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Crosslink Search Task
Manual and Test data could be found here: Click me
- Download the newest version of MetaMorpheus from https://github.com/smith-chem-wisc/MetaMorpheus/releases, install by double click ‘MetaMorpheusInstaller.msi’.
- Add (Drag) your Database and Data files to MetaMorpheus. The results will be in the same folder as the data files.
- Click the ‘Add XL SEARCH’ will lead to set the parameter for cross-link search. Detailed parameter description as follows. Then ‘Add the XLSearch Task’ to the Tasks panel of the main window. If you have an old .toml file (parameter setting file), you can add (drag) it to MetaMorpheus.
Crosslink Search panel:
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Crosslinker Type: choose the cross-linker the data used. You can also add novel crosslinker in Main panel -> settings -> Create New Crosslinker.
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Quench Methods: this is used to find dead-end crosslinks.
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Search top N candidates: The ion-indexed open search will give a list of candidate alpha peptides per MS2 scan. the number here is to limit the number of candidates for crosslink search. The number is better to be <= 50.
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MS2 Dissociation Type: What fragmentation method is used for MS2 scan.
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MS2 Child Scan Dissociation: If use combined fragmentation methods, choose this for the other fragmentation method. (For example, if use HCD trigger MS2 ETD, set Dissociation Type: HCD, Child Scan Dissociation: ETD).
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MS3 Child Scan Dissociation: If use combined fragmentation methods, choose this for the other fragmentation method. (For example, if use HCD trigger MS3 HCD, set MS2 Dissociation Type: HCD, MS3 Child Scan Dissociation: HCD).
We realize that in rare cases data sets could not be correctly read in, please contact developer for help.
- Crosslink At Cleavage Site: The popular crosslinker DSS or DSSO crosslink lysines (K), the trypsin cleaves at lysines. In default, the crosslinks cannot be cleaved.
Search Parameters Panel & Modifications Panel:
- Similar to the parameters in Search Task, please check the definition there.
- Pay attention to 'Numberof Database Partitions'. If large database (for example human database from uniprot) is used, please change the number to 50 or 100.
- pay attention to 'Max Threads'. The parameter decides the parallel of the program. The larger the number, the faster the search. In default, the number is the number of logical processors of the computer minus 1.
Output Parameters panel:
- Write .pep.XML will generate .pep.XML file for ProXL, which is a cool web-based program for visualizing results.
If you have any suggestions or problems, you can leave a message to the developers (via GitHub or email the author llu56@wisc.edu), we appreciate any help from you to improve the software program.
You may or may not want to cite the paper:
Lu, Lei, Robert J. Millikin, Stefan K. Solntsev, Zach Rolfs, Mark Scalf, Michael R. Shortreed, and Lloyd M. Smith. "Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus." Journal of proteome research 17, no. 7 (2018): 2370-2376. link
Bottom-up E. coli ribosome and yeast Pol2: Click me