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, https://doi.org/10.5061/dryad.f7m0cfxxj
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 https://sourceforge.net/p/calis-p/wiki/Home/ and the research article.
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