Table I Listing and main features of software tools for analysis of MS and MS/MS data from cross-linking experiments

“MS1” indicates assignment of cross-links based on MS1-level information only; “MS/MS” indicates functionality to assign peaks of MS/MS spectra to theoretical spectra of candidate cross-links. “Batch search” indicates whether consecutive searching of multiple MS/MS spectra is possible. “Database size” indicates whether the search space is restricted to a “small” number of sequences (<100) or whether it has been demonstrated that large sequence databases may be searched (“large”). In the “Cross-linker” column, “#” indicates that the generic mass shift of the cross-linker may be defined by the user, “PIR” indicates that it was designed for protein interaction reporter cross-linking reagents, and “iso” indicates that software may be used with isotopically labeled cross-linkers. GPMAW, General Protein/Mass Analysis for Windows; ASAP, Automated Spectrum Assignment Program; CLPM, Cross-Linked Peptide Mapping Algorithm for Mass Spectrometric Analysis. ✓, available/possible; —, not available/not possible.

AlgorithmMS dataDatabase sizeCross-linkerScoringRef.
MS1MS/MSBatch searchSmallLarge
ProteinXXX (GPMAW)#37
X-linksPIR78
Links and MS2Links (formerly ASAP and MS2assign)ab#1, 5
CLPM#39
Pro-CrossLink (for 16O/18O-labeled samples)#79
xQuest, xBobcat#/iso26
XLink (for 16O/18O-labeled samples, LC-MALDI)#80
Protein Prospector (open mass modification search)#41
Popitam (CXMS) (open mass modification search)#29
X!Links#28, 81
XDB approach (+search engine), Phenyx#27