Table 1.
Programs employed to support the MS-based identification of probing products. Summarized are features that determine their performance, such as maximum number of supported sequences, customizability of modifications, integrated spectrum processing, ability to output theoretical mass lists, support for tandem MS analysis, availability of scoring functions to evaluate assignments, and user accessibility. Refer to the text or the provided citation for more details.
| Software | Max # of sequences |
Customizable search |
Spectrum Processing |
Output theoretical mass list |
MS2 data |
Scoring function |
Unique feature | Availability | Ref. |
|---|---|---|---|---|---|---|---|---|---|
| NIH-XL | 2 | limited | offline | - | - | stand alone | 89 | ||
| GPMAW | 2 | limited | offline | - | - | stand alone | 131 | ||
| FindLink | 2 | yes | offline | - | - | - | stand alone | 137 | |
| LINKS/ MS2LINKS |
20 | yes | yes§ | yes | yes | - | customizable MS2 ion search; nucleic acids MS & MS2 data analysis |
CMS3D portal https://ms3d.org/ |
139 |
| X-Link | 2 | yes | offline | no | yes | - | MIX-tagged mass marker peaks for crosslink ID |
stand alone | 135 |
| SEARCHXLINKS | multiple | yes | offline | no | yes | yes | integrated MS & MS2 data analysis; adjustable parameters in MS2 scoring scheme |
webserver* | 136 |
| CLPM | 2 | yes | offline | no | no | - | outputs best match only | webserver http://bioinformatics.ualr.edu/mbc/services/CLPM.html |
138 |
| Pro-CrossLink | 2 | yes | yes¶ | no | yes | yes | streamlined workflow to identify crosslinks |
stand alone http://goodlett.proteomics.washington.edu/helpful_links/ |
155 |
| VIRTUALMSLAB | proteome | yes | offline | yes | no | - | multi-stage experiment editor; integrated output sorting |
stand alone | 134 |
| X!Link | proteome | yes | offline | no | yes | yes | shotgun method | stand alone | 147 |
| MS-Bridge | proteome | yes | offline | yes | no | - | webserver http://prospector.ucsf.edu/mshome.htm |
133 | |
| CrossSearch | 2 | limited | offline | no | no | - | webserver http://talmud.umkc.edu/prot_cross3/ |
144 | |
| iLINK/doLink | multiple | limited ( only bis-NHS ester crosslinkers) |
yes¶ | no | yes | yes | integrated spectrum processing, data viewer and annotation |
stand alone http://tools.proteomecenter.org/wiki/index.php?title=Software:Xlink |
156 |
| XQUEST | proteome | yes | yes¶ | no | yes | yes | search engine with stringent spectrum matching |
stand alone | 145 |
| MSX-3D | 2 | yes | offline | no | no | - | with integrated 3D viewer (PDB file input) |
PBIL portal http://proteomics-pbil.ibcp.fr |
179 |
§
Webserver does not include data reduction component.
¶
Spectrum processing supports identification of isotope pairs.
*
URL link is not available.