compared with
Current by Louis Felix Nothias
on Apr 25, 2018 11:13.

Key
This line was removed.
This word was removed. This word was added.
This line was added.

Changes (17)

View page history
The _Insilico Peptidic Natural Products Dereplicator_ is a bioinformatic tool that allows the annotation of known peptidic natural products in MS/MS data using in silico fragmentation tree.

Please cite the following if you are using Dereplicator:
For more informations, see the Dereplicator and VarQuest manuscripts:


Hosein Mohimani, Alexey Gurevich, Alla Mikheenko, Neha Garg, Louis-Felix Nothias, Akihiro Ninomiya, Kentaro Takada, Pieter C. Dorrestein, Pavel A. Pevzner, {color:#000000}{_}Dereplication of Peptidic Natural Products Through Database Search of Mass Spectra, Nature Chemical Biology, 2016,_{color} 13, 30--37 (2017) doi:[10.1038/nchembio.2219|http://www.nature.com/nchembio/journal/v13/n1/abs/nchembio.2219.html]

*Dereplicator*: Hosein Mohimani, Alexey Gurevich, Alla Mikheenko, Neha Garg, Louis-Felix Nothias, Akihiro Ninomiya, Kentaro Takada, Pieter C. Dorrestein, Pavel A. Pevzner, {color:#000000}{_}Dereplication of Peptidic Natural Products Through Database Search of Mass Spectra, Nature Chemical Biology,_{color} {color:#000000}{*}2016{*}{color}{color:#000000},{color} 13, 30--37 (2017) doi:[10.1038/nchembio.2219|http://www.nature.com/nchembio/journal/v13/n1/abs/nchembio.2219.html]










*Dereplicator with VarQuest*: Gurevich, A.; Mikheenko, A.; Shlemov, A.; Korobeynikov, A.; Mohimani, H.; Pevzner, P. A. Increased Diversity of Peptidic Natural Products Revealed by Modification-Tolerant Database Search of Mass Spectra. _Nat Microbiol_ *2018*, _3_ (3), 319--327. [https://www.nature.com/articles/s41564-017-0094-2|https://www.nature.com/articles/s41564-017-0094-2]






{toc}










h2. Running the Dereplicator on GNPS

{color:#000000}{*}BASIC OPTIONS:*{color}

*  \-\- Precursor Ion Mass Tolerance: * {color:#000000}This value specifies how much fragment ions can be shifted from their expected{color} {color:#000000}m{color}{color:#000000}/{color}{color:#000000}z{color} {color:#000000}values. Default value is ± 0.02 Da for high-resolution instruments (q-TOF, q-Orbitrap) and ± 2.0 0.5 Da for low-resolution instruments (ion traps, QqQ).{color}

*  \-\- Fragment ion Mass Tolerance:* {color:#000000}This value specifies how much fragment ions can be shifted from their expected{color} {color:#000000}m{color}{color:#000000}/{color}{color:#000000}z{color} {color:#000000}values. Default value is ± 0.02 Da for high-resolution instruments (q-TOF, q-Orbitrap) and ± 2.0 0.5 Da for low-resolution instruments (ion traps, QqQ).{color}

{color:#000000}*  \-\- Search analog (VarQuest)*{color} {color:#000000}\[RECOMMENDED TO USE\]: The VarQuest algorithm can search for analogs of known natural products in MS/MS data using Dereplicator. VarQuest is a modification-tolerant database search tool that discovers unexpected modifications in a blind mode. Since the computational space for variable PNP identification is computationally expensive, VarQuest first constructs a set of feasible PSM using a simple scoring approach and further filters out this set using a rigorous scoring method. Using VarQuest will increase the job time. The use of VarQuest analogs option is recommended as it expands the search space, and it reduces the overall run time.{color}


{color:#000000}{*}ADVANCED OPTIONS:*{color}



\-  The *adducts* detected must be confirmed using the MS1 spectrum (mono-charged, di-charged ?, protonated adduct ?, ...)

\- The *molecular formula* must be verified. Chemcalc can be used for that, [see here|http://www.chemcalc.org/mf_finder]. As well as Sirius, [here|https://bio.informatik.uni-jena.de/software/sirius/].
\- If genome sequence(s) are available, *genome mining* can be performed to search potential biogenetic gene clusters.

h3. How to cite the In silico Peptidic Natural Product Dereplicator
h3. Mapping Dereplicator results on GNPS molecular networks

1. Run molecular networks with the spectral data (Files can be .MGF or mzML/mzXML) [See the following documentation|https://bix-lab.ucsd.edu/display/Public/Molecular+Networking+Documentation].



2. Download the molecular networks clustered data (.MGF file). Click on "Download Clustered Spectra as MGF".

!Screen Shot 2018-04-25 at 11.03.03 AM.png|border=1,width=717,height=402!


3. Upload the .MGF file, and run a Dereplicator job. Note that alternatively, the .MGF obtained with MZmine can be used (GNPS export module).


4. When the job is completed click on  "View Unique Peptides".

!Screen Shot 2018-04-25 at 10.19.43 AM.png|border=1,width=754,height=177!

5. In the "View unique Peptide" page, download the .TSV annotation file. Click on download with Download button and unzip the file.

!Screen Shot 2018-04-25 at 10.27.10 AM.png|border=1,width=754,height=186!

6. Open the molecular networks with Cytoscape. [See documentation here.|https://bix-lab.ucsd.edu/display/Public/Cytoscape+3.4+Visualization+and+Analysis+Documentation]





7. In Cytoscape, import the .TSV table as attribute table. In Cytoscape go to "File / Import / Table / File" and select the .TSV annotation file for the dereplicator (see above).

8. In the preview window, click on the "Scan" header to set the meaning to "Key".

!Screen Shot 2018-04-25 at 10.07.21 AM.png|border=1,width=762,height=567!

9. Select/Unselect column as needed, and eventually change the name for table header if they are already in the molecular networks (otherwise, they will be replaced with the new table imported).

10. Change the column header "SMILES" into "SMILES_derepl"


11. Click on import. Now the attribute table is mapped into the networks.

12. The structure can be viewed with the [ChemViz2 plugin|http://www.cgl.ucsf.edu/cytoscape/chemViz2/index.shtml] . [See the Network Annotation Propagation documentation for documentation.|https://github.com/DorresteinLaboratory/NAP_ProteoSAFe/blob/master/supplementar_tool_manual_documentation.pdf]










h3. How to cite the In silico Peptidic Natural Product Dereplicator and VarQuest

Please cite the following if you are using Dereplicator:

Hosein Mohimani, Alexey Gurevich, Alla Mikheenko, Neha Garg, Louis-Felix Nothias, Akihiro Ninomiya, Kentaro Takada, Pieter C. Dorrestein, Pavel A. Pevzner, Dereplication of Peptidic Natural Products Through Database Search of Mass Spectra, Nature Chemical Biology, 2016, in press.
*Dereplicator*: Hosein Mohimani, Alexey Gurevich, Alla Mikheenko, Neha Garg, Louis-Felix Nothias, Akihiro Ninomiya, Kentaro Takada, Pieter C. Dorrestein, Pavel A. Pevzner, {color:#000000}{_}Dereplication of Peptidic Natural Products Through Database Search of Mass Spectra, Nature Chemical Biology,_{color} {color:#000000}{*}2016{*}{color}{color:#000000},{color} 13, 30--37 (2017) doi:[10.1038/nchembio.2219|http://www.nature.com/nchembio/journal/v13/n1/abs/nchembio.2219.html]









*Dereplicator with VarQuest*: Gurevich, A.; Mikheenko, A.; Shlemov, A.; Korobeynikov, A.; Mohimani, H.; Pevzner, P. A. Increased Diversity of Peptidic Natural Products Revealed by Modification-Tolerant Database Search of Mass Spectra. _Nat Microbiol_ *2018*, _3_ (3), 319--327. [https://www.nature.com/articles/s41564-017-0094-2|https://www.nature.com/articles/s41564-017-0094-2]









h3. Troubleshooting

*If you have any problem with running the Dereplicator you can contact Hosein Mohimani* [(homohimani@eng.ucsd.edu)|mailto:homohimani@eng.ucsd.edu] , *for feedback on this page, contact* *Louis-Félix Nothias* ([nothias@ucsd.edu|mailto:])