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Protocols

SpecOMS specifications

Information


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

Subtools


  • SpecFit
  • SpecTrees
  • SpecXtract

Versioning


No version available

Documentation


Maintainers


This tool is not available anymore.

Additional information


https://hal.archives-ouvertes.fr/hal-01337288

Publication for Spectra Open Modification Search

SpecOMS citations

 (27)
library_books

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

2018
Beilstein J Org Chem
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 from GlobalF […]

library_books

White light emission from discrete heterometallic lanthanide directed self assembled complexes in solution† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00739f Click here for additional data file.

2017
PMCID: 5417009
PMID: 28507713
DOI: 10.1039/c7sc00739f

[…] of the 1 : 1 (Ln : L, where Ln = lanthanide and L = EDTA) complexes, Ln(EDTA)·(H2O)3. The UV-visible data were then treated and fitted using the non-linear least squares regression analysis program, SPECFIT® to determine the stoichiometry of the metal species formed in solution as well as their corresponding stability constants. Residuals calculated for UV-visible data are equal to 1.6 × 10–3 and […]

library_books

Interactions between photoacidic 3 hydroxynaphtho[1,2 b]quinolizinium and cucurbit[7]uril: Influence on acidity in the ground and excited state

2017
Beilstein J Org Chem
PMCID: 5301965
PMID: 28228861
DOI: 10.3762/bjoc.13.23

[…] The data from the titrations were plotted as absorption or emission intensity versus concentration of CB[7], and the resulting binding isotherms were used to obtain the binding constants K b with the SpecFit 32 program. […]

library_books

Template directed synthesis of linear porphyrin oligomers: classical, Vernier and mutual Vernier† †Electronic supplementary information (ESI) available: Synthesis and characterization of new compounds, ladder complexes, UV vis NIR titrations and binding data for reference compounds and for the formation of linear oligomer complexes, calculation of effective molarities, analytical GPC calibration and molar absorption coefficients. See DOI: 10.1039/c6sc05355f Click here for additional data file.

2017
PMCID: 5426366
PMID: 28553508
DOI: 10.1039/c6sc05355f

[…] 1.0 equivalents of NiP6 indicates formation of a series of self-assembled complexes with NiP6 : ZnP4 stoichiometries of 1 : 2, 2 : 3 and 1 : 1 as illustrated in . The titration data were analyzed by SPECFIT in term of six colored species as predicted in , NiP6, ZnP4, 1 : 1, 1 : 2, 2 : 2 and 2 : 3 complexes. The predicted β N : N values as listed in were used to fit to the experimental data by SP […]

library_books

Plugging a Bipyridinium Axle into Multichromophoric Calix[6]arene Wheels Bearing Naphthyl Units at Different Rims

2017
PMCID: 5288757
PMID: 28168152
DOI: 10.1002/open.201600128

[…] ing 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 workin […]

call_split

In Vitro Antioxidant versus Metal Ion Chelating Properties of Flavonoids: A Structure Activity Investigation

2016
PLoS One
PMCID: 5082868
PMID: 27788249
DOI: 10.1371/journal.pone.0165575
call_split See protocol

[…] 30 nm to 800 nm to follow the evolution of complexation on a Cary 50 (Varian) or a Cary 5000 (Agilent) spectrophotometer maintained at (25.0 ± 2°C. The spectrophotometric data were then analyzed with Specfit [] program which adjusts the absorptivities and the stability constants of the species formed at equilibrium. Specfit uses factor analysis to reduce the absorbance matrix and to extract the ei […]

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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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