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Protocols

MS-Viewer specifications

Information


Unique identifier OMICS_27507
Name MS-Viewer
Interface Web user interface
Restrictions to use None
Input data A peak list file that contains the spectrum information, and a results file that contains the peptide assignments to each spectrum.
Input format XML
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Peter Baker

Publication for MS-Viewer

MS-Viewer citations

 (19)
library_books

Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

2018
BMC Genomics
PMCID: 5859498
PMID: 29554870
DOI: 10.1186/s12864-018-4604-2

[…] 9 cultured in SupT1 cells (Additional file : Figure S3, Additional file : Figure S4). Shotgun proteomic analysis produced 350 unique spectra covering 39 different HHV-6 proteins that may be viewed in MS Viewer (Additional file : Table S2 and Additional file : Table S3).Intriguingly, three novel U79 mRNA isoforms were found, one of which also demonstrated divergent splicing based on culture in SupT […]

library_books

Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment*

2017
PMCID: 5795391
PMID: 29141914
DOI: 10.1074/mcp.RA117.000400

[…] ein mass spectrometry data were deposited at PRIDE Accession No. PXD006138 (supplemental Table S1) and PXD008047 (proteomic analyses of conditioned media of TU and TAM). Data can also be accessed via MS-viewer (http://msviewer.ucsf.edu/prospector/cgi-bin/msform.cgi?form_msviewer), a web-based spectral viewer for proteomics results (), by entering the search keys “tvk5oek0to” or “y40gjy2o1y” (prote […]

call_split

Crosstalk between proteins expression and lysine acetylation in response to patulin stress in Rhodotorula mucilaginosa

2017
Sci Rep
PMCID: 5647337
PMID: 29044224
DOI: 10.1038/s41598-017-14078-5
call_split See protocol

[…] ed. All the other parameters in MaxQuant were set to default values. The site localization probability was set as >0.75. All the peptide sequences was deposited in the public protein peptide database MS-Viewer: http://msviewer.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msviewer. […]

library_books

Prediction of Protein Complexes in Trypanosoma brucei by Protein Correlation Profiling Mass Spectrometry and Machine Learning*

2017
PMCID: 5724185
PMID: 29042480
DOI: 10.1074/mcp.O117.068122

[…] ntifier PXD005968, https://www.ebi.ac.uk/pride/archive/. Processed data and data exploration tools can be found at http://134.36.66.166:8083/complex_explorer. Annotated spectra can be viewed from the MS-Viewer website (http://msviewer.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msviewer) by entering the following search keys: SAX: czyi4m7zoe; SEC300: esvc3krys1; SEC1000: 5gt8lsrrv7. […]

library_books

Global Analysis of Membrane associated Protein Oligomerization Using Protein Correlation Profiling*

2017
PMCID: 5672003
PMID: 28887381
DOI: 10.1074/mcp.RA117.000276

[…] ode was deposited (https://github.com/dlchenstat/Gaussian-fitting), the raw data and MaxQuant search outputs were deposited at JPOST (PXD006694), and spectra for single peptide hits were deposited at MS-Viewer () (http://msviewer.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msviewer) (Search keys: uerfksr5dl, sceybigrnm, osakjoppm2). […]

library_books

Detection and identification of Criegee intermediates from the ozonolysis of biogenic and anthropogenic VOCs: comparison between experimental measurements and theoretical calculations† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7fd00025a

2017
Faraday Discuss
PMCID: 5708353
PMID: 28580994
DOI: 10.1039/c7fd00025a

[…] (1 Td = 10–17 V cm2). The PTR-ToF-MS inlet (a 1 m long inert PEEK tube, ID = 1 mm, OD = 1.59 mm) was kept at 100 °C and the sampling flow rate was 100 cm3 min–1. Data analysis was conducted using PTR-MS Viewer 3.2 (Ionicon Analytik). The concentration of the olefinic precursors were estimated on the basis of the rate constants of the proton transfer reaction, which were: 2.33 × 10–9 cm3 per molecu […]

Citations

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MS-Viewer institution(s)
Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
MS-Viewer funding source(s)
Supported by Grant No. 8P41GM103481 from NIGMS, National Institutes of Health.

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