ASAPRatio pipeline

ASAPRatio specifications

Information


Unique identifier OMICS_02486
Name ASAPRatio
Alternative name Automated Statistical Analysis on Protein Ratio
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Medium
Stability Stable
Maintained Yes

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  • ASAPRatio

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Publication for Automated Statistical Analysis on Protein Ratio

ASAPRatio IN pipelines

 (5)
2013
PMCID: 3591400
PMID: 23505477
DOI: 10.1371/journal.pone.0058285

[…] [87]). peptide identifications were validated with peptideprophet filtering out peptide hits with probabilities below 0.70. retained peptide identifications were subsequently quantified via the asapratio tool using a fixed scan range for light and heavy labeled peptides and a 6.02013 da label mass for both arginine and lysine. mass tolerance was set to 0.01 da. for each individual lc-run, […]

2011
PMCID: 3046137
PMID: 21386990
DOI: 10.1371/journal.pone.0016975

[…] which corresponds to a false identification rate of 3.5% in iron chelation experiment and 5.3% in p160 co-immunoprecipitation experiment, respectively. protein abundance ratios were calculated using asapratio software tool [22]., immunoprecipitation was performed as described [23]. the indicated amounts of cell lysates were separated by sds-page and were analyzed by immunoblotting as described […]

2010
PMCID: 2848867
PMID: 20368813
DOI: 10.1371/journal.pone.0010015

[…] the sensitivity of peptide identification was above 50% (i.e. more than 50% “true” peptides were identified) and the error rate was 4% (i.e. 4% of the peptides in the results could be errors). asapratio [17] was used to integrate the peak of the peptide in the extracted ion current (xic) for quantifying the signals. taking the peptide tfcqlildpifk from elongation factor 2 (swiss-prot, […]

2010
PMCID: 2848867
PMID: 20368813
DOI: 10.1371/journal.pone.0010015

[…] of light isotope-labeled peptides. the heavy isotope-labeled peptides in green have a +3 m/z shift because the [13c6]-lys is +6 da heavier in mass compared to [12c6]-lys. the ratio calculated by asapratio was 1.0. thus the quantity of s-nitrosation of the cys in tfcqlildpifk from elongation factor 2 was 2.0 since the treated cells were mixed with control group cells in a ratio of 1∶2 based […]

2010
PMCID: 2996310
PMID: 21151997
DOI: 10.1371/journal.pone.0015132

[…] of between 300–500 unique proteins (data not shown)., to determine proteins whose expression was altered by march-viii, ratios between heavy and light peptide peaks were determined using the asapratio algorithm [32]. ratios of individual peptides belonging to the same protein were grouped together using proteinprophet to obtain a ratio for the expression of each identified protein [32]. […]

ASAPRatio institution(s)
The Institute for Systems Biology, Seattle, WA, USA

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