Next Article in Journal
A Computer-Vision-Guided Robot Arm for Automatically Placing Grids in Pioloform Film Preparation
Previous Article in Journal
A Software Architecture to Mimic a Ventricular Tachycardia in Intact Murine Hearts by Means of an All-Optical Platform
Article Menu
Issue 1 (March) cover image

Export Article

Open AccessProtocol

Fast Proteome Identification and Quantification from Data-Dependent Acquisition–Tandem Mass Spectrometry (DDA MS/MS) Using Free Software Tools

1
Department of Chemistry, University of Wisconsin—Madison, Madison, WI 53706, USA
2
Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI 53706, USA
3
National Center for Quantitative Biology of Complex Systems, University of Wisconsin—Madison, Madison, WI 53706, USA
Methods Protoc. 2019, 2(1), 8; https://doi.org/10.3390/mps2010008
Received: 26 November 2018 / Revised: 7 January 2019 / Accepted: 15 January 2019 / Published: 17 January 2019
  |  
PDF [3622 KB, uploaded 17 January 2019]
  |     |  

Abstract

The identification of nearly all proteins in a biological system using data-dependent acquisition (DDA) tandem mass spectrometry has become routine for organisms with relatively small genomes such as bacteria and yeast. Still, the quantification of the identified proteins may be a complex process and often requires multiple different software packages. In this protocol, I describe a flexible strategy for the identification and label-free quantification of proteins from bottom-up proteomics experiments. This method can be used to quantify all the detectable proteins in any DDA dataset collected with high-resolution precursor scans and may be used to quantify proteome remodeling in response to drug treatment or a gene knockout. Notably, the method is statistically rigorous, uses the latest and fastest freely-available software, and the entire protocol can be completed in a few hours with a small number of data files from the analysis of yeast. View Full-Text
Keywords: shotgun proteomics; mass spectrometry; protein quantification; peptide quantification; data-dependent acquisition shotgun proteomics; mass spectrometry; protein quantification; peptide quantification; data-dependent acquisition
Figures

Graphical abstract

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 (CC BY 4.0).

Supplementary material

SciFeed

Share & Cite This Article

MDPI and ACS Style

Meyer, J.G. Fast Proteome Identification and Quantification from Data-Dependent Acquisition–Tandem Mass Spectrometry (DDA MS/MS) Using Free Software Tools. Methods Protoc. 2019, 2, 8.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Methods Protoc. EISSN 2409-9279 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top