scholarly journals Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book

2004 ◽  
Vol 1 (3) ◽  
pp. 195-202 ◽  
Author(s):  
Rovshan G Sadygov ◽  
Daniel Cociorva ◽  
John R Yates
Keyword(s):  
Mass Spectra ◽  
Large Scale ◽  
Database Searching ◽  
Tandem Mass ◽  
Tandem Mass Spectra

pClean: An Algorithm To Preprocess High-Resolution Tandem Mass Spectra for Database Searching

2019 ◽  
Vol 18 (9) ◽  
pp. 3235-3244
Author(s):  
Yamei Deng ◽  
Zhe Ren ◽  
Qingfei Pan ◽  
Da Qi ◽  
Bo Wen ◽  
...  
Keyword(s):  
High Resolution ◽  
Mass Spectra ◽  
Database Searching ◽  
Tandem Mass ◽  
Tandem Mass Spectra

scholarly journals MAZIE: A mass and charge inference engine to enhance database searching of tandem mass spectra

2010 ◽  
Vol 21 (1) ◽  
pp. 80-87 ◽  
Author(s):  
Ken G. Victor ◽  
Meera Murgai ◽  
Charles E. Lyons ◽  
Thaddeus A. B. Templeton ◽  
Sergey A. Moshnikov ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Inference Engine ◽  
Database Searching ◽  
Tandem Mass ◽  
Tandem Mass Spectra

Authentication of Fish Products by Large-Scale Comparison of Tandem Mass Spectra

2013 ◽  
Vol 12 (11) ◽  
pp. 5253-5259 ◽  
Author(s):  
Tune Wulff ◽  
Michael Engelbrecht Nielsen ◽  
André M. Deelder ◽  
Flemming Jessen ◽  
Magnus Palmblad
Keyword(s):  
Mass Spectra ◽  
Large Scale ◽  
Tandem Mass ◽  
Fish Products ◽  
Tandem Mass Spectra

Statistical Model for Large-Scale Peptide Identification in Databases from Tandem Mass Spectra Using SEQUEST

2004 ◽  
Vol 76 (23) ◽  
pp. 6853-6860 ◽  
Author(s):  
Daniel López-Ferrer ◽  
Salvador Martínez-Bartolomé ◽  
Margarita Villar ◽  
Mónica Campillos ◽  
Fernando Martín-Maroto ◽  
...  
Keyword(s):  
Statistical Model ◽  
Mass Spectra ◽  
Large Scale ◽  
Peptide Identification ◽  
Tandem Mass ◽  
Tandem Mass Spectra

scholarly journals MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

2017 ◽  
Author(s):  
Hosein Mohimani ◽  
Alexey Gurevich ◽  
Kelsey L. Alexander ◽  
C. Benjamin Naman ◽  
Tiago Leão ◽  
...  
Keyword(s):  
Natural Products ◽  
Mass Spectra ◽  
Large Scale ◽  
Software Tool ◽  
Tandem Mass ◽  
Tandem Mass Spectra ◽  
Modified Peptides ◽  
New Algorithms ◽  
Large Scale Screening ◽  
Metagenome Mining

AbstractRibosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that include many antibiotics and a variety of other bioactive compounds. While recent breakthroughs in RiPP discovery raised the challenge of developing new algorithms for their analysis, peptidogenomic-based identification of RiPPs by combining genome/metagenome mining with analysis of tandem mass spectra remains an open problem. We present here MetaRiPPquest, a software tool for addressing this challenge that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just six genomic and metagenomic datasets, MetaRiPPquest identified 27 known and discovered 5 novel RiPP natural products.

scholarly journals Analysis of Tandem Mass Spectra by FTMS for Improved Large-Scale Proteomics with Superior Protein Quantification

2010 ◽  
Vol 82 (1) ◽  
pp. 316-322 ◽  
Author(s):  
Graeme C. McAlister ◽  
Doug Phanstiel ◽  
Craig D. Wenger ◽  
M. Violet Lee ◽  
Joshua J. Coon
Keyword(s):  
Mass Spectra ◽  
Large Scale ◽  
Protein Quantification ◽  
Tandem Mass ◽  
Tandem Mass Spectra
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