sapFinder 1.7.0 – Variant Peptides Detection and Visualization in Shotgun Proteomics.

sapFinder 1.7.0

:: DESCRIPTION

sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.

::DEVELOPER

Shaohang Xu <xsh.skye at gmail.com>, Bo Wen <wenbo at genomics.cn>

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux /Windows / MacOs
  • R
  • BioConductor

:: DOWNLOAD

 sapFinder

:: MORE INFORMATION

Citation

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
Wen B, Xu S, Sheynkman GM, Feng Q, Lin L, Wang Q, Xu X, Wang J, Liu S.
Bioinformatics. 2014 Nov 1;30(21):3136-8. doi: 10.1093/bioinformatics/btu397.

sapFinder 1.7.0 – Detection of Variant Peptides in Shotgun Proteomics Experiments

sapFinder 1.7.0

:: DESCRIPTION

sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.

::DEVELOPER

 Shaohang Xu <xsh.skye at gmail.com>, Bo Wen <wenbo at genomics.cn>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R
  • BioCOnductor

:: DOWNLOAD

 sapFinder

:: MORE INFORMATION

Citation

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
Wen B, Xu S, Sheynkman GM, Feng Q, Lin L, Wang Q, Xu X, Wang J, Liu S.
Bioinformatics. 2014 Jul 22. pii: btu397.

Vonode – de novo Sequencing algorithm for Shotgun Proteomics using high-resolution Tandem Mass Spectrometry

Vonode

:: DESCRIPTION

Vonode is a new de novo sequencing algorithm which has been developed specifically for analysis of such high-resolution tandem mass spectra.

:: DESCRIPTION

Omics Bio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Vonode

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Mar 5;11:118. doi: 10.1186/1471-2105-11-118.
A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry.
Pan C1, Park BH, McDonald WH, Carey PA, Banfield JF, VerBerkmoes NC, Hettich RL, Samatova NF.

MUMAL – Multivariate Analysis in Shotgun Proteomics

MUMAL

:: DESCRIPTION

MUMAL is a new method, termed for PSM assessment that is based on machine learning techniques. The method can establish nonlinear decision boundaries, leading to a higher chance to retrieve more true positives.

:: DEVELOPER

Fabio R. Cerqueira  (fabio.cerqueira@ufv.br); Ricardo S. Ferreira; Alcione P. Oliveira; Humberto J. O. Ramo; Christian Baumgartner.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • JAVA

:: DOWNLOAD

 MUMAL

:: MORE INFORMATION

Citation

BMC Genomics. 2012;13 Suppl 5:S4. doi: 10.1186/1471-2164-13-S5-S4. Epub 2012 Oct 19.
MUMAL: multivariate analysis in shotgun proteomics using machine learning techniques.
Cerqueira FR, Ferreira RS, Oliveira AP, Gomes AP, Ramos HJ, Graber A, Baumgartner C.