Tag: Shotgun Proteomics

sapFinder 1.26.0 – Detection of Variant Peptides in Shotgun Proteomics Experiments

sapFinder 1.26.0

:: 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.

sapFinder 1.20.1 – Variant Peptides Detection and Visualization in Shotgun Proteomics.

sapFinder 1.20.1

:: 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.

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.