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PIA specifications

Information


Unique identifier OMICS_09158
Name PIA
Alternative name Protein Inference Algorithms
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Julian Uszkoreit <>

Information


Unique identifier OMICS_09158
Name PIA
Alternative name Protein Inference Algorithms
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Julian Uszkoreit <>

Publication for Protein Inference Algorithms

PIA in publications

 (7)
PMCID: 5500760
PMID: 28515314
DOI: 10.1074/mcp.M117.068429

[…] solutions, waterloo, canada) (), scaffold (proteome software, portland, or) (), byonic (protein metrics), myrimatch (), peptideshaker (), crux (), openms (), mzid in bioconductor (), and pia (protein inference algorithms) (). it is also planned that proteomediscoverer (thermo fisher scientific, waltham, ma) will export the format natively in its next version, to be released later […]

PMCID: 4955376
PMID: 27493641
DOI: 10.3389/fmicb.2016.01103

[…] exoproteome samples were searched setting trypsin as the enzyme and allowing two missed cleavages. peptide analyses were carried out with no enzyme set., after database search, peptideshaker uses protein inference algorithms for protein characterization. peptide spectrum matches (psm), peptides and proteins were validated at 1% fdr estimated using the decoy hit distribution. […]

PMCID: 4992032
PMID: 27393313
DOI: 10.1007/s00401-016-1592-7

[…] of cysteine was set as fixed modification. one tryptic mis-cleavage was considered in the analysis. confidence of peptide identification was determined using a protein inference algorithm (pia) []. the filter cut-off for the identified peptides was set to targeted false discovery rates of <1 %., ion intensity-based label-free quantification was performed using progenesis lc-ms […]

PMCID: 4833187
PMID: 25347964
DOI: 10.1002/prca.201400107

[…] publication. if this effect is not taken into consideration, differences may appear that are only caused by changing protein accessions. additionally, analysis pipelines generally use different protein inference algorithms as well as different models for protein homologues and isoforms and potentially different false discovery rate thresholds —details that are often not reported. […]

PMCID: 4156250
PMID: 25026199
DOI: 10.1021/pr500496p

[…] searching is comparing ms/ms spectra to peptide sequences to identify the best matching peptide for each spectrum, referred to as peptide-to-spectrum matches (psms). these psms are then processed by protein inference algorithms to produce a minimal list of proteins that would need to be present in the sample to explain the identified psms. the proteins in this list are also assigned a confidence […]


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PIA institution(s)
Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany

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