AutoRT v1.0 – Peptide Retention Time Prediction using Deep Learning

AutoRT v1.0

:: DESCRIPTION

AutoRT is a peptide sequence-based RT prediction tool developed using automated deep learning and transfer learning. It can provide high accurate RT prediction with models trained using a small number of peptides (~1000) with transfer learning.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

AutoRT

:: MORE INFORMATION

Citation

Wen B, Li K, Zhang Y, Zhang B.
Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis.
Nat Commun. 2020 Apr 9;11(1):1759. doi: 10.1038/s41467-020-15456-w. PMID: 32273506; PMCID: PMC7145864.

ProteinDecision 1.0 – Protein Identification using Peptide-Mass Fingerprinting Data

ProteinDecision 1.0

:: DESCRIPTION

ProteinDecision is a computer software for identifying protein by serching against protein database with the input Peptide-Mass Fingerprinting Data. It can handle the issues of selecting peaks from mass spectrum, transforming database format, displaying the top ranks of identification result, and detailed information for each ranking.

::DEVELOPER

Digital Biology Laboratory, University Of Missouri-Columbia

:: SCREENSHOTS

ProteinDecision

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 ProteinDecision

:: MORE INFORMATION

Citation

Methods Mol Biol. 2010;604:7-22. doi: 10.1007/978-1-60761-444-9_2.
Bioinformatics methods for protein identification using Peptide mass fingerprinting.
Song Z1, Chen L, Xu D.

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

pLink-SS – Identification of Disulfide Bond Peptides

pLink-SS

:: DESCRIPTION

pLink-SS is a high-throughput mass spectrometry method for precise identification of disulfide-linked peptides.

::DEVELOPER

pLink-SS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

 pLink-SS

:: MORE INFORMATION

Citation

Mapping native disulfide bonds at a proteome scale.
Lu S, Fan SB, Yang B, Li YX, Meng JM, Wu L, Li P, Zhang K, Zhang MJ, Fu Y, Luo J, Sun RX, He SM, Dong MQ.
Nat Methods. 2015 Feb 9. doi: 10.1038/nmeth.3283.

SAROTUP 3.1 – Target-Unrelated Peptides Scanners

SAROTUP 3.1

:: DESCRIPTION

SAROTUP is a suite of web tools that can scan, report and exclude possible target-unrelated peptides from the noisy experiment results of phage display.

::DEVELOPER

HLAB: Huang’s LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

SAROTUP

:: MORE INFORMATION

Citation

J Biomed Biotechnol. 2010;2010:101932. doi: 10.1155/2010/101932. Epub 2010 Mar 21.
SAROTUP: scanner and reporter of target-unrelated peptides.
Huang J1, Ru B, Li S, Lin H, Guo FB.

PAComplex – Infer Peptide Antigen Family and TCR-pMHC Binding Model

PAComplex

:: DESCRIPTION

PAComplex is a web server investigating and visualizing both TCR-peptide / peptide-MHC interfaces; furthermore, it provides biological insights of TCR-pMHC binding models.

::DEVELOPER

PAComplex team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W254-60. doi: 10.1093/nar/gkr434. Epub 2011 Jun 11.
PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes.
Liu IH1, Lo YS, Yang JM.

GPMAW 12.5 – Mass Spectrometric Analysis of Proteins and Peptides

GPMAW 12.5

:: DESCRIPTION

GPMAW (General Protein/Mass Analysis for Windows) is primarily intended as a tool for mass spectrometric analysis of proteins and peptides. However, a number of other bioinformatics tools have been included, so the use of the program extends far beyond simple mass analysis.

::DEVELOPER

Lighthouse data

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GPMAW

:: MORE INFORMATION

Citation

GPMAW–a software tool for analyzing proteins and peptides.
Peri S, Steen H, Pandey A.
Trends Biochem Sci. 2001 Nov;26(11):687-9.

X!TandemPipeline 0.4.34 – Peptide / Protein Identifications from MS/MS Mass Spectra

X!TandemPipeline 0.4.34

:: DESCRIPTION

X!TandemPipeline is a free software that helps you to filter and group your peptide/protein identifications from MS/MS mass spectra.

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

XTandemPipeline

:: REQUIREMENTS

  • Windows/ MacOsX / Linux
  • Java

:: DOWNLOAD

  X!TandemPipeline

:: MORE INFORMATION

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.

iSuc-PseAAC – Predicting Lysine Succinylation in proteins by incorporating Peptide Position-specific Propensity

iSuc-PseAAC

:: DESCRIPTION

The web-server iSuc-PseAAC is established for predicting the lysine succinylation sites in proteins.

::DEVELOPER

Yan Xu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

iSuc-PseAAC: predicting lysine succinylation in proteins by incorporating peptide position-specific propensity.
Xu Y, Ding YX, Ding J, Lei YH, Wu LY, Deng NY.
Sci Rep. 2015 Jun 18;5:10184. doi: 10.1038/srep10184.