scholarly journals Optimization and testing of mass spectral library search algorithms for compound identification

1994 ◽  
Vol 5 (9) ◽  
pp. 859-866 ◽  
Author(s):  
Stephen E. Stein ◽  
Donald R. Scott
Keyword(s):  
Search Algorithms ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Compound Identification ◽  
Library Search ◽  
Mass Spectral

Evaluation of mass spectral library search algorithms implemented in commercial software

2015 ◽  
Vol 50 (6) ◽  
pp. 820-825 ◽  
Author(s):  
Andrey Samokhin ◽  
Ksenia Sotnezova ◽  
Vitaly Lashin ◽  
Igor Revelsky
Keyword(s):  
Search Algorithms ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Commercial Software ◽  
Library Search ◽  
Mass Spectral

scholarly journals N-Linked Glycopeptide Identification Based on Open Mass Spectral Library Search

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Zhiwu An ◽  
Qingbo Shu ◽  
Hao Lv ◽  
Lian Shu ◽  
Jifeng Wang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Human Cancer ◽  
Cancer Cell Line ◽  
Peptide Identification ◽  
High Energy ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Data Set ◽  
Library Search ◽  
Mass Spectral

Confident characterization of intact glycopeptides is a challenging task in mass spectrometry-based glycoproteomics due to microheterogeneity of glycosylation, complexity of glycans, and insufficient fragmentation of peptide bones. Open mass spectral library search is a promising computational approach to peptide identification, but its potential in the identification of glycopeptides has not been fully explored. Here we present pMatchGlyco, a new spectral library search tool for intact N-linked glycopeptide identification using high-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS) data. In pMatchGlyco, (1) MS/MS spectra of deglycopeptides are used to create spectral library, (2) MS/MS spectra of glycopeptides are matched to the spectra in library in an open (precursor tolerant) manner and the glycans are inferred, and (3) a false discovery rate is estimated for top-scored matches above a threshold. The efficiency and reliability of pMatchGlyco were demonstrated on a data set of mixture sample of six standard glycoproteins and a complex glycoprotein data set generated from human cancer cell line OVCAR3.

False Discovery Rate Estimation for Hybrid Mass Spectral Library Search Identifications in Bottom-up Proteomics

2019 ◽  
Vol 18 (9) ◽  
pp. 3223-3234 ◽  
Author(s):  
Meghan C. Burke ◽  
Zheng Zhang ◽  
Yuri A. Mirokhin ◽  
Dmitrii V. Tchekovskoi ◽  
Yuxue Liang ◽  
...  
Keyword(s):  
False Discovery Rate ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Bottom Up ◽  
Library Search ◽  
Mass Spectral ◽  
Rate Estimation ◽  
False Discovery ◽  
False Discovery Rate Estimation

The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics

2017 ◽  
Vol 16 (5) ◽  
pp. 1924-1935 ◽  
Author(s):  
Meghan C. Burke ◽  
Yuri A. Mirokhin ◽  
Dmitrii V. Tchekhovskoi ◽  
Sanford P. Markey ◽  
Jenny Heidbrink Thompson ◽  
...  
Keyword(s):  
Search Method ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Hybrid Search ◽  
Library Search ◽  
Mass Spectral
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