TY - JOUR
T1 - A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis
AU - Gonzalez-Galarza, Faviel F.
AU - Lawless, Craig
AU - Hubbard, Simon J.
AU - Fan, Jun
AU - Bessant, Conrad
AU - Hermjakob, Henning
AU - Jones, Andrew R.
PY - 2012/9/1
Y1 - 2012/9/1
N2 - New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool (http://www.proteosuite.org/?q=other-resources) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology. © Copyright 2012, Mary Ann Liebert, Inc. 2012.
AB - New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool (http://www.proteosuite.org/?q=other-resources) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology. © Copyright 2012, Mary Ann Liebert, Inc. 2012.
U2 - 10.1089/omi.2012.0022
DO - 10.1089/omi.2012.0022
M3 - Article
C2 - 22804616
SN - 1536-2310
VL - 16
SP - 431
EP - 442
JO - Omics : a journal of integrative biology
JF - Omics : a journal of integrative biology
IS - 9
ER -