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Protocols

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 citations

 (6)
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A novel non canonical PIP box mediates PARG interaction with PCNA

2017
Nucleic Acids Res
PMCID: 5766153
PMID: 28934471
DOI: 10.1093/nar/gkx604
call_split See protocol

[…] etained. 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 . […]

library_books

Deciphering the Translation Initiation Factor 5A Modification Pathway in Halophilic Archaea

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

[…] d 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/). […]

call_split

Protein RNA linkage and posttranslational modifications of feline calicivirus and murine norovirus VPg proteins

2016
PeerJ
PMCID: 4928471
PMID: 27375966
DOI: 10.7717/peerj.2134
call_split See protocol

[…] spho (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, h […]

call_split

Mto2 multisite phosphorylation inactivates non spindle microtubule nucleation complexes during mitosis

2015
Nat Commun
PMCID: 4918325
PMID: 26243668
DOI: 10.1038/ncomms8929
call_split See protocol

[…] e data 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. […]

library_books

Deletion of Genes Encoding Arginase Improves Use of “Heavy” Isotope Labeled Arginine for Mass Spectrometry in Fission Yeast

2015
PLoS One
PMCID: 4468061
PMID: 26075619
DOI: 10.1371/journal.pone.0129548

[…] FT 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 in the pepti […]

library_books

Characterization of Ribosomal Frameshifting in Theiler's Murine Encephalomyelitis Virus

2015
J Virol
PMCID: 4524249
PMID: 26063423
DOI: 10.1128/JVI.01043-15

[…] es, and trypsin cleavage before proline plus a number of variable modifications, such as oxidation (M), oxidation (HW), phospho (ST), and phospho (Y). For the figures, spectra were autoannotated with xiSPEC (http://spectrumviewer.org). […]

Citations

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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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