Supported pyXLMS I/O

The following section gives an overview of the supported crosslink search engines and input file formats for reading crosslink results, as well as the supported export options.

The following abbreviations are used:

CSMs: crosslink-spectrum-matches
XLs: crosslinks/residue pairs

Supported Search Engines and Formats

The following crosslink search engines and formats are currently supported:

Search Engine/Format	Parser	CSMs	XLs	Supported Formats	API Docs
MaxQuant/MaxLynx	`read_maxquant()`	✅	❌	`.txt`, any text-like	link
MeroX	`read_merox()`	✅	❌	`.csv`, `.zhrm`, any text-like	link
MS Annika	`read_msannika()`	✅	✅	`.pdResult`, `.xlsx`, `.txt`, any text-like	link
pLink 2 & 3	`read_plink()`	✅	✅	`.csv`, any text-like	link
Scout	`read_scout()`	✅	✅	`.csv`, any text-like	link
xiSearch & xiFDR	`read_xi()`	✅	✅	`.csv`, any text-like	link
XlinkX	`read_xlinkx()`	✅	✅	`.pdResult`, `.xlsx`, `.txt`, any text-like	link
mzIdentML	`read_mzid()`	✅	❌	`.mzid`	link
pyXLMS/custom	`read_custom()`	✅	✅	`.xlsx`, `.parquet`, `.csv`, any text-like	link

*any text-like denotes all .csv like file formats that use a character delimiter e.g. .csv, .tsv and tab-delimited .txt.

Supported Export Formats

The following export options are currently available:

Tool/Format	Exporter	CSMs	XLs	API Docs	Tool Link
pandas.DataFrame/`.csv`/`.xlsx`/`.json`	`transform.to_dataframe()`	✅	✅	link
AlphaLink2	`exporter.to_alphalink2()`	❌	✅	link	link
IMP-X-FDR	`exporter.to_impxfdr()`	✅	✅	link	link
MS Annika	`exporter.to_msannika()`	✅	✅	link	link
ProXL	`exporter.to_proxl()`	✅	❌	link	link
PyXlinkViewer (PyMOL)	`exporter.to_pyxlinkviewer()`	❌	✅	link	link
xiFDR	`exporter.to_xifdr()`	✅	❌	link	link
xiNET	`exporter.to_xinet()`	❌	✅	link	link
xiVIEW	`exporter.to_xiview()`	❌	✅	link	link
XlinkDB	`exporter.to_xlinkdb()`	❌	✅	link	link
xlms-tools	`exporter.to_xlmstools()`	❌	✅	link	link
XMAS (ChimeraX)	`exporter.to_xmas()`	❌	✅	link	link