ProteomeScout – Visualization and Analysis Framework for Proteins

ProteomeScout

:: DESCRIPTION

ProteomeScout is a database of proteins and post-translational modifications.

::DEVELOPER

The Naegle Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Web Server
  • MySQL

:: DOWNLOAD

ProteomeScout

:: MORE INFORMATION

Citation:

Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM.
ProteomeScout: A web resource for analysis of high-throughput post-translational proteomic studies.
Molecular and Cellular Proteomics, 2010.

Mol Cell Proteomics. 2010 Nov;9(11):2558-70. doi: 10.1074/mcp.M110.001206.
PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies.
Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM.

Specialize 1.0 – Identification of Peptides with complex PTM from Tandem Mass Spectra

Specialize 1.0

:: DESCRIPTION

Specialize is a novel approach to enable the expedited development of new algorithms for any types of PTM (post-translational modifications) peptide fragmentation.

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Specialize

:: MORE INFORMATION

Citation

A Turn-key Approach for Large-scale Identification of Complex Post-translational Modifications
Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. J
Proteome Res. 2014 Mar 7;13(3):1190-9. doi: 10.1021/pr400368u. Epub 2014 Jan 29.

Tremolo 20130821 – Spectral Library Search

Tremolo 20130821

:: DESCRIPTION

Tremolo is a spectral library search tool that leverages the Spectral Library Generating Function (SLGF) concept to identify spectrum-spectrum matches (SSMs).

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Tremolo

:: MORE INFORMATION

Citation

J Proteome Res. 2013 Sep 6;12(9):3944-51. doi: 10.1021/pr400230p. Epub 2013 Jul 31.
Spectral library generating function for assessing spectrum-spectrum match significance.
Wang M1, Bandeira N.

SpliceDB 1.0 – Splice Graph Proteomics Tools

SpliceDB 1.0

:: DESCRIPTION

SpliceDB is a software of incorporation of RNA-seq for MS database search

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 SpliceDB

:: MORE INFORMATION

Citation

J Proteome Res. 2014 Jan 3;13(1):21-8. doi: 10.1021/pr400294c. Epub 2013 Jul 17.
Proteogenomic database construction driven from large scale RNA-seq data.
Woo S1, Cha SW, Merrihew G, He Y, Castellana N, Guest C, MacCoss M, Bafna V.

MixGF 1.0r – Computing Statistical Significance of Peptide-spectrum-matches for multiplexed MS/MS Spectra

MixGF 1.0r

:: DESCRIPTION

MixGF computes the statistical significance of peptide identifications for mixture spectra and show that this approach improves the sensitivity of current mixture spectra database search tools by a ≈30-390%.

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 MixGF

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2014 Dec;13(12):3688-97. doi: 10.1074/mcp.O113.037218. Epub 2014 Sep 15.
MixGF: Spectral Probabilities for Mixture Spectra from more than One Peptide.
Wang J, Bourne PE, Bandeira N

MSPLIT 1.0 – Multiplexed Spectral Library Search

MSPLIT 1.0

:: DESCRIPTION

M-SPLIT is a spectral-library search tool for identification of mixture spectra of up to two peptides.

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 MSPLIT

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2010 Jul;9(7):1476-85. doi: 10.1074/mcp.M000136-MCP201. Epub 2010 Mar 27.
Peptide identification from mixture tandem mass spectra.
Wang J1, Pérez-Santiago J, Katz JE, Mallick P, Bandeira N.

MS-GF+ 20140630 – Database search for Peptide Identification

MS-GF+ 20140630

:: DESCRIPTION

MS-GF+ is a new MS/MS database search tool that is sensitive (it identifies more peptides than other database search tools and as many peptides as spectral library search tools) and universal (works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols).

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 MS-GF+

:: MORE INFORMATION

Citation

MS-GF+ makes progress towards a universal database search tool for proteomics.
Kim S, Pevzner PA.
Nat Commun. 2014 Oct 31;5:5277. doi: 10.1038/ncomms6277.

MetaSPS 7.332 – De novo Protein Sequencing

MetaSPS 7.332

:: DESCRIPTION

MetaSPS was shown to yield the longest and most accurate de novo sequences from tandem mass spectrometry data at nearly full sequence coverage.

::DEVELOPER

Nuno BandeiraAdrian Guthals [aguthals (at) cs.ucsd.edu] ,CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX

:: DOWNLOAD

 MetaSPS

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2012 Oct;11(10):1084-96. Epub 2012 Jul 13.
Shotgun protein sequencing with meta-contig assembly.
Guthals A1, Clauser KR, Bandeira N.

UniNovo 20130520 – Universal tool for de novo Peptide Sequencing

UniNovo 20130520

:: DESCRIPTION

UniNovo is a universal de novo peptide sequencing tool that works well for various types of spectra and spectral pairs (e.g., CID, ETD, HCD, CID/ETD, etc). The accuracy of de novo reconstructions generated by UniNovo is better than or comparable to PepNovo+ or PEAKS. Moreover, UniNovo also estimates the error rate of the reported reconstruction.

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 UniNovo

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 15;29(16):1953-62. doi: 10.1093/bioinformatics/btt338. Epub 2013 Jun 12.
UniNovo: a universal tool for de novo peptide sequencing.
Jeong K1, Kim S, Pevzner PA.