GlycoPeptideSearch 1.3.12 – Interpretation of N-glycopeptide by searching for Glycopeptide Results consistent with MS/MS spectra

GlycoPeptideSearch 1.3.12

:: DESCRIPTION

GlycoPeptideSearch (or GPS) is a siimplifies data interpretation of N-glycopeptide CID MS/MS datasets by searching for glycopeptide results consistent with MS/MS spectra. Results are tabulated in Excel format.

::DEVELOPER

Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

GlycoPeptideSearch

:: MORE INFORMATION

Citation

J Proteome Res. 2012 Mar 2;11(3):1728-40. doi: 10.1021/pr201183w. Epub 2012 Feb 6.
Semi-automated identification of N-Glycopeptides by hydrophilic interaction chromatography, nano-reverse-phase LC-MS/MS, and glycan database search.
Pompach P, Chandler KB, Lan R, Edwards N, Goldman R.

MixDB 1.0r – Identify Mixture MS/MS Spectra from more than one Peptide

MixDB 1.0r

:: DESCRIPTION

MixDB is a database search tool that able to identify mixture MS/MS spectra from more than one peptide.

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/windows
Java
Perl

:: DOWNLOAD

MixDB

:: MORE INFORMATION

Citation:

Peptide identification by database search of mixture tandem mass spectra.
Wang, J., Bourne, P. E., Bandeira, N.
Mol. Cell. Proteomics, 2011

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

MUDE 1.0 – Assess MS/MS Spectra Assignments

MUDE 1.0

:: DESCRIPTION

mude (multivariate decoy database analysis) is a set of programs implementing the framework to assess MS/MS spectra assignments

:: DEVELOPER

By Cerqueira, Fabio (fabio.cerqueira@ufv.br); Graber, Armin; Schwikowski, Benno; Baumgartner, Christian.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux / MacOsX
JAVA

:: DOWNLOAD

MUDE

:: MORE INFORMATION

Citation

MUDE: a new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification.
Cerqueira FR, Graber A, Schwikowski B, Baumgartner C.
J Proteome Res. 2010 May 7;9(5):2265-77. doi: 10.1021/pr901023v.

Tag-DB 0.4.0 – de novo Sequencing and Tag-based database Searching of MS/MS Spectra

Tag-DB 0.4.0

:: DESCRIPTION

Tag-DB provides a user-friendly, lightweight and open-source graphical user interface for running the de novo sequencing algorithm PepNovo+ and also holds the possibiliy to search derived short amino acid sequences (so-called tags) against a protein database in order to retrieve peptide and protein identifications.

::DEVELOPER

Thilo Muth and Harald Barsnes.

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux
Java

:: DOWNLOAD

Tag-DB

:: MORE INFORMATION