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platforms, pipelines and libraries
related sites
bio.tools
CPFP
CompOmics
ExPASy tools
Nesvizhskii lab
PNNL Tools
SPC Proteomic Tools
GenePattern
Central Proteomics Facilities Pipeline [1]
(demo here )
platform for integrative genomics and proteomics (includes PEPPeR
[2]
and other
tools for proteomics)
Java
InSilicoSpectro
open source proteomics library (of Perl functions) [3]
Perl
libmgf
a flex/bison-based Mascot Generic Format (MGF) parser library
C++
MALDIquant
analysis pipeline for MALDI-TOF profiling [4]
C, R
Mass-up
utility with full GUI for proteomics data analysis, particularly MALDI-TOF [5]
Java
MASSyPup
MetaProteomeAnalyzer
mspire
a lightweight Linux live distribution prepackaged with a wide range of tools for MS and
MS/MS data analysis
pipeline to analyze metaproteomics data, supporting MGF and X!Tandem, OMSSA and
Mascot [6]
MS data processing in Ruby, including mzML reader/writer, in-silico digestion, isotopic
pattern calculation etc. [7]
MSFileReader_Python_bindings Python bindings for the (non-free) ThermoFisher Scientific MSFileReader
mzAccess
MzJava
Open source web-service software for remote interactive access to the large collections
of mass spectrometry data [8]
library for the analysis of mass spectrometry data from large scale proteomics and
glycomics experiments
Java
Ruby
Python
C#, R
Java
OpenMS
library for the analysis, reduction and visualization of LC-MS(/MS) data
C++
PAPPSO
Plateforme d'Analyse Protéomique de Paris Sud-Ouest
Java
PatternLab
suite of pattern recognition software for interpretation of quantiative proteomics data [9] .NET
pFind Studio
PeptideShaker
platform for mass spectrometry-based proteomics, including pFind [10] , pNovo [11] ,
pQuant [12]
and pLink [13]
platform for interpretation of proteomics identification results from multiple search
engines [14]
Java
Java
PRIDE Toolsuite
a selection of tools and libraries for interacting with data in PRIDE
Proline
a free and open source software suite for mass spectrometry based proteomics.
Proteios
pipeline/LIMS for proteomics experiments and analysis
Java
Proteomatic
platform for creating MS/MS data analysis workflows using scripts [15]
C++
ProteoWizard
open source library for proteomics tools development (supports mzML) [16]
C++
pymzML
Python module to parse mzML data based on cElementTree [17]
Python
Pyteomics
framework for proteomics data analysis, supporting mzML, MGF, pepXML and more [18]Python
QuanTP
resource for quantitative proteotranscriptomic data analysis [19]
QuPE
Rproteomics
Ursgal
integrated environment for storage, analysis and integration of proteomics data
(requires login) [20]
set of routines for analyzing proteomics data, an XML database to store the results and
a user interface
Python module providing a generalized interface to several common bottom-up
proteomics tools [21]
TPP
Institute for Systems Biology
XCMS
software package (in R) for metabolite profiling from LC-MS data
Java
R
Java
R
Python
"Trans-Proteomic Pipeline"
R
data visualization and analysis
BatMass
platform for multiplexed LC–MS data visualization and exploration in proteomics and
metabolomics [22]
Java
cdfread
a simple reader of mass spectra in netCDF
C
COMSPARI
compares two datasets in netCDF or ASCII format
C
imDEV
data exploration and visualization in Excel
Insilicos Viewer
basic viewer of LC-MS/MS data in mzXML
LA-iMageS
generates 2D/3D images for elements in ICP-MS [23]
Java
MapQuant
image analysis" of LC-MS features, deconvolution etc. [24]
C
format
web
mMass
MoverZ
msaccess
MSGraph
MSPicturePerfect
msXpertSuite
user-friendly and free software to view MS data in a range of formats [25]
formats
creates a psuedo-2D-gel representation [26]
an MS-DOS program to visualize LC-MS data in 2D and 3D (converter from mzXML
available)
C++
C
visualize mzXML data in 2D
tools for analysis of polymer and peptide/protein mass spectra, including ion mobility
data
MZmine
toolbox for visualization and analysis of LC-MS data in netCDF or mzXML [27]
mzXMLplot
plots mzXML LC-MS data as virtual gels or heat maps
mzXML Viewer
mzXML viewer from Seattle Proteome Center
OpenChrom
open source tool for mass spectrometry and chromatography [28]
Pep3D
plots LC-MS and LC-MS/MS data in a 2D m/z vs time plot [29]
Peppy
proteogenomic, proteomic search tool [30]
ProteomicsDB
explorable, interactive human proteome database, including MS/MS data [31]
PROTICdb
proteomic database to store, track, query and compare proteome data [32]
Protter
Python
free version of MoverZ for viewing and manipulating single mass spectra in many
interactive protein feature visualization and integration with experimental proteomic data
[33]
C++
C
Java
Java
web
Java
web
Java
web
Scaffold Viewer
free viewer to share and visualize Scaffold-analyzed data
Sirius
tool for metabolite identification using mass spectrometry
Java
Skyline
builds SRM/MRM methods and analyzes resulting data
C#
Spectrum Look
tool for viewing and annotating MS/MS spectra
C
TAPIR
visualization of targeted/SWATH proteomics LC-MS(/MS) data
Python
Taverna
Taverna4Proteomics
powerful, scalable, open source and domain independent tools for designing and
executing workflows [34]
Taverna workflows for integrated proteomics data analysis, a.k.a. Workflow4Proteomics
[35]
VIPER
visualizes features from LC-MS analyses, particularly AMTs
WinICR
reads and analyzes single FTICR and TOF spectra in various older vendor formats
Java
Java, C/C++
format conversion
APLToMGFConverter
collect_mgf
converts MaxQuant APL (Andromeda peak lists) to MGF
collects MGF
files and dd_results from an XMass setup_QDD.tcl experiment to a
single MGF file
CompassXport
converts Bruker analysis.baf and analysis.yep files to mzXML or mzML
dat2mgf
converts Mascot results files back to MGF
DataAnalysis2TPP
converts MGF from Bruker DataAnalysis to TPP-friendly format for use with XPRESS
and ASAPRatio
MassWolf
converts MassLynx format to mzXML
.dta to MGF File Converter
converts .dta to MGF
MSD File Reader
C#
C
AWK
VC++
read, display and save data from the original HP MSD based on the HP Pascal
Chemstation (replaced with Quadfiles )
mspire/mspire-sequest
mzML to imzML and Bioworks Sequest results files (.srf) to pepXML (mspire-sequest)
Ruby
multiplierz
scriptable framework for access to manufacturers' formats via mzAPI [36]
Python
msconvert
converts from RAW/WIFF/T2D/Agilent/Bruker/Waters/mzML/mzXML/MGF/MS2 to
mzML/mzXML/MGF/MS2 [37]
msgfdb2pepxml
converter from MS-GFDB
mz2mgf
converts mzData files to MGF
mzBruker
converts Bruker analysis.baf files to mzXML
VC++
mzStar
converts SCIEX/ABI Analyst format (WIFF) to mzXML
VC++
mzXML2Other
converts mzXML to SEQUEST .dta, MGF, and Micromass .pkl
VC++
Out2Summary
collects Sequest and TurboSequest *.out files to HTML for use with INTERACT
VC/VC++
PklFileMerger
merges individual Q-TOF .pkl files into a single file for database searching
C++
ProCon
converts ProteomeDiscovere 1.X .msf to mzIdentML
Java
PyMS
tools for reading LC-MS data in the ANDI-MS and JCAMP-DX formats [38]
Python
pyteomics.pepxmltk
converts X!Tandem t.XML files to pepXML (without enzyme limitations) [39]
Python
Quadfiles
output to pepXML
C++
Python
(formerly Mass Hunder File Reader) exports raw quadrupole MS data from Agilent
Chemstation or MassHunter to plain text
RawTools
package to parse Thermo Orbitrap raw data [40]
C#
ReAdW
converts Xcalibur native acquisition files to mzXML
VC++
T2D converter
converts ABI SCIEX 4700/4800 t2d files to mzXML
Python
unfinnigan
reading Thermo .raw files without MsFileReader
Perl
wiff2dta
converts ABI WIFF to .dta [41]
X2XML
converts from almost any format (Thermo, Bruker, Agilent and Micromass) to mzXML
.NET
small molecules/lipidomics
CEU Mass Mediator
Chrombox D
Chrombox Q
LipidXplorer
MSC Pro
annotation of metabolites in MS1 spectra with R and REST APIs [42]
J2EE
identification and quantitation, particularly of polar lipids, from LC-MS or direct infusion
data in most formats [43] [44]
deconvolution, search and identification of peaks in GC-MS data [45]
MATLAB
MATLAB
high-throughput lipid identification from shotgun mass spectra in mzML, mzXML, CSV
and .dta formats [46]
Python
mass spectrometry calculator for interpreting mass spectra integrated with NIST
MSSearch
msPurity
precursor purity evaluation for tandem mass spectrometry in metabolomics [47]
R
statTarget
statistical analysis of molecular profiles and signal drift correction [48]
R
SpiderMass
web
semantic chemical database generation, metabolite identification and de novo formula
generation
Python/C/C++
peak picking /deconvolution
DeconMSn
DeconTools
tool for accurate precursor ion monoisotopic mass determination for tandem mass
spectra [49]
advanced peak picking of MS and LC-MS(/MS) data using THRASH
and other
algorithms
.NET
.NET
esimsa
simple deconvolution of electrospray ionization peak lists [50]
C
esimsa2D
simple deconvolution and 2D peak picking of LC-MS data
C
ESIprot
charge state determination and molecular weight calculation for low resolution
electrospray ionization data [51]
Python
libmprc
library for analysis of high resolution mass spectrometry data (including THRASH)
C++
massifquant
Kalman filter based on binless peak picking and quantitation in XCMS
R
MS-DIAL
data independent MS/MS deconvolution for metabolomics [52]
.NET
nontarget
R function for compound, adducts and ion series detection using isotopic distributions
R
UniDec
universal deconvolution and visualization of (ion mobility) mass spectra [53]
C/Python
Xtractor
extracts pre-defined peaks or regions into a uniform array
C
Y.A.D.A.
tool for deconvoluting MS/MS spectra [54]
.NET
adjust (recalibrate ) PKL peak lists
Java
web
calibration /alignment
adjustPKL
CPM
ID-Align
msalign
alignment
of time-series data [as in LC-MS(/MS)] using Continuous Profile Models
[55]
aligns
metabolite data from multiple files to single spreadsheet
aligns
LC-MS and LC-MS/MS datasets using peptides identified by MS/MS and
accurate mass MS [56]
msalign2
aligns
mzRecal
recalibrate
two CE-MS or LC-MS datasets using accurate mass information [57]
OBI-Warp
aligns
recal2
recalibrate
SpecArray
aligns
LC-MS datasets using peptides identified by MS/MS [58]
multiple LC-MS(/MS) datasets in retention time by dynamic time warping [59]
LC-FTICRMS(/MS) datasets using peptides identified by MS/MS [60]
multiple LC-MS datasets and much more [61]
MATLAB
Python
C
C
Go
C++
C
C++
retention time prediction
BioLCCC
an analytic model of peptide retention [62]
web
hplcsimulator
a general tool for simulating and optimizing HPLC gradients
web
retentionprediction
a related web utility for projecting/predicting retention times [63]
rt
retention time prediction using LC-MS data with improved user interface [64]
SSRCalc
sequence-specific retention time calculator [65]
de novo sequencing /PTMs
web
C
web
CrossTalkDB
Delta Mass
DeNovoGUI
histone modification database designed to store, analyze and compare histone
modifications determined by MS [66]
the ABRF
Java
database of protein post-translational modifications
A nice GUI for running the PepNovo
and DirecTag
under Windows, Mac or Linux
[67]
web
Java
GlycoMod
predicts oligosaccharide structures from experimental masses
InSpecT
"blind" spectral search of tandem mass spectra of peptides [68]
C/Python
lutefisk
de novo peptide sequencing from MS/MS data [69]
C
MSNovo
de novo peptide sequencing from MS/MS data [70]
Novor
fast, real-time peptide de novo sequencing engine [71]
PEAKS De Novo
[74]
web
Java
integrated de novo peptide sequencing [72] , PTM finder [73] , and homology search
(demo available)
web
web
web
Java
PepNovo
de novo sequencing using probabilistic network modeling [75]
Popitam
searches for unknown post-translational modifications [76]
C++
POSTMan
post-translational modification software [77]
ProSight PTM
web portal for PTM search in top-down experiments [78]
ProSight PTM Ion Predictor
generate exact masses for CID/ECD fragments with PTMs
ProteoSushi
transformation of peptide-centric PTM data into annotated PTM-site output
Sequit!
free (non-batch) version of a de novo/BLAST tool [79]
SPS
shotgun protein sequencing assembling multiple MS/MS spectra [80]
MATLAB
theospec
command line tool for predicting MS/MS spectra
C
UniMod
database of simple protein modifications
web
aldente
web based peptide mass fingerprinting
web
MASCOT
free version of the Matrix Science
web
web
C++
web
web
Python
web
protein identification
peptide mass fingerprinting
ms1searchpy
MASCOT Peptide Mass Fingerprinting
an open-source Python proteomics search engine for the LC-MS spectra (also LCMS/MS data can be used) [82]
suite
Python
MS-Fit
peptide mass fingerpriting tool in the ProteinProspector
PepMAPPER
multi-experiment peptide mass fingerprinting
C++
web
web
ProFound
free web version of ProFound (peptide mass fingerprinting)
web
ProteinGuru
several on-line tools, including OLMAT for peptide mass fingerprinting
web
ProteinProspector
the ProteinProspector suite of protein identification tools
web
tandem mass spectrometry (MS/MS)
Comet
open source tandem mass spectrometry (MS/MS) sequence database search tool [83] C++
EasyProt
graphical and software platform for the analysis of MS/MS data
greylag
free MS/MS search engine
MASCOT
free, web-based version of the MASCOT MS/MS Ions Search
web
MassMatrix
web based tools for peptide identification and quantitation
web
MassAI
free (Windows/WINE) tool for analysis of MS/MS, bottom-up proteomics data, including
non-standard PTMs and more
Python/C++
Delphi
MassWiz
peptide identification and FDR calculation [84]
Perl
MS Amanda
algorithm optimized for high accuracy tandem mass spectra [85]
C#
MSFragger
ultrafast database search for peptide identification, including from TIMS-TOF data [86]
Java
MS-GFDB
peptide identification using a combination of de novo and database search [87]
Java
MS-GF+
latest version of MS-GFDB above [88]
MSPolygraph
open source hybrid database and spectral library MS/MS search engine [89]
C
MyriMatch
another free MS/MS search engine
C++
OMSSA
mass spectrometry search algorithm from NIH (also searches ETD MS/MS data) [90]
PEAKS DB
de novo-assisted database search [91]
Percolator
semi-supervised learning for peptide identification from MS/MS data [92]
PepProbe
web-based MS/MS search engine [93]
PepSplice
cache-optimized search algorithm [94]
C++
ProLuCID
improved SEQUEST-like algorithm with enhanced sensitivity and specificity [95]
Java
ProLuCID GUI
user-friendly graphical user interface for the ProLuCID database search engine
Python, Java
ProteinProspector
the ProteinProspector suite of protein identification tools
Proteome ARTworks
SearchGUI
TopPIC
web
Java
web
web
predicts detectability and tandem mass spectra of peptides and addresses the protein
web
inference problem [96]
graphical user interface to several common search engines, such as X!Tandem, Mascot
and OMSSA. [97]
proteoform identification/characterizaion at the proteome level using database search
Java
C++
web
[98] [99] [100]
VEMS
platform for protein identification and characterization [101]
X!Tandem
matches tandem mass spectra with peptide sequences
C++
MS/MS library search
ProMEX
matches tandem mass spectra against A. thaliana and M. truncatula libraries
SpectraST
matches peptide MS/MS spectra with library spectra
X! Hunter
matches tandem mass spectra with library spectra from same organism
web
C++
(result) parsers/validation /fragment spectrum processing
goa_gubbar
sorts protein identifications under GOA slim terms
C
Mascot Parser
PDOM and MASCOT parser [103]
Java
Mayu
estimates protein identification false discovery rates
Perl/R
libmgf (formerly mgfp) - a flex/bison-based Mascot Generic Format (MGF) parser library
libmgf
[104]
C++
ms2preproc
ms2preproc - MGF and dta fragment spectrum preprocessing [105]
C++
mres2x
a tool to process MASCOT results [106]
C
PAnalyzer
rearranges Waters PLGS XML or mzIdentML peptide data into inferred proteins
C#
PeptideProphet
(TPP )
validation of peptide identifications by MS/MS and database searches [107]
C++/Perl
ProteinProphet
(TPP )
validation of protein identifications by MS/MS and database searches [108]
C/Perl
XTandem Parser
Java-based parser for X!Tandem result files [109]
Java
X!TandemPipeline
filter, edit and group peptide/protein identifications from X!Tandem (and MASCOT)
Java
data-independent acquisition (DIA)
DIA-Umpire
computational framework for data-independent acquisition proteomics [110]
Java
EncylcopeDIA
library searching for DIA data [111]
Java
Workflow for targeted data analysis of data-independent acquisition (DIA) or SWATH-
OpenSWATH
MS proteomics data [112]
PECAN
C++
library-free peptide detection for DIA data [113]
Python
protein abundance estimate from LC-MS/MS data [114]
Java
statistical analysis of protein ratios from ICAT, cICAT or SILAC experiments
VC++
DAnTE
protein quantitation, statistical analysis and visualization
.NET
Diffprot
non-parametric statistical analysis of differential proteomics data [115]
Perl
FlashLFQ
label-free quantification algorithm for mass spectrometry-based proteomics [116]
C#
ICPLQuant
tool for processing and analyzing ICPL LC-MALDI data [117]
Java
ICPL_ESIQuant
tool for processing and analyzing ICPL LC-MS/MS (ESI) data [118]
Java
isobar
quantitation of TMT and iTRAQ data and LaTeX report generation [119]
R
IsobariQ
quantitation of IPTL, iTRAQ and TMT-labeled peptides [120]
C++
Libra
analyzes 4- and 8-channel iTRAQ
protein quantitation
APEX
ASAPRatio
(TPP )
(TPP )
data [121]
MassChroQ
XIC extraction and quantitation from LC-MS data [122]
MaxQuant
quantitation from SILAC data from Thermo Orbitrap and FTICR
MFPaQ
Mascot file parsing and quantitation using ICAT and SILAC [123]
MSQuant
protein quantitation combining Mascot results and raw data from stable isotope labeling .NET
MS-Spectre
quantitiave analysis of multiple LC-MS(/MS) analyses in mzXML
Java
MSstats
statistical tool for quantitative mass spectrometry-based proteomics [124]
R
Multi-Q
tool for multiplexed iTRAQ-based quantitation [125]
.NET/Perl
muxQuant
multiplexed quantitiave proteomics using differential stable isotope labeling [126]
C
PeakQuant
an integrated platform of quantitative proteomics tools, including for SILAC and
metabolic labeling
C++
Perl/.NET
Java
PEAKS Q
peptide/protein quantification by iTRAQ, ICAT, SILAC or label-free
Java
pepXML2Excel
converts output from PeptideProphet to protein level information in Excel
AWK
ProRata
differential proteomics analysis using for various stable isotope labeling schemes [127]
ProteoClade
taxonomic-based annotation and quantification of bottom-up metaproteomics data [128] Python
PVIEW
pyQms
isotope labeled, label-free, and XIC-based quantitation for high resolution LC-ESIMS/MS data [129]
generalized mass spectrometry data quantification module using isotopic distributions
[130]
Quant
MATLAB program for protein quantitation by iTRAQ [131]
QUIL
another program for relative quantitation using stable isotope labeling [132]
C++
Python
MATLAB
RAAMS
algorithm for interpreting O-16/O-18 differential proteomics data
RelEx
calculation of ion current ratios from LC-MS data (requires Xcalibur) [134]
XINA
network integration of kinetic proteomics data [135]
XPRESS
(TPP )
calculates relative abundances from ICAT, cICAT, SILAC and other N-14/N-15
experiments [136]
C++
R
VC++
protein structure
Cross-linking
ASAP
automatic peptide identification in crosslinking experiments [137]
CCdigest
digest proteins with intact disulfide bridges
Perl
web
CCfind
find peptides with disulfide bridges from ETD data
Perl
web
Crosslinx
identify cross-linked peptides from mzML files feasible for larger databases with a twostep approach [138]
Kojak
application for identification of cross-linked peptides from mass spectra [139]
MassMatrix
MassMatrix also allows cross-linked peptide identification
Python
C++
web
assigns crosslinked or non-crosslinked fragments in whole protein MS/MS (top-down)
MS2Pro
web
spectra [140]
tool for protein-protein cross-linking using MS-cleavable cross-linking reagents (DSBU,
MeroX
DSSO, CDI or PIR) [141]
MS2Assign
assigns crosslinked or non-crosslinked peptides in MS/MS spectra [142]
MS-Studio
analysis of crosslinking, H/D exchange and covalent labeling data [143] [144]
SIM-XL
Spectrum Identification Machine for Cross-Linked Peptides [145]
analyses peptide-peptide cross-links for protein-protein interaction or protein structure
StavroX
analysis [146]
interogate protein-protein interactions and protein structure using cross-links FASTA
xComb
databases [147]
Xilmass
XLink
web
algorithm for identifying cross-linked peptides [148]
(TPP )
xQuest/xProphet
Java
web
Java
Perl
web
Java
set of tools for analysis of data from crosslinked and digested protein complexes
analysis of lysine-specific cross-linking [149]
H/D exchange
AUTOHD
analysis of H/D-exchange data using isotopic distributions [150]
C
Deuterator
web based software platform for determining backbone amide H/D ratios
Java/JSP
DEX
another program (similar to AUTOHD) for analysis of H/D-exchange spectra [152]
C/C++
ExMS
MATLAB program for analyzing H/D-exchange data [153]
MATLAB
HDX WorkBench
integrated software platform for HDX data analysis [154]
Java/JSP
hydrogen_bondifier
PyMOL script for retrieving hydrogen bond characteristics from protein structures
PyMOL
HX-Express
an Excel spreadsheet for analysis of H/D exchange mass spectra [155]
Excel
web
web
in silico digestion
bash
sed 1d|tr -d '\n'|awk 'BEGIN{RS="[RK]"}(NR==1)&&/.{5,}/{print $1
RT;next}/[^P].{4,}/{print $1 RT}'
bash
dig
digests or fragments protein sequences [156]
C
dig2
updated version of dig
C
InDigestion
iOS app for in-silico digestion and more
MS-Digest
digests a protein sequence
web
PChopper
multiple-enzyme in silico digester for experimental design
web
PeptideCutter
another web based protein digestion applet
web
Protein Digestion Simulator
Basic
ProteomeDigestSim
mobile
app
calculates theoretical enzymatic peptides and AMTs
R classes for prediction of proteome coverage based on iterative digestion by MEDFASP
or similar [157]
R
mass spectrometry imaging (MSI)
Axima2Analyze
converts imaging data from the Axima formats to the Analyze format used in BioMap
BioMap
biomedical image analysis software (also MSI)
IDL™
Cardinal
a MSI toolbox for statistical analysis [158]
C++
Datacube Explorer
vendor-neutral visualization program for mass spectrometry imaging data (including
C# (.NET)
imzML ) [159]
R package for annotation and interpretation of lipidomics mass spectrometry imaging
massPix
data [160]
R
microMS
Python platform for image-guided mass spectrometry profiling [161]
MSImageView
generate images from WIFF data and export to imzML
Python
msIQuant
fast access, visualization, and analysis of MSI data in imzML [162]
C++ (.NET)
MSI.R
Collection of R scripts for processing mass spectrometry imaging [163]
R
MSiReader
vendor-neutral MATLAB program to view analyze mass spectrometry imaging data [164]MATLAB
OpenMZxy
open mass spectrometry imaging control software [165]
Python
pyImagingMSpec
Python library for processing imaging mass spectrometry data
Python
rMSI
R package for mass spectrometry imaging data handling and visualization [166]
R
SPUTNIK
R package for filtering spatially correlated peaks in MSI data [167]
R
isotopic distributions
algorithm for calculating aggregated isotope distributions and corresponding center-
BRAIN
C++
masses (R package )
enviPat
batch fine structure, profile and centroid calculation with resolution settings provided
R
IDCalc
isotope distribution and theoretical spectrum calculation with GUI
VB
iso2l
calculates the isotopic distribution of a chemical formula or a amino acid chain
Java
IsoSpec
calculates isotopic fine structure (with bindings for C, Python and R)
C++
isotop
MATLAB code for calculating the isotopic distribution of a molecule (e.g. insulin) [168]
MATLAB
isotop
the same program in R
R
Isotope calculator
console application for calculating isotope distributions based on Yergey's method [169]
isotop_fs
MATLAB code for calculating isotopic fine structure
MATLAB
isotope.py
the same program in Python
Python
libipaca
Isotopic PAttern CAlculation library (MIT license)
C++
Molecular Weight Calculator
calculates molecular masses and isotopic distributions
VB
MS-Isotope
calculates the isotopic distribution from a peptide sequence
C++/Java
web
VB
web
online calculator of physicochemical parameters of peptides/proteins, including isotopic
Prot pi
distributions
web
random database generation
Database Manager
sequence database manager, including random database generation
Java
decoy.pl
decoy database generator from Matrix Science
Perl
make_random
generate random database through Markov process
C
simulation /other
compareMS2
Graph Extract
calculates overlap between two LC-MS/MS datasets in MGF [170]
tool for digitizing data from images, similar to the classic Data Grabber, DataThief
C
and
WebPlotDigitizer
mspire-simulator
simulates peptide retention times and chromatographic profiles
Ruby
NGP
simulation of next-generation proteomics experiments
R
Prot pi
online calculation (simulation) of many physicochemical parameters of peptides/proteins VB
web
The categorization of the software and algorithms here is somewhat arbitrary and may change over time. Many programs belong to multiple
categories. If you have any suggestions on how to better organize this website - please let us know (see below).
The goal is to continuously improve the website while not moving too far beyond being a classic link collection and repository of free software
for data analysis in mass spectrometry-based proteomics and protein analysis. The idea is to maximize the usefulness to anyone facing an
analytical or computational problem in proteomics who first would like to know if a solution to the problem already exists and is in the public
domain. The list will therefore always be an eclectic mix of full software suites with advanced graphical user interfaces, web-based software,
libraries, scripts
and pieces of source code to accomplish anything from reading a file in a particular format to providing a complete package
for a proteomic analysis pipeline, from sample tracking to storing, viewing and comparing results from protein identification search engines.
The ambition should be to maintain only functional links to tested, useful and gratis software.
IMPORTANT - BY INSTALLING, COPYING OR USING ANY OF THE SOFTWARE YOU (EITHER AN INDIVIDUAL OR A SINGLE ENTITY)
AGREE THAT YOU HAVE READ THESE TERMS , UNDERSTAND THEM AND AGREE TO BE LEGALLY BOUND BY THEM. IF YOU DO
NOT AGREE TO ALL OF THE TERMS, DO NOT INSTALL, USE OR COPY ANY OF THE SOFTWARE.
This page was last edited on April 16, 2021, at 05:26 AM
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