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 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 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 High Mass Accuracy Phosphopeptide Identification Using Tandem Mass Spectra

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Rovshan G. Sadygov
Keyword(s):  
Mass Spectra ◽  
Search Algorithm ◽  
Neutral Loss ◽  
Search Space ◽  
High Mass ◽  
Tandem Mass ◽  
Tandem Mass Spectra ◽  
Candidate Peptide ◽  
Phosphorylated Peptides ◽  
Database Size

Phosphoproteomics is a powerful analytical platform for identification and quantification of phosphorylated peptides and assignment of phosphorylation sites. Bioinformatics tools to identify phosphorylated peptides from their tandem mass spectra and protein sequence databases are important part of phosphoproteomics. In this work, we discuss general informatics aspects of mass-spectrometry-based phosphoproteomics. Some of the specifics of phosphopeptide identifications stem from the labile nature of phosphor groups and expanded peptide search space. Allowing for modifications of Ser, Thr, and Tyr residues exponentially increases effective database size. High mass resolution and accuracy measurements of precursor mass-to-charge ratios help to restrict the search space of candidate peptide sequences. The higher-order fragmentations of neutral loss ions enhance the fragment ion mass spectra of phosphorylated peptides. We show an example of a phosphopeptide identification where accounting for fragmentation from neutral loss species improves the identification scores in a database search algorithm by 50%.

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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