SIM-XL very slow?

[franc...@gmail.com]

Hi,

we are relatively new to cross-linking mass spec. we have been doing crosslinking of a 3 protein complex with BS3, and processing the data with SIM-XL. The output is great, and very easy to work with. However, it takes several days (4-6) to run each file (my computer has 8 cores and 32 GB of RAM). By comparison, to analyze the same data with pLink takes less than 1 hour. is this normal or is it possible that we are not setting up the run properly?

Thanks,

Nicole

[Diogo Borges]

Hi Nicole,

We've improved our search engine core to reduce the processing time. However, each search has a particularity. In general, we recommend some default parameters which you can set up on SIM-XL.

Please find attached a robust benchmark that we made during this last 6 weeks. You can see that we got to improve our results compared to the previous version. The benchmarks were made using a classical XL (DSS) and using a new XPlex strategy.

We're continue improving our core to reduce the processing time and to increase the sensibility of identifications.

Should you have any doubts, please contact us.

Best,

Diogo

_____________________________________

Diogo Borges Lima

Postdoctoral fellow in Computational Biology

Mass Spectrometry for Biology Unit

Institut Pasteur - CNRS USR 2000

28 rue du Dr. Roux - Paris - France

Computational Mass Spectrometry Group - Fiocruz / Brazil

About me: @diogobor | diogobor
URL: diogobor

diogo.bo...@pasteur.fr

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[Paulo C Carvalho]

It is nice to note that we will continue to improve the speed of our search engine.  We are already experimenting on a faster spectral predictor to eventually replace the existing one and resulting in significant gains, but this will still take some time.

Paulo 

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Paulo Costa Carvalho

http://pcarvalho.com

[Nicole Francis]

Hi,

thanks for this--we are eager to try the new version. the modifications you suggested previously have already helped reduce our processing time by ~ 30%.
Best,

Nicole

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