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Protocols

ChopNSpice specifications

Information


Unique identifier OMICS_06898
Name ChopNSpice
Interface Web user interface
Restrictions to use None
License GNU General Public License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

ChopNSpice citations

 (4)
library_books

Proteome wide Mapping of Endogenous SUMOylation Sites in Mouse Testis*

2017
PMCID: 5417816
PMID: 28289178
DOI: 10.1074/mcp.M116.062125

[…] ion series within complex MS/MS spectra (). This kind of software was developed to interpret MS2 spectra of branched SUMOylated peptides. In addition, Hsiao et al. developed a database search tool (“ChopNSpice”) that can successfully allow the identification of SUMO acceptor sites from endogenous SUMOylated proteins (). Nevertheless, the application of these two search strategies is not widely us […]

library_books

The Human Cytomegalovirus DNA Polymerase Processivity Factor UL44 Is Modified by SUMO in a DNA Dependent Manner

2012
PLoS One
PMCID: 3499415
PMID: 23166733
DOI: 10.1371/journal.pone.0049630

[…] Extracted peptides were analyzed by LC-MSMS on an Orbitrap Velos (ThermoFisherScientific) exactly under the conditions described in Hsiao et al. . Data analysis was performed by the use of software “ChopNSpice” in combination with MASCOT as search engine. See Supplementary Material and Methods in for details. […]

library_books

Global SUMO Proteome Responses Guide Gene Regulation, mRNA Biogenesis, and Plant Stress Responses

2012
Front Plant Sci
PMCID: 3443746
PMID: 23060889
DOI: 10.3389/fpls.2012.00215

[…] tified for each target separately using often MS/MS data obtained from in vitro sumoylated proteins. Such relatively simple MS/MS spectra are then analyzed with specific algorithms such as SUMmOn and ChopNSpice to facilitate annotation of both in vitro and biological data (Pedrioli et al., ; Hsiao et al., ; Jeram et al., ). A second problem is that tryptic digestion of SUMO leaves a large signatur […]

call_split

Sumoylation inhibits α synuclein aggregation and toxicity

2011
PMCID: 3135405
PMID: 21746851
DOI: 10.1083/jcb.201010117
call_split See protocol

[…] with the Orbitrap detector, a lock-mass ion from ambient air (m/z = 445.120025) was used for internal calibration.Identification of sumoylated lysine residues was performed exactly as described in . ChopNSpice software () was used to generate a concatenated protein sequence in order to identify the actual SUMO sites with the MASCOT search engine. For this, the FASTA sequence of α-synuclein was ch […]


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