Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Quantitative analysis of proteome and phosphoproteome

WX Weiling Xu
SC Suzy A. A. Comhair
RC Ruoying Chen
BH Bo Hu
YH Yuan Hou
YZ Yadi Zhou
LM Lori A. Mavrakis
AJ Allison J. Janocha
LL Ling Li
DZ Dongmei Zhang
BW Belinda B. Willard
KA Kewal Asosingh
FC Feixiong Cheng
SE Serpil C. Erzurum
request Request a Protocol
ask Ask a question
Favorite

Patient characteristics were summarized with appropriate descriptive statistics. For the protein expression analysis, the variance-stabilizing transformation (VSN) was first performed to normalize the proteomics and phosphoproteomics data, respectively. Missing data were imputed using the nearest neighbor approach. The comparison between PAH and healthy controls was then performed using the moderated t-test (limma package in R). The results were controlled for multiple comparisons with the false discovery rate (FDR) approach, and proteins with significantly different expressions were identified with FDR < 0.05. All analyses were conducted using R-studio (Boston, MA).

Copyright and License information: The Author(s) ©2019
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A