Morpheus statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool Morpheus

Tool usage distribution map

This map represents all the scientific publications referring to Morpheus per scientific context
info info

Associated diseases


Popular tool citations

chevron_left PTM identification chevron_right
Want to access the full stats & trends on this tool?

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




No version available


  • person_outline Lloyd Smith

Publications for Morpheus

Morpheus citations


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

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

[…] [, ]. The inclusion of the Gencode database allows for identification of any peptides derived from transcripts that may not have been detected in the PacBio data. The MS searching was done using the Morpheus algorithm [], wherein all theoretical peptides resulting from an in silico tryptic digestion of protein entries (from Gencode, PacBio, or contaminants database) were matched against the raw m […]


Proteomics in non human primates: utilizing RNA Seq data to improve protein identification by mass spectrometry in vervet monkeys

BMC Genomics
PMCID: 5683380
PMID: 29132314
DOI: 10.1186/s12864-017-4279-0

[…] es (PSMs) or unique peptides identified in the samples when searched by the SSdb. Restricting the size of SSdb to transcripts with an abundance of 1 TPM or more condensed the search database size and Morpheus compute time when compared to the REFdb. On average, the SSdbs were 77% of the size of the REFdb, and compute times in Morpheus averaged 53% faster for SSdbs compared to the REFdb (defined by […]


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

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

[…] etter 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, the target-deco […]


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

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

[…] des. 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 and quan […]


Human Proteomic Variation Revealed by Combining RNA Seq Proteogenomics and Global Post Translational Modification (G PTM) Search Strategy

J Proteome Res
PMCID: 4779408
PMID: 26704769
DOI: 10.1021/acs.jproteome.5b00817

[…] ching, and identifies high-quality PTM peptide spectral matches that are missed during sequence-only searches. We developed this Global PTM (G-PTM) search strategy using the proteomic search software Morpheus along with PTM information available in UniProt to identify candidate PTM peptides in a single-pass search that can then be further validated. While G-PTM does not detect unannotated PTMs, it […]


Universal database search tool for proteomics

Nat Commun
PMCID: 5036525
PMID: 25358478
DOI: 10.1038/ncomms6277

[…] rch tools such as SEQUEST [] and Mascot [] have not kept pace with the increased diversity of the data. While several new MS/MS database search engines were recently developed including Andromeda [], Morpheus [], and MS Amanda []), they have resulted in only minor improvements as compared to SEQUEST and Mascot.Many efforts have been invested into making existing MS/MS search tools compatible with […]

Want to access the full list of citations?
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.

Morpheus reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Morpheus