scholarly journals Exploring Site-Specific N-Glycosylation Microheterogeneity of Haptoglobin Using Glycopeptide CID Tandem Mass Spectra and Glycan Database Search

2013 ◽  
Vol 12 (8) ◽  
pp. 3652-3666 ◽  
Author(s):  
Kevin Brown Chandler ◽  
Petr Pompach ◽  
Radoslav Goldman ◽  
Nathan Edwards
Keyword(s):  
Mass Spectra ◽  
Database Search ◽  
Tandem Mass ◽  
Site Specific ◽  
Tandem Mass Spectra

scholarly journals A hierarchical MS2 /MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra

PROTEOMICS ◽  
2009 ◽  
Vol 9 (7) ◽  
pp. 1763-1770 ◽  
Author(s):  
Hua Xu ◽  
Liwen Wang ◽  
Larry Sallans ◽  
Michael A. Freitas
Keyword(s):  
Mass Spectra ◽  
Search Algorithm ◽  
Automated Analysis ◽  
Database Search ◽  
Tandem Mass ◽  
Tandem Mass Spectra

Gapped Spectral Dictionaries and Their Applications for Database Search of Tandem Mass Spectra

SciVee ◽  
2011 ◽  
Author(s):  
Kyowon Jeong ◽  
Sangtae Kim ◽  
Nuno Bandeira ◽  
Pavel Pevzner
Keyword(s):  
Mass Spectra ◽  
Database Search ◽  
Tandem Mass ◽  
Tandem Mass Spectra

scholarly journals Deconvolution and Database Search of Complex Tandem Mass Spectra of Intact Proteins

2010 ◽  
Vol 9 (12) ◽  
pp. 2772-2782 ◽  
Author(s):  
Xiaowen Liu ◽  
Yuval Inbar ◽  
Pieter C. Dorrestein ◽  
Colin Wynne ◽  
Nathan Edwards ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Database Search ◽  
Tandem Mass ◽  
Intact Proteins ◽  
Tandem Mass Spectra

scholarly journals Peptide Identification by Database Search of Mixture Tandem Mass Spectra

2011 ◽  
Vol 10 (12) ◽  
pp. M111.010017 ◽  
Author(s):  
Jian Wang ◽  
Philip E. Bourne ◽  
Nuno Bandeira
Keyword(s):  
Mass Spectra ◽  
Peptide Identification ◽  
Database Search ◽  
Tandem Mass ◽  
Tandem Mass Spectra

scholarly journals The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search

2010 ◽  
Vol 9 (12) ◽  
pp. 2840-2852 ◽  
Author(s):  
Sangtae Kim ◽  
Nikolai Mischerikow ◽  
Nuno Bandeira ◽  
J. Daniel Navarro ◽  
Louis Wich ◽  
...  
Keyword(s):  
Generating Function ◽  
Mass Spectra ◽  
Database Search ◽  
Tandem Mass ◽  
Tandem Mass Spectra

scholarly journals GPQuest: A Spectral Library Matching Algorithm for Site-Specific Assignment of Tandem Mass Spectra to Intact N-glycopeptides

2015 ◽  
Vol 87 (10) ◽  
pp. 5181-5188 ◽  
Author(s):  
Shadi Toghi Eshghi ◽  
Punit Shah ◽  
Weiming Yang ◽  
Xingde Li ◽  
Hui Zhang
Keyword(s):  
Mass Spectra ◽  
Tandem Mass ◽  
Spectral Library ◽  
Site Specific ◽  
Matching Algorithm ◽  
Tandem Mass Spectra ◽  
Specific Assignment

PhoStar: Identifying Tandem Mass Spectra of Phosphorylated Peptides before Database Search

2017 ◽  
Vol 17 (1) ◽  
pp. 290-295 ◽  
Author(s):  
Sebastian Dorl ◽  
Stephan Winkler ◽  
Karl Mechtler ◽  
Viktoria Dorfer
Keyword(s):  
Mass Spectra ◽  
Database Search ◽  
Tandem Mass ◽  
Tandem Mass Spectra ◽  
Phosphorylated Peptides

scholarly journals Protocol for analysis of glycoproteomics LC-MS data using GlycReSoft

2020 ◽  
Author(s):  
Joshua A. Klein ◽  
Joseph Zaia
Keyword(s):  
Mass Spectra ◽  
Software Tool ◽  
Database Search ◽  
Peptide Sequence ◽  
Data Sets ◽  
Tandem Mass ◽  
Exact Mass ◽  
Tandem Mass Spectra ◽  
Search Results ◽  
Data Files

Summary/AbstractThe GlycReSoft software tool allows users to process glycoproteomics LC-MS data sets. The tool accepts proteomics database search results or a user-defined list of proteins in the sample. GlycReSoft processes LC-MS data to yield deconvoluted exact mass values. The user has the option to import a list of theoretical glycans from an external database, a curated glycan list, or a measured glycome. The tool assembles a list of theoretical glycopeptides from the lists of theoretical glycans and proteins, respectively. The program then scores the tandem mass spectra in the LC-MS data files and provides graphical views of the identified glycopeptides for each protein in the sample, and the set of glycoforms identified for each peptide sequence.

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