Added by Louis Felix Nothias, last edited by Louis Felix Nothias on Oct 24, 2016  (view change)

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Introduction

For the documentation on the Insilico Peptidic Natural Products Dereplicator, see here.

For more details, see and 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.

Methods

The Dereplicator found 1643 potential annotations on GNPS Massives datasets (April 2016). 59.7% of these annotations were manually curated by looking at the dereplicator results, and cross-validated the sample with the known biological sources of the peptide. 35% of these annotations were found in four Massivedatasets: the Cyanobacteria dataset from the Gerwick lab (MSV000078568) and the Kerry lab (MSV000079050); the fungi samples from the Cichewicz lab collection (MSV000079098) and Pseudomonas samples (MSV000079619).

Annotations were then classified in four categories:

Level 1 (identification): the peptide has been isolated and has been characterized by NMR from the same sample.

Level 2 or 3 (annotation): the peptide has been previously isolated in the same species or genus.

Unlikely: the peptide has been isolated in an other micro-organism familly.

Unsetteled: the biological source or the sample origin is not clear.

Results

Results are showed in the following tables and figures.

Conclusion

Automatic annotations of the Dereplicator must be confirmed manually:

- The MS/MS spectrum from the raw file must be inspected (consistency, noise level, ...)

-  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. As well as Sirius, here.

- Main non-annotated fragment ions should be manually annotated.

- Look at the biological source(s) of the peptide (Google scholar, Dictionnary of Natural Products, AntiMarin, MarinLit, ...), to see if it is consistent with the sample type.

- If genome sequence(s) are available, genome mining can be performed to search potential biogenetic gene clusters.

How to cite the Peptidic Dereplicator

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.

Troubleshooting

If you have any problem with running the Dereplicator you can contact Hosein Mohimani (homohimani@eng.ucsd.edu) , for feedback on this page and the evaluation, contact Louis-FĂ©lix Nothias (nothias@ucsd.edu).