Statistical Analysis of Spectral Count Data Generated by Label-Free Tandem Mass Spectrometry-Based Proteomics

2011 ◽  
pp. 297-309
Author(s):  
Thang V. Pham ◽  
Connie R. Jimenez
Keyword(s):  
Mass Spectrometry ◽  
Statistical Analysis ◽  
Tandem Mass Spectrometry ◽  
Count Data ◽  
Tandem Mass ◽  
Label Free ◽  
Spectral Count

scholarly journals On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics

2009 ◽  
Vol 26 (3) ◽  
pp. 363-369 ◽  
Author(s):  
Thang V. Pham ◽  
Sander R. Piersma ◽  
Marc Warmoes ◽  
Connie R. Jimenez
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Count Data ◽  
Binomial Model ◽  
Tandem Mass ◽  
Label Free ◽  
Spectral Count

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

2019 ◽  
Vol 2 (1) ◽  
pp. 8 ◽  
Author(s):  
Jesse Meyer
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Gene Knockout ◽  
Tandem Mass ◽  
Label Free ◽  
Software Packages ◽  
Complex Process ◽  
Data Files ◽  
Using Data ◽  
Free Quantification

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.

Ultrasensitive and simultaneous determination of RNA modified nucleotides by sheathless interfaced capillary electrophoresis–tandem mass spectrometry

2019 ◽  
Vol 55 (53) ◽  
pp. 7595-7598 ◽  
Author(s):  
Yue Yu ◽  
Si-Hao Zhu ◽  
Fang Yuan ◽  
Xiao-Hui Zhang ◽  
Yan-Ye Lu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Capillary Electrophoresis ◽  
Tandem Mass Spectrometry ◽  
Simultaneous Determination ◽  
Tandem Mass ◽  
Label Free ◽  
Modified Nucleotides ◽  
Nickel Ions ◽  
Mass Spectrometry System

A label-free ultrasensitive method was established for the simultaneous determination of RNA modified nucleotides based on a sheathless capillary electrophoresis–tandem mass spectrometry system and successfully applied to investigate the effects of exposure to nickel ions on RNA epigenetics.

Analysis of the human pituitary proteome by data independent label-free liquid chromatography tandem mass spectrometry

PROTEOMICS ◽  
2011 ◽  
Vol 11 (3) ◽  
pp. 495-500 ◽  
Author(s):  
Divya Krishnamurthy ◽  
Yishai Levin ◽  
Laura W. Harris ◽  
Yagnesh Umrania ◽  
Sabine Bahn ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Label Free ◽  
Human Pituitary ◽  
Chromatography Tandem Mass Spectrometry ◽  
Liquid Chromatography Tandem Mass
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