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SpecOMS specifications


Unique identifier OMICS_19250
Name SpecOMS
Alternative name Spectra Open Modification Search
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A database source file, a contaminants file and an experimental spectra file.
Input format MGF
Output data A collection of PSM.
Operating system Windows
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained No


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Publication for Spectra Open Modification Search

SpecOMS in publications

PMCID: 5789433
PMID: 29441133
DOI: 10.3762/bjoc.14.5

[…] since it allows a model-free determination of the number of linearly independent components in a given matrix of data []. furthermore, several commercially available programs (e.g., hyperquad [] or specfit []) offer versatile approaches to multicomponent spectra analysis, whereby the introduction of at least some known parameters (binding constants for dominant binding sites derived […]

PMCID: 5288757
PMID: 28168152
DOI: 10.1002/open.201600128

[…] small aliquots (typically 20 μl) of a concentrated solution of dov×2 tso to a dilute solution of the calixarene. the titration curves were fitted according to a 1:1 association model by using the specfit software. cyclic voltammetric experiments were carried out at room temperature in ar‐purged dichloromethane with an autolab30 multipurpose instrument interfaced to a pc. a glassy carbon […]

PMCID: 4912637
PMID: 27302144
DOI: 10.1038/ncomms11978

[…] the association of fluoride was fitted to the equilibria:, , , taking the water concentration as constant during the titration, analysis of the ultraviolet–visible absorption data by the specfit software using and afforded stability constants of 6.1(3) and 13.0(2) log units, respectively, for β1er and β2er. the results for the cumulative stability constant β2er are in excellent […]

PMCID: 4736451
PMID: 26500150
DOI: 10.1002/chem.201504236

[…] isosbestic point at 320 nm suggesting the formation of a single rotaxane–anion complex in solution. the 1:1 stoichiometric anion association constants were determined by a global fit procedure using specfit and are shown in table  together with quantitative anion‐binding data obtained with an acyclic bis‐iodotriazole rei receptor 7 (figure ) with pendent octyl chains., importantly, the neutral […]

PMCID: 4691337
PMID: 26508679
DOI: 10.1002/chem.201502721

[…] point at 418.5 nm, along with approximately 9 and 4 % increases in the intensities of the emission maxima at 595 nm and 650 nm, respectively (figure ). analysis of the uv/vis titration data by using specfit software revealed a 1:1 stoichiometric association constant of log k=3.38±0.04 (k=2396 m−1), which is in good agreement with the value determined by 1h nmr spectroscopy. by comparison, […]

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SpecOMS institution(s)
LS2N UMR CNRS 6004, Université de Nantes, Nantes, France; INRA UR1268 Biopolymères Interactions Assemblages, Nantes, France
SpecOMS funding source(s)
This work was partly funded by the Région Pays de la Loire (France) GRIOTE program (2013-2018).

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