Perseus protocols

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chevron_left Protein-protein interaction prediction Proteome analysis Differential protein expression chevron_right
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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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Maintainer


This tool is not maintained anymore.

Additional information


Add info: A registration is needed to access to the issues. http://www.coxdocs.org/doku.php?id=perseus:user:tutorials http://www.coxdocs.org/doku.php?id=perseus:common:google_groups

Publications for Perseus

Perseus in pipelines

 (73)
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) (), 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: 5805371
PMID: 29377895
DOI: 10.1371/journal.pgen.1007189

[…] between runs” option was enabled. for the identification of peptides and proteins the uniprot human fasta database (from september 2014) was used. bioinformatics analyses were performed with the perseus software (version 1.5.4.1) []. after removing potential contaminants as well as reverse sequences, label free intensities were transformed to logarithm with base 2 and entries that contained […]

2018
PMCID: 5830946
PMID: 29358085
DOI: 10.1016/j.stemcr.2017.12.016

[…] intensities across samples, the options “match between runs”, and label-free quantification (lfq) were selected to obtain maxlfq. the output file “proteingroup.txt” was further analyzed using perseus version 1.5.6.0 for downstream statistical analyses of the normalized protein intensities. protein lists were filtered to remove potential contaminants, hits to the reverse decoy database, […]

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, ). 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 with a location […]


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Perseus in publications

 (818)
PMCID: 5954169
PMID: 29780279
DOI: 10.1007/s41114-018-0013-8

[…] sur de solides fondements; dh. 8, 1; luc. de fond en comble ( )the greek–english lexicon by liddell & scott, gives similar definitions. the short version can be consulted at the website of the perseus project., surface servant de fondement, d’où: 1 base hdt. 1, 183; part. piédestal d’une statue, hdt. 5, 85; esch. pers. 811; xén. eq. 1, 1 // 2 degré, marche, hdt. 7, 23; soph. o. c. 1591; […]

PMCID: 5935685
PMID: 29728570
DOI: 10.1038/s41598-018-25391-y

[…] acetylation (n-terminal) as variable modifications. the output contained a list of proteins identified below 1% false discovery rate, and their abundances were further filtered and processed using perseus v1.5.6.0 platform. all reverse hits that identified proteins were removed from further analysis, and the data were log2-transformed in order to approximate normal distribution. two […]

PMCID: 5934373
PMID: 29725059
DOI: 10.1038/s41598-018-25450-4

[…] (france)., the 16s rrna gene pyrotags were analysed using qiime version 1.9.1 and r (r project 3.3.2). briefly, the flowgrams were denoised with ampliconnoise, and chimeras were removed using perseus. all reads shorter than 250 bp were discarded and the remaining reads were clustered into operational taxonomic units (otus) at 97% similarity using uclust. representative sequences […]

PMCID: 5943503
PMID: 29774024
DOI: 10.3389/fimmu.2018.00872

[…] usa) was used for statistical analysis of quantitative western blot. variance was calculated with the two-way anova method. the null hypothesis was rejected when the p-value was lower than 0.05., perseus software () was mainly used to analyze the ms data. either peptides (peak volumes) or epitopes (% intensity from the total ion current) determined by plateau were loaded as matrices. all data […]

PMCID: 5932012
PMID: 29720585
DOI: 10.1038/s41467-018-04180-1

[…] transcriptomic signatures, average log2 protein ratios and average mrna ratios (as compared to kmt2a-mllt3 + empty-gfp) were combined for matching gene symbols and 2d enrichment was performed using perseus (v1.5.5.3) with an benjamini-hochberg fdr of 0.02., for the cytokine assay, established mouse kmt2a-mllt3 + empty-gfp leukemic cells were washed once in cold pbs (ge healthcare life […]


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Perseus institution(s)
Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany
Perseus funding source(s)
Supported by the European Union′s Horizon 2020 research and innovation program under grant agreement no. 686547 and from the FP7 grant agreement GA ERC-2012-SyG_318987-ToPAG.

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