Calis-p (The CALgary approach to ISotopes in proteomics) is a java application to estimate isotopic composition (e.g. delta13C or delta15N) of individual species in a microbial community from a proteomic dataset. Calis-p 2.0 handles both natural isotope abundances and data from labelling experiments such as stable isotope probing (SIP). It requires a mzIdent (or target spectrum match) and mzML files as the input and requires about 1 min per mzML file with 10 threads and needs <10 Gb of RAM. It has been tested with data from various nano liquid chromatography/Orbitrap platforms. For successful SIP, it is extremely sensitive, but requires the 13C fraction to remain below 10%.

A newer version is available at github and we strongly recommend to try it out: https://github.com/kinestetika/Calisp.

Features

  • delta13C is estimated from a standard metaproteomic dataset
  • Efficently and reliably obtain delta13C for many species in a microbiome samples.

Project Samples

calisp.summary.csv

Project Activity

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Categories

Bio-Informatics

License

Academic Free License (AFL)

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Calis-p Web Site

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Additional Project Details

Operating Systems

Linux, Mac, Windows

Registered

2017-04-24
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