RHybridFinder 0.2.0 – Identification of Hybrid Peptides in Immunopeptidomic Analyses

RHybridFinder 0.2.0

:: DESCRIPTION

RHybridFinder (RHF) is an R package to process immunopeptidomic data for putative hybrid peptide discovery

::DEVELOPER

Frederic Saab <frederic.saab at umontreal.ca>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux
R

:: DOWNLOAD

RHybridFinder

:: MORE INFORMATION

Citation:

Saab F, Hamelin DJ, Ma Q, Kovalchik KA, Sirois I, Faridi P, Li C, Purcell AW, Kubiniok P, Caron E.
RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery.
STAR Protoc. 2021 Oct 21;2(4):100875. doi: 10.1016/j.xpro.2021.100875. PMID: 34746858; PMCID: PMC8551247.

PIUS 1.0 – Peptide Identification by Unbiased Search

PIUS 1.0

:: DESCRIPTION

PIUS is an open source tool that performs peptide identification from tandem mass spectrograms using the six-frame translation of the complete genome. Differently from peptidomics methods that also allow a search against the complete genome, PIUS does not limit analysis of the genome to a small set of sequences that match a list of de novo reconstructions. Instead, it performs an exhaustive scan of the translation of the six reading frames of the complete genome. Therefore, this search is not biased towards a subset of candidates.

::DEVELOPER

PIUS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux

:: DOWNLOAD

PIUS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1913-4. doi: 10.1093/bioinformatics/btt298. Epub 2013 May 24.
PIUS: peptide identification by unbiased search.
Costa EP1, Menschaert G, Luyten W, De Grave K, Ramon J.

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

:: 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

:: 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

:: REQUIREMENTS

Windows/ MacOsX / Linux
Java

:: DOWNLOAD

X!TandemPipeline

:: MORE INFORMATION