False discovery rate estimation for cross-linked peptides identified by mass spectrometry

2012 ◽  
Vol 9 (9) ◽  
pp. 901-903 ◽  
Author(s):  
Thomas Walzthoeni ◽  
Manfred Claassen ◽  
Alexander Leitner ◽  
Franz Herzog ◽  
Stefan Bohn ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
False Discovery Rate ◽  
Rate Estimation ◽  
False Discovery ◽  
False Discovery Rate Estimation

Bias in False Discovery Rate Estimation in Mass-Spectrometry-Based Peptide Identification

2019 ◽  
Vol 18 (5) ◽  
pp. 2354-2358 ◽  
Author(s):  
Yulia Danilova ◽  
Anastasia Voronkova ◽  
Pavel Sulimov ◽  
Attila Kertész-Farkas
Keyword(s):  
Mass Spectrometry ◽  
False Discovery Rate ◽  
Peptide Identification ◽  
Rate Estimation ◽  
False Discovery ◽  
False Discovery Rate Estimation

scholarly journals False discovery rate estimation and heterobifunctional cross-linkers

2017 ◽  
Author(s):  
Lutz Fischer ◽  
Juri Rappsilber
Keyword(s):  
Mass Spectrometry ◽  
False Discovery Rate ◽  
Cross Linking ◽  
Rate Estimation ◽  
False Discovery ◽  
False Discovery Rate Estimation ◽  
The Many ◽  
Single Formula ◽  
The Impact

AbstractFalse discovery rate (FDR) estimation is a cornerstone of proteomics that has recently been adapted to cross-linking/mass spectrometry. Here we demonstrate that heterobifunctional cross-linkers, while theoretically different from homobifunctional cross-linkers, need not be considered separately in practice. We develop and then evaluate the impact of applying a correct FDR formula for use of heterobifunctional cross-linkers and conclude that there are minimal practical advantages. Hence a single formula can be applied to data generated from the many different non-cleavable cross-linkers.

scholarly journals The effect of correlation in false discovery rate estimation

Biometrika ◽  
2011 ◽  
Vol 98 (1) ◽  
pp. 199-214 ◽  
Author(s):  
A. Schwartzman ◽  
X. Lin
Keyword(s):  
False Discovery Rate ◽  
Rate Estimation ◽  
False Discovery ◽  
False Discovery Rate Estimation

scholarly journals A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

2015 ◽  
Vol 14 (9) ◽  
pp. 2394-2404 ◽  
Author(s):  
Mikhail M. Savitski ◽  
Mathias Wilhelm ◽  
Hannes Hahne ◽  
Bernhard Kuster ◽  
Marcus Bantscheff
Keyword(s):  
False Discovery Rate ◽  
Data Sets ◽  
Rate Estimation ◽  
Proteomic Data ◽  
False Discovery ◽  
False Discovery Rate Estimation

Reverse and Random Decoy Methods for False Discovery Rate Estimation in High Mass Accuracy Peptide Spectral Library Searches

2018 ◽  
Vol 17 (2) ◽  
pp. 846-857 ◽  
Author(s):  
Zheng Zhang ◽  
Meghan Burke ◽  
Yuri A. Mirokhin ◽  
Dmitrii V. Tchekhovskoi ◽  
Sanford P. Markey ◽  
...  
Keyword(s):  
False Discovery Rate ◽  
Mass Accuracy ◽  
High Mass ◽  
High Mass Accuracy ◽  
Spectral Library ◽  
Rate Estimation ◽  
False Discovery ◽  
False Discovery Rate Estimation

scholarly journals Local false discovery rate estimation using feature reliability in LC/MS metabolomics data

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Elizabeth Y. Chong ◽  
Yijian Huang ◽  
Hao Wu ◽  
Nima Ghasemzadeh ◽  
Karan Uppal ◽  
...  
Keyword(s):  
False Discovery Rate ◽  
Local False Discovery Rate ◽  
Metabolomics Data ◽  
Rate Estimation ◽  
False Discovery ◽  
False Discovery Rate Estimation
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