CCMS Software Tools

Tool	Purpose	Research Area	ProteoSAFe	Downloadables	Publications	Contact
Cancer Proteogenomics	Tool-sets developed during the Cancer Proteogenomics project	Proteogenomics		CancerProteogenomicsTools	23802565 25263569 25263569	Sunghee Woo Seong Cha Stefano Bonissone Vineet Bafna
MXDB	Identification of cross-linked peptides	Universal Tools for Mass Spectrometry	Workflow: MXDB	MXDB	24493012	Jian Wang Nuno Bandeira
Specialize	Identification of peptides with complex PTMs (e.g. SUMOylation)	Universal Tools for Mass Spectrometry	Workflow: Specialize	Specialize	24437954	Jian Wang Nuno Bandeira
Enosi	Pipeline for proteogenomic event calling	Proteogenomics	Workflow: Enosi	V0.1 Executable Jar Python files	24142994 23802565 20164058	Vineet Bafna Sunghee Woo Seong Cha
MetaSPS	De novo protein sequencing	Shotgun Protein Sequencing	Workflow: MetaSPS	Windows executable Linux executable source code	23679345 22798278, PMC3494147	Nuno Bandeira Adrian Guthals
GenoMS	Reconstructing monoclonal antibody	Proteogenomics		Runnable Jar file package for execution(here) source(here)	20164058	Vineet Bafna
MixDB	Multiplexed database search	Multiplexed Mass Spectrometry	Workflow: MixDB	Runnable Jar file Source Code	21862760	Nuno Bandeira
Molecular networks	Spectral networks of any type of molecule to explore the molecular diversity present in biological samples	Spectral Networks	Workflow: Molecular networks	Windows executable Linux executable Source code	27504778 22586093, PMC3387089 22869730, PMC3427086 23798442, PMC3710860	Nuno Bandeira Mingxun Wang
MS-Align+	Database search of top-down spectra	Top-Down Proteomics	Workflow: MS-Align+	Runnable Jar file Source Code	22027200, PMC3433905	Pavel Pevzner
MS-Cluster/Archives	Clustering multiple spectra from the same precursor	Spectral Networks	Workflow: MS-Cluster/Archives	Source Code	18067247 21572408, PMC3128193	Pavel Pevzner
MS-Deconv	Deconvolution of top-down spectra	Top-Down Proteomics		Windows executable Runnable Jar file Source Code	20855543, PMC310195	Pavel Pevzner
MS-GF+	Database search for peptide identification	Universal Tools for Mass Spectrometry	Workflow: MS-GF+	Runnable Jar File Source Files	25358478 18597511	Pavel Pevzner
MSPLIT	Multiplexed spectral library search	Multiplexed Mass Spectrometry	Workflow: MSPLIT	Runnable Jar file Source Code	20348588, PMC2938093	Nuno Bandeira
MSPLIT-DIA	Multiplexed spectral library search for data independent acquisition data	Multiplexed Mass Spectrometry		MSPLIT-DIA	20348588, PMC2938093	Jian Wang Nuno Bandeira
MixGF	Computing statistical significance of peptide-spectrum-matches for multiplexed MS/MS spectra	Multiplexed Mass Spectrometry		Runnable Jar file	PMID:25225354	Jian Wang Nuno Bandeira
AMASS for MS-Imaging	Tools for querying and segmenting MS Image data	MS Imaging		Linux executable Source	21800894, PMC3190602	Vineet Bafna Doruk Beyter
Pepnovo	De novo peptide sequencing	Universal Tools for Mass Spectrometry	Workflow: Pepnovo	Source Code + Windows executable	19256476 19231891	Pavel Pevzner
Spectral Networks	Analysis of Post-Translational Modifications (PTMs)	Spectral Networks	Workflow: Spectral Networks	Windows executable Linux executable Source Code	21082434	Nuno Bandeira
SpliceDB: Splice Graph Proteomics Tools	Incorporation of RNA-seq for MS database search	Proteogenomics	Workflow: SpliceDB: Splice Graph Proteomics Tools	Executable Jar Python files Source Files	23802565	Vineet Bafna
Tremolo	Spectral library search	Spectral Networks	Workflow: Tremolo	Linux executable Source Code	23808827, PMC3766387	Nuno Bandeira Mingxun Wang

Tool	Purpose	Recommended CCMS alternative(s)	Downloadables	Contact
MS-Gapped Dictionary	Huge database search		[Runnable Jar File]	Kyowon Jeong
Multistage Sequencing of Cyclic Peptides				Julio Ng
Shotgun Protein Sequencing (see MetaSPS)	De novo protein sequencing	MetaSPS	[Windows Executable] [Linux Executable] [source]	Nuno Bandeira
Uninovo	Universal De novo peptide sequencing	Pepnovo MetaSPS	[Runnable Jar File and source]	Kyowon Jeong

Tool	Purpose	Recommended CCMS alternative(s)	Downloadables	Publications	Contact
Comparative Shotgun Protein Sequencing (see MetaSPS)	Homology-based de novo protein sequencing	MetaSPS	MetaSPS	19060866	Nuno Bandeira
InsPecT/MS-Alignment	Database search with sequence tags (InsPecT) and unknown modifications (MS-Alignment)	MS-GF+ MODa on ProteoSAFe			Sunghee Woo
MS-Dictionary	Huge database search using de novo sequences	MS-GappedDictionary MS-GF+			Sangtae Kim
MS-GF	Rescoring Peptide-Spectrum Matches using spectral probabilities	MS-GF+			Sangtae Kim
MS-GFDB	Database search using spectral probabilities	MS-GF+			Sangtae Kim

Center for Computational Mass Spectrometry

Software Tools Developed at CCMS