分子網(wǎng)絡(luò)【GNPS-Spectral Library Search】

GNPS-Spectral Library Search

Spectral Library Search?

One of the major limitations in discovering new chemical entities is determining which metabolites are known compounds within complex biological samples. A way to overcome this limitation is to compare the MS2 spectra of the unknown metabolite with a library of MS/MS spectra generated from structurally characterized metabolites. Herein, this comparison is based upon the similarity cosine scoring of MS/MS spectra.

Dereplication Workflow?

From the main?GNPS page, click the?"Match Search"?button.

This will bring you to the workflow input to start library searching your data.

Selecting Input Files?

Please refer to the file selection?documentation?from networking.

Selecting Spectral Libraries to Search?

By default all the public spectral libraries are selected under the folder "speclibs". This includes many different spectral libraries. You can read about and browse these libraries on?GNPS.

NOTE: Do not change the selection of libraries unless you are an advanced user. Proteomics Spectral libraries will not work with GNPS and cause problems.

Parameters Walkthrough?

Search Options?

ParameterDescriptionDefaultParent Mass ToleranceParent mass peak tolerance2.0 Ion ToleranceMS2 peak tolerance 0.5 Score ThresholdCosine score threshold to make a match0.5Min Matched PeaksMinimum matched peaks to make a match 6

Advanced Search Options?

ParameterDescriptionDefaultLibrary ClassMinimum Library Class to Consider in SearchBronzeTop Hits Per SpectrumNumber of results to return per query spectrum1Search analogsWill search data for analogs to library spectraDon't SearchMaximum analog Search Mass DifferenceMaximum mass shift between library and putative analog found100 (Da)

Advanced Filtering Options?

ParameterDescriptionDefaultNotesFilter stdDev IntensityDeprecated0Not recommended to changeMinimum Fragment Ion IntensityAll fragment ions in the MS/MS spectrum below this raw intensity will be deleted. By default, no filter.0Reduce to 0 if your data's raw intensities are very low.Filter Precursor Ion WindowAll peaks in a +/- 17 Da around precursor ion mass are deleted. By default, yes filter. This removes the residual precursor ion, which is frequently observed in MS/MS spectra acquired on qTOFs.FilterFilter libraryApply peak filters to libraryFilterFilter peaks in 50Da WindowFilter out peaks that are not top 6 most intense peaks in a +/- 50Da windowFilterTurn off if your data is very small molecules as it might filter out a lot peaks in the lower mass ranges that might be signal.

Exploration of Results?

To access your data, either click the link in the email or click the DONE link under Status on the jobs menu page.

ViewDescriptionView All Spectra HitsView all library matchesView Top HitsView only top hit per query spectrumView All CompoundsUnique set of compounds in matches