Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry.
To facilitate structural analysis of proteins and protein-protein interactions, we developed Pro-CrossLink, a suite of software tools consisting of three programs (Figure 1), DetectShift, IdentifyXLink, and AssignXLink. DetectShift was developed to detect ions of cross-linked peptide pairs in a mixture of 18O-labeled peptides obtained from protein proteolytic digests. The selected candidate ions of cross-linked peptide pairs subsequently undergo tandem mass spectrometric (MS/MS) analysis for sequence determination. Based on the masses of candidate ions as well as y- and b-type ions in the tandem mass spectra, IdentifyXLink assigns the candidate ions to cross-linked peptide pairs. For an identified cross-linked peptide pair, AssignXLink generates an extensive fragment ion list, including a-, b-, c-type, x-, y-, z-type, internal, and immonium ions with associated common losses of H2O, NH3, CO, and CO2, and facilitates a precise location of the cross-linked residues. Pro-CrossLink is automated, highly configurable by the user, and applicable to many studies that map low-resolution protein structures and molecular interfaces in protein complexes.
Gao
Qiuxia
Q
Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, Washington 98195, USA.
Xue
Song
S
Doneanu
Catalin E
CE
Shaffer
Scott A
SA
Goodlett
David R
DR
Nelson
Sidney D
SD
D000595:Amino Acid Sequence; D000641:Ammonia / Q000737:chemistry; D001331:Automation; D002245:Carbon Dioxide / Q000737:chemistry; D002248:Carbon Monoxide / Q000737:chemistry; D003432:Cross-Linking Reagents / Q000737:chemistry*; D007477:Ions; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis*; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D012984:Software; D014867:Water / Q000737:chemistry
D003432:Cross-Linking Reagents; D007477:Ions; D010455:Peptides; D011506:Proteins; D014867:Water; D002245:Carbon Dioxide; D000641:Ammonia; D002248:Carbon Monoxide