SRPI – Score Regularization for Peptide Identification

SRPI

:: DESCRIPTION

SRPI is a score regularization method which can be used as a general post-processing step for improving peptide identifications.

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 SRPI

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S2. doi: 10.1186/1471-2105-12-S1-S2.
Score regularization for peptide identification.
He Z1, Zhao H, Yu W.

MSblender – Integrating Peptide Identifications from multiple database search engines

MSblender

:: DESCRIPTION

MSblender is a software for integrating peptide identifications from multiple database search engines. MSblender rescores unique peptide-spectrum matches by multivariate mixture modeling of score distributions from multiple search engines.

::DEVELOPER

the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 MSblender 

:: MORE INFORMATION

Citation:

T. Kwon, H. Choi, C. Vogel, A.I. Nesvizhskii, and E.M. Marcotte,
MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines.
J. Proteome Res., 2011, 10 (7), pp 2949–2958

MSFragger / FragPipe 12.1 – Peptide Identification in Mass Spectrometry-based Proteomics

MSFragger / FragPipe 12.1

:: DESCRIPTION

MSFragger is an ultrafast database search tool that uses a fragment ion indexing method to rapidly perform spectra similarity comparisons.

FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger – an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

MSFragger / FragPipe

:: MORE INFORMATION

Citation:

Andy Kong, Felipe Leprevost, Dmitry Avtonomov, Dattatreya Mellacheruvu, Alexey Nesvizhskii.
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics
Nat Meth, May 2017. DOI: 10.1038/nmeth.4256

DeNovoPTM – MS-based Peptide Identification software tool

DeNovoPTM

:: DESCRIPTION

DeNovoPTM is a MS-based peptide identification software tool, which is the first available tool to do de novo sequencing with limited number of PTM occurrences per peptide while considering many types of PTMs.

::DEVELOPER

Lin He

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 DeNovoPTM

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Aug;11(4):1350007. doi: 10.1142/S0219720013500078. Epub 2013 Apr 11.
De novo sequencing with limited number of post-translational modifications per peptide.
He L1, Han X, Ma B.

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.

PepDistiller 1.26 – Improve Sensitivity & Accuracy of Peptide Identifications in Shotgun Proteomics

PepDistiller 1.26

:: DESCRIPTION

PepDistiller is a software designed to validate the peptide identifications obtained from MASCOT search results.

::DEVELOPER

Beijing Proteome Research Center Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • ActivePerl

:: DOWNLOAD

 PepDistiller

:: MORE INFORMATION

Citation

Proteomics. 2012 Jun;12(11):1720-5. doi: 10.1002/pmic.201100167.
PepDistiller: A quality control tool to improve the sensitivity and accuracy of peptide identifications in shotgun proteomics.
Li N, Wu S, Zhang C, Chang C, Zhang J, Ma J, Li L, Qian X, Xu P, Zhu Y, He F.

Percolator 2.04 – Confident Peptide Identifications from a collection of Tandem Mass Spectra

Percolator 2.04

:: DESCRIPTION

Percolator post-processes the results of a shotgun proteomics database search program, re-ranking peptide-spectrum matches so that the top of the list is enriched for correct matches.

::DEVELOPER

Noble Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX

:: DOWNLOAD

 Percolator

:: MORE INFORMATION

Citation

Semi-supervised learning for peptide identification from shotgun proteomics datasets
Lukas Kall, Jesse D. Canterbury, Jason Weston, William Stafford Noble and Michael J. MacCoss
Nature Methods 4:923 – 925, November 2007