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Protocols

MS-Cluster specifications

Information


Unique identifier OMICS_04041
Name MS-Cluster
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for MS-Cluster

MS-Cluster citations

 (6)
call_split

A protocol for high‐throughput, untargeted forest community metabolomics using mass spectrometry molecular networks

2018
Appl Plant Sci
PMCID: 5895185
PMID: 29732263
DOI: 10.1002/aps3.1033
call_split See protocol

[…] peaks within ±17 Da of the precursor m/z. We then window‐filtered the MS/MS spectra by choosing only the top six peaks in each ±50 Da window throughout the spectrum. The data were then clustered with MS‐Cluster (Frank et al., ) with a parent mass tolerance of 2.0 Da and an MS/MS fragment ion tolerance of 0.5 Da to generate consensus spectra representing putative unique molecular structures. Consen […]

call_split

A novel quantification driven proteomic strategy identifies an endogenous peptide of pleiotrophin as a new biomarker of Alzheimer’s disease

2017
Sci Rep
PMCID: 5645330
PMID: 29042634
DOI: 10.1038/s41598-017-13831-0
call_split See protocol

[…] Spectral clustering was performed using MS-Cluster v2, an open source software for TMT dataset clustering. MS-Cluster uses a hierarchical clustering algorithm similar to the Pep-Miner algorithm, but is optimized for analysis of large number […]

library_books

Mass Spectrometry Based Molecular 3D Cartography of Plant Metabolites

2017
Front Plant Sci
PMCID: 5370242
PMID: 28405197
DOI: 10.3389/fpls.2017.00429

[…] was filtered by removing all MS/MS peaks within a 17 Da window of the precursor m/z and MS/MS spectra were filtered by choosing only the top 6 peaks in 50 Da windows. The data was then clustered with MS-Cluster (), with a precursor mass tolerance of 0.02 Da and a MS/MS fragment ion tolerance of 0.02 Da. Consensus spectra with less than 2 spectra were discarded. A spectral network was then created […]

call_split

Multi species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks*

2016
PMCID: 5098046
PMID: 27609420
DOI: 10.1074/mcp.O116.060913
call_split See protocol

[…] Typically, MS/MS data sets contain substantial amounts of redundancy, with multiple spectra coming from the same peptide. We used MS-Cluster (ver. 2.0) () to group spectra of the same peptides and compute cluster consensus spectra prior to spectral networks analysis. In brief, MS-Cluster retains peaks in a cluster consensus spec […]

call_split

Using Molecular Networking for Microbial Secondary Metabolite Bioprospecting

2016
PMCID: 4812331
PMID: 26761036
DOI: 10.3390/metabo6010002
call_split See protocol

[…] ed using Xcalibur version 2.2.HR-MS/MS raw data files were converted from .RAW to .mzXML file format using the Trans-Proteomic pipeline (Institute for Systems Biology, Seattle) [], and clustered with MS-Cluster using Global Natural Products Social (GNPS) Molecular Networking [,,,]. A molecular network was created using the online workflow at GNPS. The data was filtered by removing all MS/MS peaks […]

library_books

Spectral Archives: Extending Spectral Libraries to Analyze both Identified and Unidentified Spectra

2011
Nat Methods
PMCID: 3128193
PMID: 21572408
DOI: 10.1038/nmeth.1609

[…] ering often yields 5–10% more peptide identifications, at a given false discovery rate, compared to the number of peptides identified without using it. See for more details about the running time of MS-Cluster.We note that our current implementation focuses on ion-trap data. Using our algorithm with other types of instruments that display significantly different fragmentation patterns can require […]

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MS-Cluster institution(s)
Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA

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