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A Scala Implementation of ProInfer

Limsoon Wong
12 April 2023
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Reference:

Hui Peng, Limsoon Wong, Wilson Wen Bin Goh. 
ProInfer: An interpretable protein inference tool 
leveraging on biological networks. 
PLoS Computational Biology, 19(3):e1010961, 2023

In mass spectrometry (MS)-based proteomics, protein inference from
identified peptides (protein fragments) is a critical step. 
We present ProInfer (Protein Inference), a novel protein assembly
method that takes advantage of information in biological networks.
ProInfer assists recovery of proteins supported only by ambiguous
peptides (a peptide which maps to more than one candidate protein) 
and enhances the statistical confidence for proteins supported by 
both unique and ambiguous peptides. Consequently, ProInfer rescues 
weakly supported proteins thereby improving proteome coverage. 
Evaluated across THP1 cell line, lung cancer and RAW267.4 datasets, 
ProInfer always infers the most numbers of true positives, in 
comparison to mainstream protein inference tools Fido, EPIFANY and 
PIA. ProInfer is also adept at retrieving differentially expressed 
proteins, signifying its usefulness for functional analysis and 
phenotype profiling. Python Source codes of ProInfer are available 
at https://github.com/PennHui2016/ProInfer.



To see instructions for this Scala implementation of ProInfer
for Windows platforms:


   scala.bat -cp proteomics.jar proteomics.proinfer --help

 

To run ProInfer:


  scala.bat -cp proteomics.jar proteomics.proinfer <PROTEINS.fasta> <CORUM.txt> <DDA.txt> <OUTPUT.txt> <Organism> <Prefix> <PEP-threshold> <QVAL-threshold>

 

E.g., explicitly specifying all input parameter values,


  scala.bat -cp proteomics.jar proteomics.proinfer human-proteins-n-decoys.fasta complexes.txt results.txt Human myruns 0.999 0.01

 

E.g., using all defaults,


  scala.bat -cp proteomics.jar proteomics.proinfer human-proteins-n-decoys.fasta complexes.txt results.txt

 

The codes have been tested for Scala3.  They should run also for Scala2,
but I have not tested this.

 
Limsoon Wong
12 April 2023



