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Calis-p 2.1 a software for protein-based stable isotope fingerprinting (Protein-SIF) and probing (Protein-SIP)


Kleiner, Manuel; Strous, Marc; Dong, Xiaoli (2023), Calis-p 2.1 a software for protein-based stable isotope fingerprinting (Protein-SIF) and probing (Protein-SIP), Dryad, Dataset,


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 2.1 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%.

Detailed documentation can be found in the Wiki on and the research article.

Usage notes

The files are either tables in tab-delimited or comma-delimited format and can be opened with a text editor or they are in Microsoft Excel format and can be opened with Excel or Open Office.


U.S. Department of Agriculture, Award: 1014212

National Institute of General Medical Sciences, Award: R35GM138362

National Science Foundation, Award: OIA #1934844

Novo Nordisk Fonden, Award: NNF19SA0059360

Foundation for Food and Agriculture Research, Award: 593607

Canadian Foundation for Innovation, Award: 32181

Natural Sciences and Engineering Research Council of Canada

Canada First Research Excellence Fund

Government of Alberta

U.S. Department of Energy, Award: DE-SC0022996