The Comprehensive Systems Biology Project (CSB)
- A Comprehensive Systems-Biology Database -
Hosted at Max Planck Institute of Molecular Plant Physiology
Databases: Associated DB | Transcriptome DB | Metabolome DB | Co-Response DB | BestFit
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NOTIFICATION: Permanent migration of all CSB.DB services and functionalities on 1.1.2016.
Herewith we inform you that all CSB.DB databases have been migrated at the beginning of 2016. This includes all gene correlation and expression databases, the GMD@CSB.DB module and all associated databases
The BestFit software, a tool for non-aqueous fractionation data analysis, will also be available by the Experimental Systems Biology Research Group headed by Dr. Patrick Giavalisco.
We thank all users, contributors, and collaborators of CSB.DB at the Max Planck Institute for their long-standing support.
Yours sincerely, the CSB.DB Curator and the CSB.DB Developmental Core Team
Help@CSB.DB: Metabolome - GMD Queries
tCoR query
If you want to get help directly related to a page/query, use the Info Pages / Medium Info Pages. Direct links are available at each (Query) Page.

If you are completely lost, here is link to a short description of what CSB.DB is and is not. Enter this page.

GMD@CSB.DB: Query Types
MSRI: Single Compound Query (sCQ):

Mass Spectra Query: Single Compound Query (sCQ) back to top

The compound search tool allows searching by a (part of a) compound or metabolite name and provides access to the mass spectra information harboured at GMD. Various available filter options enabled the user to limit the result set to the available technology platforms, particular libraries or methods. Filter options can be simultaneous applied to limit the result set. Following filter options can be applied.

The Platform Filter option allows restricting search to mass spectra obtained by gas chromatography mass spectrometry (GC-MS) based on time-of-flight (GC-TOF) or quadrupole (GC-Quad) technology platform. With the default setting the search is performed among all available GC-MS technology platforms.

The Library Filter option allows restricting search to curated libraries available for download, namely 'T_MSRI_ID' which base on GC-TOF-MS platform or 'Q_MSRI_ID' which based on quadrupole GC-MS platform. With the default setting the search is not restricted to any of the available libraries. The curated as well as additional non-curated libraries are available for download. A detailed description of the libraries can be found here: MSRI library page.

The Method Filter option allows restricting search to those compound names were the spectral information are obtained by a particular method. Currently, the search can be restricted to the method M[1], which base on GC-TOF-MS platform, or to the method M[2], which based on quadrupole GC-MS platform. With the default setting the search is not restricted to the method available.

MSRI: Single Mass Spectrum Search (sSPQ):

Mass Spectra Query: Single Mass Spectrum Search (sSPQ) back to top

The Mass Spectrum Search page allows searching by a user provided mass spectrum to ask weather we know something about this spectrum or about related spectra. Following filter options can be applied to restrict the search:

The Platform Filter option allows restricting search to mass spectra obtained by gas chromatography mass spectrometry (GC-MS) based on time-of-flight (GC-TOF) or quadrupole (GC-Quad) technology platform. With the default setting the search is performed among all available GC-MS technology platforms.

The RI Filter allows restricted search to those mass spectra which are characterized by a retention time index (RI) within the user defined RI window wide. The observed RI for the input spectrum is required and should be a float number or single number. The accepted formats are: [dddd] or [dddd.ddd], e.g. 1000 or 1000.000. The window wide should be an absolute float number less than 1000. Before using restricted search by RI filter options you should check if your RI system and the method settings fit to our RI system / method settings. Otherwise ignore this option or increase the default window wide. RI system and settings: GC-MS-TOF | GC-MS-QUAD

The Fragment Filter allows search limited to masses and / or intensities which fit to the applied filter. Following Fragment Filter options can be selected or no filter applied:
The Search can be restricted to highest relative intensities according user input, e.g. the masses with the highest 10 intensities. The required input must be an absolute float number of at least 1 up to max. 50. Masses which do not fit are ignored.
Moreover, the search can be restricted to masses with relative intensities higher than a user specified value, e.g. 20. The required fragment filter input must be less or equal than 100. The search is restricted to masses with a particular relative or normalized relative intensity defined by the user input. It can be used to limit the search to abundant relative intensities.
Additionally, the search can be restricted to particular mass range, e.g. 100-300. The range is limited from 10 to 650. The input must be specified as follows: Value1-Value2. The search is restricted to masses which are in the specified range.

Normalization: The mass spectral search can be computed on the relative intensities or on the normalized relative intensities for all mass spectra. If your input spectra not in relative intensity range we recommended usage of the normalized relative intensities. If you select this option all intensities of the mass spectrum are normalized to the unit intensity of 1000 to allow comparison.

With the output option you can limit the number of obtained hits to 50, 100 or 250 according the fragment-intensity or the fragment agreement. The fragment-intensity agreement is computed as the Euclidean distance and takes the mass as well as the intensity into account. If a particular mass absent for the query or a subject spectrum the intensity is set to 0. In contrast, the fragment agreement compares only the masses among a query and a subject spectrum and is computed as the binary distance measure S12.

MSRI: Customized Library Generation (CLG):

Mass Spectra Query: Customized Library Generation (CGL) back to top

GMD allows the user to generate customized mass spectral library from the list of curated mass spectral entries. The input must be a list of MPIMP-IDs which can be obtained by using the Compound Name Conversion Tool. The mass spectra used for generation of a customized library can be restricted to the technology platform or a particular method (see above).
Tool: Compound Name Converter:

Tools: Compound Name Converter back to top

The Compound Name Conversion allows converting compound names to MapMan names or MPIMP-IDs. The output will be a list of possible matches which must be curated by user for the exact assignments. The curated list can be downloaded. The input is limited to 25 compound names. The type of conversion must be selected. As mentioned above to types are currently available.

Convert to MapMan Names: The conversion of your compound names to MapMan names allows visualizing your obtained results in the software MapMan. For visualization in MapMan the MapMan mapping file, kindly provided by Y.Gibon (Research group Stitt, MPI-MP), is required, which can be obtained from the parent Tools@GMD page.

Convert to MPIMP-IDs: The conversion of your compound names to MPIMP-IDs allows generating customized mass spectra and retention time index (MSRI) libraries of your favourite compounds to use it with the NIST software for compound identification.
Profiles: Single Metabolite Profil Search (sMPQ):

Profiles: Single Metabolite Profil Search (sMPQ) back to top

The profiles can be queried by a particular compound name and allows searching for the co-responding compound levels within a particular experiment. Various filter options are available to restrict computation to high-quality mass traces / mass trace entries by using the default or user modified values.

Organism: Restrict search to metabolite profiles obtained from a particular organism which can be selected from the list of available organisms.

Profile Sets: You can restrict the search to metabolite profile generated on a particular technology platform as well as limited to specific profile sets.

RI Regression: With the retention time index (RI) regression option you determine the procedure hwo to compute the RIs from the observed retention time (RT). You can select between a quintic regression and a step-wise linear regression. The qunitic regression assumes a quintic relation between the RT and the RI for the measured fragments. The regression is performed among all added standard substances for RI computation (RI system for: method 1 | method 2). The step-wise linear regression assume a linear behaviour among to added standard substances. Furthermore, define the RI window wide or use the default. If the RI for a particular profile higher than the tolerated range, the compound is not valid measured in the co-responding profile and values will be set to 'NA'.

Area Filter: Define the minimal area threshold (Min. Area Thresh.) and maximum area threshold (Max. Area thresh.). This filter option allows you to ignore raw areas which are near the background as well as to filter out saturated peaks. If a area value lower / higher than the defined threshold the values will be set to 'NA'.

Match Filter: Define the thresholds for the forward match (For. Match Thresh.) and the reverse match (Rev. Match Thresh.). Theses matches are obtained by matching a mass spectrum against library of mass spectra and vice verse. We recommend using the default settings.

Statistics: Select the statistical procedure which do you want to apply. If you select arithmetic mean you should select the parametric t-test statistic. The non-parametric Wilcoxon's two-sample test should be selected if you have selected the median, the non-parametric version of the arithmetic mean. The selected statistic will be applied to compute the average of the replicates for a particular condition as well as used to compute the probability (p.value) for the significant changes of the treatment vs. the respective control. Please remember when interpreting the results, that the obtained p.value is not corrected for multiple comparisons. The simplest but very conservative way is correction as follows (Bonferroni procedure): Accept the changes as significant, if the obtained probability less than (0.05 / number of comparisons).

For suggestions and questions feel free to contact the CSB.DB curator.
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