Introduction

pyXLMS supports the following crosslink search engines and input file formats for reading crosslink results at both crosslink-spectrum-match and crosslink/residue pair level.

Available Parsers with Documented Tutorial Pages

Overview of Supported Search Engines and Formats

The following abbreviations are used:

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

The following crosslink search engines and formats are currently supported:

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

Tip

➡️ All search engine parsers also support any text-like file format that uses a character delimiter e.g. .csv, .tsv and tab-delimited .txt.

API Summary

Here’s a quick summary of the available functions, their page links and their API documentations:

Function Name	Page	API Docs
`parser.pyxlms_modification_str_parser()`		link
`parser.read_custom()`	link	link
`parser.parse_modifications_from_maxquant_sequence()`		link
`parser.read_maxlynx()`	link	link
`parser.read_maxquant()`	link	link
`parser.read_merox()`	link	link
`parser.read_msannika()`	link	link
`parser.parse_scan_nr_from_mzid()`		link
`parser.read_mzid()`	link	link
`parser.detect_plink_filetype()`		link
`parser.parse_scan_nr_from_plink()`		link
`parser.parse_spectrum_file_from_plink()`		link
`parser.read_plink()`	link	link
`parser.detect_scout_filetype()`		link
`parser.parse_modifications_from_scout_sequence()`		link
`parser.read_scout()`	link	link
`parser.detect_xi_filetype()`		link
`parser.parse_modifications_from_xi_sequence()`		link
`parser.parse_peptide()`		link
`parser.read_xi()`	link	link
`parser.read_xlinkx()`	link	link
`parser.format_sequence()`		link
`parser.get_bool_from_value()`		link
`parser.read()`	any of the pages	link