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xiSPEC specifications

Information


Unique identifier OMICS_29653
Name xiSPEC
Interface Web user interface
Restrictions to use None
Input data An identification file and a peak list file or a PRIDE accession number.
Input format (mzIdentML,CSV)+(mzML,mgl)
Output data Some single plots.
Programming languages Javascript
Database management system SQLite
License Apache License version 2.0
Computer skills Basic
Version 2
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Juri Rappsilber <>
  • person_outline Lars Kolbowski <>

Additional information


http://spectrumviewer.org/help.php

Publication for xiSPEC

xiSPEC in publications

 (7)
PMCID: 5766153
PMID: 28934471
DOI: 10.1093/nar/gkx604

[…] proteome discoverer analysis results were exported and converted to a summary report using custom tools. spectra of all psms with evidence for the acetylation site k409 were annotated in the xispec spectrum viewer (http://spectrumviewer.org) and are provided in ., molar ellipticity values [θ] of 0.12 mg/ml of parg 1–447aa in 10 mm k-phosphate, ph 7.3 were recorded over a range of 260–185 […]

PMCID: 5178350
PMID: 28053595
DOI: 10.1155/2016/7316725

[…] cleavages plus a number of variable modifications such as oxidation (m), hypusinylation (k), and deoxyhypusinylation (k). peptide hits returned by mascot were manually validated and annotated using xispec (http://spectrumviewer.org/)., the gene sequences were obtained from ncbi. the blast tools [] and resources at ncbi (https://www.ncbi.nlm.nih.gov/) were used routinely. multiple sequence […]

PMCID: 4928471
PMID: 27375966
DOI: 10.7717/peerj.2134

[…] (st), phospho (y), pap (sty), pgp (sty), pcp (sty) and pup (sty). for both viruses at least two independent biological samples were analyzed. for publication the spectra were auto-annotated with xispec (http://spectrumviewer.org) and images were prepared using inkscape (http://www.inkscape.org). the levels of viral rna present in the samples used for mass spec were not routinely quantified, […]

PMCID: 4918325
PMID: 26243668
DOI: 10.1038/ncomms8929

[…] set was considered being too small for meaningful fdr estimation using the target-decoy method. mto2 hits were manually validated, the weakest having a posterior error probability of pep=0.013., xispec spectrum viewer (http://spectrumviewer.org/) was used to visualize ms2 spectra for figure presentation., how to cite this article: borek, w. e. et al. mto2 multisite phosphorylation […]

PMCID: 4468061
PMID: 26075619
DOI: 10.1371/journal.pone.0129548

[…] ms/ms was set to 1.0e+05 ions. the maximum allowed time for ion accumulation were 500 ms and 200 ms, respectively., the generated peak lists were searched against protein databases using mascot 2.0. xispec spectrum viewer (http://spectrumviewer.org/) was used to visualize ms/ms spectra for figure presentation. due to xispec software design, occasionally b or y ions that are indicated […]


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xiSPEC institution(s)
Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK; Bioanalytics, Institute of Biotechnology, Technische Universitat Berlin, Berlin, Germany
xiSPEC funding source(s)
Supported by the Einstein Foundation; Wellcome Trust Senior Research Fellowship [103139]; Wellcome Trust Multi-user Equipment Grant [108504]; Wellcome Centre for Cell Biology [203149].

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