Perseus pipeline

Perseus specifications

Information


Unique identifier OMICS_18346
Name Perseus
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some Proteomic pro¬files.
Output data Some average accuracy, feature ranks.
Operating system Windows
Programming languages C
Computer skills Advanced
Version 1.5.8.5
Stability Stable

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Publication for Perseus

Perseus IN pipelines

 (18)
2018
PMCID: 5772234
PMID: 29150517
DOI: 10.1128/AEM.02091-17

[…] was taken from the output of the functional annotation of the chromosome and contained 2,486 entries. after quantification, intensities from the lfq normalization were filtered and compared with perseus (v1.5.8.5) (83), removing rows with fewer than two values under either condition (mineral or continuous). the two conditions were compared with two-sample welch's t test., dna raw sequencing […]

2018
PMCID: 5778013
PMID: 29358734
DOI: 10.1038/s41467-017-02694-8

[…] {{\sum} {\frac{{(x - {\bar{x}})^2}}{{\left( {n - 1} \right)}}} }$$\end{document}∑(x-x¯)2n-1, where x̅ is the sample mean and n is the sample size. analysis of variance was calculated using perseus (v.1.4.0.8). artificial within groups’ variance was set to zero and the p-value was used for truncation with a threshold of 0.05., ms raw data of dimethyl-labelled samples were jointly […]

2018
PMCID: 5836539
PMID: 29507054
DOI: 10.15252/msb.20177858

[…] details., to perform a pairwise comparison and filter for those proteins/phosphopeptides that have a consistent abundance level over three biological replicates, we applied a two‐sample t‐test using perseus 1.5.3.2 (cox & mann, 2008). only those proteins that had a p‐value < 0.05 and an arbitrary cutoff ratio ≥ 1.5 or ≤ −1.5 fold changes were considered. only phosphopeptides […]

2017
PMCID: 5449605
PMID: 28460002
DOI: 10.1093/nar/gkx326

[…] and the maximum number of missed cleavages was set to two. raw intensities were normalized using intensity-based absolute quantification (ibaq) (14). all subsequent data analyses were performed by perseus (version 1.5.0.19). the data was filtered to remove reverse identified, only identified by site and potential contaminants. volcano plots were generated using a two-tailed student's t-test […]

2017
PMCID: 5620370
PMID: 28794267
DOI: 10.1091/mbc.E17-02-0093

[…] in profile, and fragments were analyzed in centroid mode by xcalibur software. the lc unit was controlled by chromeleon xpress software., for data analysis, maxquant 1.5.3.30 (cox and mann, 2008), perseus 1.5.4.1 (tyanova et al., 2016), and excel (microsoft office 2013) were used. the enzyme specificity was set to trypsin, and missed cleavages were limited to 2. n-terminal acetylation (+42.01) […]

Perseus institution(s)
Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany; Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA; Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
Perseus funding source(s)
Supported by the European Union′s Horizon 2020 research and innovation programme under grant agreement no. 686547 and by the FP7 grant agreement GA ERC-2012-SyG_318987–ToPAG.

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