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Protocols

Morpheus specifications

Information


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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Maintainer


  • person_outline Lloyd Smith <>

Publications for Morpheus

Morpheus citations

 (5)
library_books

Full length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

2018
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 […]

library_books

Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences*

2017
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 […]

library_books

Performance Investigation of Proteomic Identification by HCD/CID Fragmentations in Combination with High/Low Resolution Detectors on a Tribrid, High Field Orbitrap Instrument

2016
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, […]

library_books

Faster and more accurate graphical model identification of tandem mass spectra using trellises

2016
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+‚ÄČ() 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 […]

library_books

DeMix Workflow for Efficient Identification of Cofragmented Peptides in High Resolution Data dependent Tandem Mass Spectrometry*

2014
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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