We offer ICC-CLASS (Isotopically-Coded Cleavable Cross-Linking Analysis Software Suite) for data processing of experiments with isotopically-coded cleavable crosslinkers.

 
Updated 2017.09.09
 
ICC-CLASS (Isotopically-Coded Cleavable CrossLinking Analysis Software Suite) is a collection of software tools for analysis of mass spectrometric data from experiments using isotopically-coded cleavable crosslinking reagents (BMC Bioinformatics, 2010, 11, 64) .
Main program of the suite is DXMSMS Match program (Current Protocols in Bioinformatics, 2014, 8.18.1-19) . It is designed for the automatic assignment of the crosslinked peptides from the whole LC-MS/MS run. The program searches for specific doublets of signals in mass spectra corresponding to the crosslinked peptides and performs assignment of the crosslinks based on the crosslink mass, masses of crosslink MS/MS fragments, masses of crosslink CID-cleavage products and their MS and MS/MS doublets isotopic signatures.

DXMSMS Match is available in two versions of input files: with doublets mass list of the LC-MS/MS run and .MGF file of MS/MS spectra mass lists as input (DX list+MGF version) and with .MGF file as solely input (MGF only version). Programs are primarily oriented for Thermo's Orbitrap instruments data and we provide auxillary programs to obtain doublet mass lists from XCalibur .RAW files as well as test dataset and its example input and output files. Details of the crosslinking analysis experimental setup and mass spectromeric acquisition parameters can be found in (Methods in Molecular Biology, 2014, 1156, 447-463) .

For large number of proteins and/or relaxed digestion/crosslinking sites restrictions the version of the program DXMSMS Match Sorting and DXMSMS Match Proteome employing fast sorting algorithm (Proteomics, 2014, 14, 1987-1989) are available.
For crosslinking data obtained using 15N-metabolically labeled proteins 14N15N DXMSMS Match ESI Sorting version of the program (Journal of Proteomics, 2014, 109C, 104-110) is available.
Software products are not for redistribution and are for research use only.
 
Programs for automatic processing of Orbitrap ESI LC-MS/MS crosslinking data:
DX list + MGF workflow:
Mass list from xtract txt Extracts mass list from the converted to text xtracted .raw file, creates mass list .txt.
DX ESI LCMS Searches for doublets of signals in mass list .txt file, creates DX list .txt.
DX ESI LCMS Mass List Filter Removes duplicates from DX list .txt, creates DX list filtered .txt.
DXMSMS Match ESI DXH Automatic analysis of the ESI LC-MS/MS crosslinking data including doublets scores.
DXMSMS Match ESI DXH Sorting Automatic analysis of the ESI LC-MS/MS crosslinking data with fast sorting algorithm.
MGF only workflow:
DXMSMS Match ESI MGF DXH Automatic analysis of the ESI LC-MS/MS crosslinking data from a single .MGF file.
DXMSMS Match ESI MGF DXH Sorting Analysis of the crosslinking data from a single .MGF file with fast sorting algorithm.
 
DXMSMS Match help files:
DXMSMS Match User Guide .pdf Outlines step-by-step instructions on how to use DXMSMS Match.
TP1 CBDPS PKD MT .MGF Example of the TP1 CBDPS crosslinked Proteinase K digested avidin enriched .MGF file.
Output Post-Processing.XLSB Excel workbook with macro for post-processing of the DXMSMS Match output files.
 
DXMSMS Match for cross-linking analysis of 1:1 mixtures of 14N- and 15N-labeled proteins:
14N15N DXMSMS Match ESI Sorting Accounts for number of nitrogen atoms in cross-linked peptides.
 
DXMSMS Match for crosslinking analysis of large sequence databases up to whole proteomes:
DXMSMS Match ESI DXH Sorting Proteome Analysis of proteome-wide crosslinking data.
Fasta to text file Process proteome protein sequences from .fasta to .txt file.
EcoliK12.fasta Example of E.coli proteome sequences .fasta file.
EcoliK12.txt Example of E.coli proteome sequences .txt file as input for DXMSMS Match.
 
DXMSMS Match 2nd level for crosslinking analysis of second-order crosslinks (three inter-crosslinked peptides):
DXMSMS Match ESI Sorting 2nd Level Analysis of second-order crosslinks.
 
Earlier versions of the programs and other useful programs for processing of crosslinking MS data:
DX VB Search for doublets of signals in mass list text files from MS spectra.
DXDX VB Matching the cleaved to the uncleaved crosslinks doublets in multiple pairs of MS spectra.
DXMSMS VB Crosslinks assignment based on MS/MS data.
DXMultipletFinder Search for multiplets of signals in mass list text files from MS spectra.
DXMassListFilter Removes duplicates from DX list text files of MS spectra of chromatographic fractions.
DXDX ICCL ICNTM Identification of the inter-peptide crosslinks by comparing ICCL and ICCL+ICNTM runs.
Peptides CL Prediction of the masses of the MS/MS fragments of the crosslink from two peptides.
ICCL MSMS Analysis of the MS/MS spectra of the CID-cleavable isotopically-coded crosslinks.
DX Search for doublets of signals in mass list text files from MS spectra.
DXDX Matching the cleaved to the uncleaved crosslinks doublets in multiple pairs of MS spectra.
CLMP Crosslink masses prediction.
DXMSMS Single mass crosslinks assignment based on MS/MS data.
DXMS Crosslinks assignment based on MS data of LC run.
DXMSMS Match ESI Automatic analysis of the ESI LC-MS/MS crosslinking data.
 
Programs for automatic processing of crosslinking MALDI LC-MS/MS data.
DXSet macro for ABI Data Explorer Search for doublets of signals in .T2D MS spectra. .frm file
DXSet macro for ABI Data Explorer Search for doublets of signals in .T2D MS spectra. .frx file
MGF maker ABI Data Explorer macro ABI Data Explorer macro for creating .MGF file from LC-MS/MS run. .frm file
MGF maker ABI Data Explorer macro ABI Data Explorer macro for creating .MGF file from LC-MS/MS run. .frx file
DX MSMS Match MALDI Automatic analysis of the MALDI LC-MS/MS crosslinking data.
 
HDX Match program for processing ECD-FTMS top-down hydrogen/deuterium exchange data.
HDX Match Matching the c- and z-ion fragment envelopes to the predicted non-deuterated and deuterated envelopes.
HDX Match User Guide Outlines step-by-step instructions on how to use HDX Match.
ML1 Example input mass list of the ECD-FT MS/MS spectrum for the non-deuterated sample.
ML2 Example input mass list of the ECD-FT MS/MS spectrum for the deuterated sample.
ML3 Example input mass list of the ECD-FT MS/MS spectrum for the deuterated sample in different condition.
Sequence Example input protein sequence.
Fragment Illustrator Illustrates fragment locations in a protein sequence.
Fragments Example fragments input file.