Table of Contents
International Journal of Proteomics
Volume 2010 (2010), Article ID 731582, 15 pages
Research Article

Assigning Significance in Label-Free Quantitative Proteomics to Include Single-Peptide-Hit Proteins with Low Replicates

1Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
2Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA

Received 18 March 2010; Revised 20 May 2010; Accepted 19 June 2010

Academic Editor: Andrew J. Link

Copyright © 2010 Qingbo Li. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

The Supplementary Materials contains three major parts as outlined in the Table of Contents in the PDF file of the Supplementary Materials. Part I contains the web link to download the raw data of the 20 LC/MS runs for the pH 5 (Sp) and pH 7 (Rp) samples fractionated with SDS/PAGE gel separation. Descriptions for the LC/MS runs are provided. Part II contains the details of PLGEM-STN noise modeling, the use of the combination of MPSP with the PLGEM-STN or the fold-change method, and the list of the differentially regulated proteins selected by the combination of MPSP with PLGEM-STN and fold-change methods. Part III contains the lists of peptides and proteins quantified from the 20 LC/MS runs of the SDS/PAGE gel-fractionated Sp and Rp samples.

  1. Supplementary Material