Morpheus protocols

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Morpheus specifications


Unique identifier OMICS_26445
Name Morpheus
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C#
License MIT License
Computer skills Advanced
Version 272
Stability Stable
Maintained Yes



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  • person_outline Lloyd Smith <>

Publications for Morpheus

Morpheus in pipelines

PMCID: 4908353
PMID: 27307634
DOI: 10.1093/bioinformatics/btw269

[…] advantage of both of these benefits in our trellis/dgm-based peptide-spectrum score functions., many ms/ms scoring functions, including xcorr, x!tandem, the base scores for ms-gf+ and omssa, and morpheus (), are linear in the theoretical and observed spectra (i.e. they constitute a dot product between two preprocessed vectors corresponding to the theoretical and the observed spectrum). using […]

PMCID: 4223503
PMID: 25100859
DOI: 10.1074/mcp.O114.038877

[…] intensity (ln i). the relative ratio of the probability densities of the target distribution (n3+) and decoy distribution (n3βˆ’) was calculated as which ranged from βˆ’1.0 to 1.0. as in the original morpheus algorithm, the sub score s3 was used here to smoothen the score distribution at the edge of an arbitrary cutoff (1% fdr)., duplications in the psm list were removed, with the highest-scoring […]

PMCID: 4223503
PMID: 25100859
DOI: 10.1074/mcp.O114.038877

[…] peptides in maxquant or spectra cloning in demix are allowed (+) or not (-)., b psm lists were trimmed to e-value < 0.05 for mascot, or to fdr < 0.01 for andromeda, ms-gf+ percolator and morpheus-as., c proportion of unique peptide sequences found in the confetti database ()., d protein groups supported by two or more unique peptides are considered to be strongly supported; and mean […]

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Morpheus in publications

PMCID: 5877393
PMID: 29598823
DOI: 10.1186/s13059-018-1418-0

[…] were concatenated with gencode version 19 and protein sequences representing common mass spectrometry (ms) contaminants, creating a customized fasta file (i.e. proteomics search database). the morpheus software (version 131) was employed for ms searching of the custom database against the mcf-7 thermo raw files obtained from the study by geiger et al. []. unknown precursor charge state […]

PMCID: 5417831
PMID: 28302922
DOI: 10.1074/mcp.O117.067728

[…] uniprot () reference proteome database (6720 yeast protein sequences of release 2015_12, 91618 human protein sequences of release 2015_07, and the sequence of bsa uniprot_id p02769) using morpheus search engine (ver. 165) (). carbamidomethylation of cysteine was set as a fixed modification, and oxidation of methionine was considered as a variable modification. the target-decoy […]

PMCID: 4966894
PMID: 27472422
DOI: 10.1371/journal.pone.0160160

[…] sensitivity, reproducibility and convenience for proteomics., with the rapid development of ms instruments, database search engines such as sequest[], mascot[], omssa[], myrimatch[], andromeda[], morpheus[], ms-gf+[], and ms amanda[] are subsequently developed to interpret the different types of spectra generated by ms. to achieve confident and accurate ms-based identification, […]

PMCID: 4908353
PMID: 27307634
DOI: 10.1093/bioinformatics/btw269

[…] we describe how to apply trellises to any scoring function expressible as a dgm. this includes linear scoring functions such as the sequest xcorr (), the score functions employed by x!tandem (), morpheus (), ms-gf+ () and omssa (), as well non-linear methods such as our recently proposed dbn for rapid identification of peptides (drip; )., for common ms/ms application settings, we prove […]

PMCID: 4223503
PMID: 25100859
DOI: 10.1074/mcp.O114.038877

[…] remain chimeric. processing such spectra requires a search engine tolerant to the presence of unassigned peaks, as such peaks are always expected when multiple precursors cofragment. thus, we chose morpheus () as a search engine. based on the original search algorithm, we implement a reformed scoring scheme: morpheus-as (advanced scoring). it inherits all the basic principles from morpheus […]

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Morpheus institution(s)
Department of Chemistry, University of Wisconsin, Madison, WI, USA; Department of Biochemistry, University of Wisconsin, Madison, WI, USA
Morpheus funding source(s)
Supported by National Institutes of Health Grant Nos. P50HG004952, U54DK093467, P01GM081629, and R01GM103315 and by the NIH Genomic Sciences Training Program T32HG002760 and the National Institute of Diabetes and Digestive Kidney Diseases Grant Nos.R01DK058037, R24DK091207, and R01DK066369.

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