Calis-p 2.1 a software for protein-based stable isotope fingerprinting (Protein-SIF) and probing (Protein-SIP)
Data files
Mar 16, 2023 version files 213.64 MB
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Dataset_S1_18O_SIF_Corrected_peptides.csv
107.04 MB
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Dataset_S2_2H_SIF_Corrected_peptides.csv
106.59 MB
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README_UpdatedMar8.md
6.22 KB
Abstract
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.