WORDGRAPH: Keyword-in-Context Visualization for NETSPEAK's Wildcard Search

2012 ◽  
Vol 18 (9) ◽  
pp. 1411-1423 ◽  
Author(s):  
P. Riehmann ◽  
H. Gruendl ◽  
M. Potthast ◽  
M. Trenkmann ◽  
B. Stein ◽  
...  
Keyword(s):  
Wildcard Search

Secure and efficient wildcard search over encrypted data

2020 ◽  
Author(s):  
Sanjit Chatterjee ◽  
Manish Kesarwani ◽  
Jayam Modi ◽  
Sayantan Mukherjee ◽  
Shravan Kumar Parshuram Puria ◽  
...  
Keyword(s):  
Encrypted Data ◽  
Wildcard Search

scholarly journals Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics

2020 ◽  
pp. mcp.RA120.002260 ◽  
Author(s):  
Abhishek Roushan ◽  
Gary M. Wilson ◽  
Doron Kletter ◽  
K. Ilker Sen ◽  
Wilfred H. Tang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Posttranslational Modifications ◽  
Mass Range ◽  
Peptide Sequence ◽  
Tandem Mass ◽  
Mass Spectrometry Experiment ◽  
Tandem Mass Spectra ◽  
Single Mass ◽  
Wildcard Search ◽  
Search Program

Glycopeptides in peptide or digested protein samples pose a number of analytical and bioinformatics challenges beyond those posed by unmodified peptides or peptides with smaller posttranslational modifications. Exact structural elucidation of glycans is generally beyond the capability of a single mass spectrometry experiment, so a reasonable level of identification for tandem mass spectrometry, taken by several glycopeptide software tools, is that of peptide sequence and glycan composition, meaning the number of monosaccharides of each distinct mass, for example HexNAc(2)Hex(5) rather than man5. Even at this level, however, glycopeptide analysis poses challenges:  finding glycopeptide spectra when they are a tiny fraction of the total spectra; assigning spectra with unanticipated glycans, not in the initial glycan database; and finding, scoring, and labeling diagnostic peaks in tandem mass spectra.  Here we discuss recent improvements to Byonic, a glycoproteomics search program, that address these three issues. Byonic now supports filtering spectra by m/z peaks, so that the user can limit attention to spectra with diagnostic peaks, for example, at least two out of three of 204.087 for HexNAc, 274.092 for NeuAc (with water loss), and 366.139 for HexNAc-Hex, all within a set mass tolerance, for example, ± 0.01 Daltons. Also new is glycan “wildcard” search, which allows an unspecified mass within a user-set mass range to be applied to N- or O-linked glycans and enables assignment of spectra with unanticipated glycans. Finally the next release of Byonic supports user-specified peak annotations from user-defined posttranslational modifications. We demonstrate the utility of these new software features by finding previously unrecognized glycopeptides in publicly available data, including glycosylated neuropeptides from rat brain.

Efficient wildcard search over encrypted data

2015 ◽  
Vol 15 (5) ◽  
pp. 539-547 ◽  
Author(s):  
Changhui Hu ◽  
Lidong Han
Keyword(s):  
Encrypted Data ◽  
Wildcard Search

Conjunctive Wildcard Search over Encrypted Data

2011 ◽  
pp. 114-127 ◽  
Author(s):  
Christoph Bösch ◽  
Richard Brinkman ◽  
Pieter Hartel ◽  
Willem Jonker
Keyword(s):  
Encrypted Data ◽  
Wildcard Search
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