Comet: An open-source MS/MS sequence database search tool

PROTEOMICS ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 22-24 ◽  
Author(s):  
Jimmy K. Eng ◽  
Tahmina A. Jahan ◽  
Michael R. Hoopmann
Keyword(s):  
Open Source ◽  
Database Search ◽  
Sequence Database ◽  
Search Tool ◽  
Sequence Database Search

scholarly journals A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry

2018 ◽  
Vol 18 (2) ◽  
pp. 652-663 ◽  
Author(s):  
Kristian E. Swearingen ◽  
Jimmy K. Eng ◽  
David Shteynberg ◽  
Vladimir Vigdorovich ◽  
Timothy A. Springer ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Database Search ◽  
Search Method ◽  
Tandem Mass ◽  
Sequence Database ◽  
Sequence Database Search

Human plasma proteome analysis by reversed sequence database search and molecular weight correlation based on a bacterial proteome analysis

PROTEOMICS ◽  
2006 ◽  
Vol 6 (4) ◽  
pp. 1121-1132 ◽  
Author(s):  
Gun Wook Park ◽  
Kyung-Hoon Kwon ◽  
Jin Young Kim ◽  
Jeong Hwa Lee ◽  
Sung-Ho Yun ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Human Plasma ◽  
Proteome Analysis ◽  
Database Search ◽  
Plasma Proteome ◽  
Sequence Database ◽  
Sequence Database Search ◽  
Human Plasma Proteome

scholarly journals COSS: A fast and user-friendly tool for spectral library searching

2019 ◽  
Author(s):  
Genet Abay Shiferaw ◽  
Elien Vandermarliere ◽  
Niels Hulstaert ◽  
Ralf Gabriels ◽  
Lennart Martens ◽  
...  
Keyword(s):  
Scoring Functions ◽  
Sequence Database ◽  
Spectral Library ◽  
Data Formats ◽  
Large Databases ◽  
Search Tool ◽  
Spectral Searching ◽  
Spectral Libraries ◽  
User Friendly ◽  
Sequence Database Search

ABSTRACTSpectral similarity searching to identify peptide-derived MS/MS spectra is a promising technique, and different spectrum similarity search tools have therefore been developed. Each of these tools, however, comes with some limitations, mainly due to low processing speed and issues with handling large databases. Furthermore, the number of spectral data formats supported is typically limited, which also creates a threshold to adoption. We have therefore developed COSS (CompOmics Spectral Searching), a new and user-friendly spectral library search tool supporting two scoring functions. COSS also includes decoy spectra generation for result validation. We have benchmarked COSS on three different spectral libraries and compared the results with established spectral search and sequence database search tool. Our comparison showed that COSS more reliably identifies spectra and is faster than other spectral library searching tools. COSS binaries and source code can be freely downloaded from https://github.com/compomics/COSS.

Impact of Discovery Layers on Accessing E-Resources in Academic Libraries

2016 ◽  
pp. 181-200
Author(s):  
Mayank Yuvaraj
Keyword(s):  
Developing Countries ◽  
Open Source ◽  
Research Articles ◽  
Survey Method ◽  
Library Users ◽  
Search Filters ◽  
Search Tool ◽  
The University ◽  
Descriptive Survey ◽  
The Impact

The paper discusses the implementation of the ‘CUB E-journal One Search' tool as an alternative solution to commercial discovery services, which was designed using Google Custom Search by the Central Library, Central University of Bihar and its impact on the library users. A descriptive survey method was used for the study. The present study found that library users found CUB E-journal One Search as a useful tool to get their desired information out of 9000 subscribed e-resources in the university. Most of the users used CUB E-journal One Search frequently in order to find relevant articles, write their assignments and research articles. The study indicated that the library users were influenced by Google like single search boxes and wished to have same features. Further, users expected features like document recommendation, search filters, RSS and on-screen help from the discovery tool. The paper is a first attempt to study the impact of open source discovery tools on the library users. It will further give confidence to the librarians in developing countries to deploy open source search solutions using Google Custom Search in the libraries.

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