Fido specifications

Information


Unique identifier OMICS_09170
Name Fido
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Fido

Fido in publications

 (4)
PMCID: 5691128
PMID: 29146960
DOI: 10.1038/s41467-017-01544-x

[…] clearer species-level identifications., going forward, we used two protein inference strategies for this study. the first strategy relies on the sequest algorithm for peptide identification and the fido method for protein inference (2 pup ∩ fido). fido is available as a standalone program (https://noble.gs.washington.edu/proj/fido/) and as an advanced implementation with convolution trees […]

PMCID: 5059416
PMID: 27572102
DOI: 10.1007/s13361-016-1460-7

[…] investigated efficient ways to obtain protein-level accuracy estimates. one of the major obstacles was the question of how to deal with shared peptides and protein grouping. an implementation of fido [], which has been part of the percolator package since 2012, addresses these two issues but is too computationally expensive to apply to large-scale data sets. we therefore compared four […]

PMCID: 3882664
PMID: 24432028
DOI: 10.3389/fgene.2013.00309

[…] and in gibbs et al. (). abundance measurements for 16,890 peptides mapping to 3277 proteins were recorded for 184 lc-ms runs. taking all observed peptides, protein inference was performed using the fido protein inference model (serang et al., ; serang and noble, ). inferred proteins were accepted with scores above 0.95. from the total set of proteins, 691 proteins had this score or better., […]

PMCID: 3489551
PMID: 23176300
DOI: 10.1186/1471-2105-13-S16-S4

[…] and protein grouping (for indistinguishable proteins). in the following subsections, we provide an in-depth discussion of the three major probabilistic methods: proteinprophet [], msbayespro [], and fido [], and briefly mention several other methods. we use the same notation for all models and, when possible, provide new interpretations of the algorithms. we aim to reveal inherent connections […]


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Fido institution(s)
Department of Genome Sciences, University of Washington, Seattle, Washington; Department of Genome Sciences, University of Washington, Seattle, Washington; Department of Genome Sciences, Department of Computer Science and Engineering, University of Washington, Seattle, Washington

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