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Links tagged with 'mass spectrometry'

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Found 21 links

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ARISTOTool Content

http://www.ionspectra.org/aristo [open in a new window]

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Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules

Automatic Reduction of Ion Spectra to Ontology (ARISTO) is a web tool which provides information regarding the chemical nature/ontology of the compound underlying an input electron ionization mass spectrum.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry.20111
NAR Web Server Issue 2011
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tagsmass spectrometry small molecule libraries

DeNovoIDDatabase Content

http://proteomics.mcw.edu/denovoid/ [open in a new window]

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Protein > Proteomics

DeNovoID is a tool for protein identification using de novo peptide sequence data from mass spectrometry experiments.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy200518
NAR Web Server Issue 2005
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tagsalgorithms amino acids mass spectrometry peptides protein databases protein sequence analysis proteomics

GlycoSearchMSTool Content

http://www.glycosciences.de/sweetdb/start.php?action=form_ms_search [open in a new window]

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Other Molecules > Carbohydrates

GlycoSearchMS takes a list of mass spectra peak values as input and searches for matches with the calculated fragments of SweetDB structures.

This content is being maintained by luetteke.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates200441
NAR Web Server Issue 2004
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tagsalgorithms carbohydrate sequence humans mass spectrometry polysaccharides

HMDBDatabase Content

http://www.hmdb.ca/ [open in a new window]

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Human Genome > Other Resources
Other Molecules > Metabolites

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches.

links directory index: 73
TitlePublication YearGoogle Scholar Citation Count
Metabolomics: the principles and potential applications to transplantation200573
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external linksLink on Wikipedia
tagsbiochemical phenomena biochemistry biomolecular nuclear magnetic resonance factual databases humans internet magnetic resonance spectroscopy mass spectrometry metabolic diseases metabolic networks and pathways metabolism metabolome organ transplantation quality control user-computer interface

HUPO Proteomics Standards InitiativeResource Content

http://psidev.sourceforge.net/ [open in a new window]

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Protein > Proteomics

HUPO Proteomics Standards Initiative (PSI) provides data representation standards to facilitate the exchange, comparison and validation of proteomics data.

links directory index: 516
TitlePublication YearGoogle Scholar Citation Count
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data2004405
The proteomics standards initiative2003111
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tagsbiochemistry database management systems guidelines as topic humans internationality mass spectrometry natural language processing peptide mapping protein binding protein databases protein interaction mapping proteins proteomics reference standards

ISOTOPICATool Content

http://coco.protein.osaka-u.ac.jp/isotopica/ [open in a new window]

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Protein > Proteomics

Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. A viewer for visualizing results is also available.

links directory index: 23
TitlePublication YearGoogle Scholar Citation Count
Isotopica: a tool for the calculation and viewing of complex isotopic envelopes200423
NAR Web Server Issue 2004
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tagsamino acid sequence base sequence biopolymers carbohydrate sequence ions isotopes mass spectrometry mathematical computing peptide mapping

ISPIDER CentralTool Content

http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl [open in a new window]

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Protein > Proteomics

The ISPIDER Central provides a range of services for integrative data analysis in mass spectrometry-based proteomics. It enables users to query multiple proteomic repositories and to add information to proteins retrieved from searches for integrative in silico experiments in proteomics.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
ISPIDER Central: an integrated database web-server for proteomics200814
NAR Web Server Issue 2008
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tagsmass spectrometry protein databases proteomics systems integration
setsUniversity of Manchester

MassNetTool Content

http://massnet.kr [open in a new window]

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Protein > Do-it-all Tools for Protein
Protein > Proteomics

MassNet web server provides comprehensive functional annotation of mass spectrometry data. Annotation includes physico-chemical analysis, KEGG pathway assignment, GO mapping, and protein-protein interaction prediction.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
MassNet: a functional annotation service for protein mass spectrometry data20087
NAR Web Server Issue 2008
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tagsmass spectrometry protein databases protein interaction mapping proteins

MassTRIXTool Content

http://masstrix.org [open in a new window]

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Other Molecules > Metabolites
Protein > Proteomics

With applications in metabolomics and other mass spectrometry studies, MassTRIX is a hypothesis driven approach to the annotation of mass spectrometry data. Data is output in context on a KEGG pathway map.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
MassTRIX: mass translator into pathways200849
NAR Web Server Issue 2008
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tagsgene expression mass spectrometry metabolic networks and pathways

MaXIC-QTool Content

http://ms.iis.sinica.edu.tw/MaXIC-Q [open in a new window]

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Protein > Proteomics

The MaXIC-Q web server performs various quantification analyses on large-scale datasets generated from proteomics studies using isotope labeling. For input MS data, output is given in projected ion mass spectrum and extracted ion chromatograph which can be used to generate other calculations (e.g. ion abundances and peptide-protein ratios.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS20093
NAR Web Server Issue 2009
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tagscomputational biology endothelial cells isotope labeling liquid chromatography mass spectrometry nitric acid peptides proteins reproducibility of results statistical data interpretation

MetaboAnalyst 2.0Tool Content

http://www.metaboanalyst.ca [open in a new window]

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Other Molecules > Metabolites
Protein > Networks & Interactions, Pathways and Enzymes
Protein > Proteomics

MetaboAnalyst is a web-based pipeline for metabolomic data processing, statistical analysis and functional interpretation. It performs data processing and normalization for various metabolomic data types. It provides various univariate and multivariate statistical analysis for two/multi-group, one/two-factor, as well time-series data. For targeted metabolomic data, users can also perform functional enrichment analysis and pathway analysis. New features for data filtering, editing & normalization

This content is being maintained by Jeff Xia.

links directory index: 75
TitlePublication YearGoogle Scholar Citation Count
MetaboAnalyst: a web server for metabolomic data analysis and interpretation200975
NAR Web Server Issue 2009NAR Web Server Issue 2012
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tagsbiomolecular nuclear magnetic resonance cluster analysis internet mass spectrometry metabolomics software user-computer interface

MODiTool Content

http://prix.uos.ac.kr/research.jsp [open in a new window]

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Protein > Biochemical Features
Protein > Proteomics

Modi is a tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide.

links directory index: 31
TitlePublication YearGoogle Scholar Citation Count
MODi: a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra200631
NAR Web Server Issue 2006
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tagsmass spectrometry peptides post-translational protein processing protein databases protein sequence analysis

Multi-QTool Content

http://ms.iis.sinica.edu.tw/Multi-Q-Web/ [open in a new window]

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Protein > Proteomics

Multi-Q provides an automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling.

links directory index: 66
TitlePublication YearGoogle Scholar Citation Count
The Multi-Q web server for multiplexed protein quantitation200712
Multi-Q: a fully automated tool for multiplexed protein quantitation200654
NAR Web Server Issue 2007
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tagsautomatic data processing computational biology humans ions jurkat cells liquid chromatography mass spectrometry multiprotein complexes peptides protein folding proteins proteomics

NeuropredTool Content

http://neuroproteomics.scs.uiuc.edu/neuropred.html [open in a new window]

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Protein > Proteomics
Protein > Sequence Features

NeuroPred is a tool designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. Neuropred also computes the mass of the predicted peptides with or without selected post-translational modifications.

links directory index: 81
TitlePublication YearGoogle Scholar Citation Count
NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides200654
From precursor to final peptides: a statistical sequence-based approach to predicting prohormone processing200327
NAR Web Server Issue 2006
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tagsamino acid sequence animals aplysia invertebrate hormones logistic models mass spectrometry neuropeptides protein precursors protein sequence analysis regression analysis sensitivity and specificity statistical models

PeptidomeDatabase Content

ftp://ftp.ncbi.nih.gov/pub/peptidome/ [open in a new window]

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Protein > Databases
Protein > Proteomics

Peptidome is a public repository that archives and freely distributes tandem mass spectrometry peptide and protein identification data generated by the scientific community. Data from all stages of a mass spectrometry experiment are captured, including original mass spectra files, experimental metadata and conclusion-level results.

links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
NCBI Peptidome: a new repository for mass spectrometry proteomics data201017
NAR Database Issue 2010
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tagscomputational biology gene expression profiling genetic databases humans mass spectrometry national library of medicine (u.s.) nucleic acid databases peptides protein databases proteomics tertiary protein structure united states

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