Sipros specifications


Unique identifier OMICS_06904
Name Sipros
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python
Parallelization OpenMP
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


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Publications for Sipros

Sipros in publications

PMCID: 5874766
PMID: 29385081
DOI: 10.3390/proteomes6010007

[…] we considered two approaches. one is the recently described omega (overlap-graph metagenome assembler), a software tool for assembly of shotgun metagenome data that can be used along with the sipros algorithm for database generation and matching to ms/ms data []. the second was a novel method and software (called sixgill) described by may et al. that uses a ‘metapeptide database’ derived […]

PMCID: 5702734
PMID: 28800138
DOI: 10.1038/ismej.2017.128

[…] the pride archive pxd002641., the final database used for sip searches (60 006 cds) was constructed from all cds with at least one peptide identification in regular (that is, unlabeled search mode) sipros searches of each metaproteome against the 391 847 cds from the full metagenome assembly and a reduced database consisting of 181 704 cds from only high metagenome coverage contigs. to ensure […]

PMCID: 5355156
PMID: 28118606
DOI: 10.18632/oncotarget.14753

[…] purified human pros1 protein was purchased from enzyme research laboratories (south bend, in). r428 was purchased from synkinase. scc cell lines were transiently transfected with pros1 sirna (sipros1; on-targetplus, smartpool # l-004833; dharmacon) or with non-targeting sirna (sint on-targetplus, smartpool #d-001810; dharmacon) using dharmafect transfection reagent according […]

PMCID: 4850331
PMID: 27199908
DOI: 10.3389/fmicb.2016.00563

[…] were fragmented via collision-activated dissociation (cid) using 35% collision energy, a mass exclusion width of 0.2 m/z, and a dynamic exclusion duration of 60 s., ms/ms data was searched using the sipros/prorata 3.0 program (wang et al., ); precursor mass tolerance and fragment ion mass tolerance were 0.05 da and 0.02 da for the data generated on orbitrap instruments and 3 da and 0.5 da […]

PMCID: 5069745
PMID: 27822523
DOI: 10.1128/mSystems.00027-15

[…] enrichment patterns for a wide diversity of peptides, in addition to identifying and quantifying thousands of unlabeled microbial proteins. labeled peptide detection is made possible with the sipros program (, , ), which finds peptide spectral matches (psm) across a defined range and interval of percent 13c enrichments (e.g., 0 to 100% 13c at 1% increments in this study). proteomic sip […]

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Sipros institution(s)
BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA

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