{"id":"https://openalex.org/W7212525352","doi":"https://doi.org/10.64898/2026.09.11.750886","title":"AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics","display_name":"AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics","publication_year":2026,"publication_date":"2026-09-13","ids":{"openalex":"https://openalex.org/W7212525352","doi":"https://doi.org/10.64898/2026.09.11.750886"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.11.750886","doi":"https://doi.org/10.64898/2026.09.11.750886","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.11.750886","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/13/2026.09.11.750886.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/13/2026.09.11.750886.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5095887645","display_name":"Vincenth Brennsteiner","orcid":"https://orcid.org/0009-0002-4629-481X","observed_orcids":["https://orcid.org/0009-0002-4629-481X"]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Vincenth Brennsteiner","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":"https://orcid.org/0009-0002-4629-481X","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119618188","display_name":"Lucas Diedrich","orcid":"https://orcid.org/0009-0007-4884-1422","observed_orcids":["https://orcid.org/0009-0007-4884-1422"]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lucas Diedrich","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":"https://orcid.org/0009-0007-4884-1422","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029759213","display_name":"Shani Ben\u2010Moshe","orcid":"https://orcid.org/0000-0002-7046-5423","observed_orcids":["https://orcid.org/0000-0002-7046-5423"]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Shani Ben-Moshe","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":"https://orcid.org/0000-0002-7046-5423","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111218353","display_name":"Magnus Schw\u00f6rer","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Magnus Schw\u00f6rer","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046421282","display_name":"Georg Wallmann","orcid":"https://orcid.org/0000-0003-4749-3730","observed_orcids":["https://orcid.org/0000-0003-4749-3730"]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Georg Wallmann","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":"https://orcid.org/0000-0003-4749-3730","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005083304","display_name":"Wen\u2010Feng Zeng","orcid":"https://orcid.org/0000-0003-4325-2147","observed_orcids":["https://orcid.org/0000-0003-4325-2147"]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Wen-Feng Zeng","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":"https://orcid.org/0000-0003-4325-2147","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083128670","display_name":"Fabian Joachim Theis","orcid":"https://orcid.org/0000-0002-2419-1943","observed_orcids":["https://orcid.org/0000-0002-2419-1943"]},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Munich","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I4405263983","display_name":"Institute of Computational Biology","ror":"https://ror.org/00kg2yq63","country_code":"DE","type":"education","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672","https://openalex.org/I4405263983"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Fabian J Theis","raw_affiliation_strings":["Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany"],"raw_orcid":"https://orcid.org/0000-0002-2419-1943","affiliations":[{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany","institution_ids":["https://openalex.org/I3018134672","https://openalex.org/I4405263983"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090940750","display_name":"Matthias Mann","orcid":"https://orcid.org/0000-0003-1292-4799","observed_orcids":["https://orcid.org/0000-0003-1292-4799","https://orcid.org/0000-0002-7122-6379"]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Matthias Mann","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1292-4799","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5090940750"],"corresponding_institution_ids":["https://openalex.org/I4210150093"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9940999746322632,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9940999746322632,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.0010999999940395355,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/mass-spectrometry-based-proteomics","display_name":"mass spectrometry-based proteomics","score":0.8349999785423279},{"id":"https://openalex.org/keywords/single-cell-proteomics","display_name":"single-cell proteomics","score":0.800000011920929},{"id":"https://openalex.org/keywords/anndata","display_name":"AnnData","score":0.9789999723434448},{"id":"https://openalex.org/keywords/python-library","display_name":"Python library","score":0.7149999737739563},{"id":"https://openalex.org/keywords/data-quality-control","display_name":"data quality control","score":0.8230000138282776},{"id":"https://openalex.org/keywords/multimodal-data-integration","display_name":"multimodal data integration","score":0.8050000071525574},{"id":"https://openalex.org/keywords/spatial-proteomics","display_name":"spatial proteomics","score":0.8289999961853027},{"id":"https://openalex.org/keywords/single-cell-multi-omics","display_name":"single-cell multi-omics","score":0.5139999985694885}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6003999710083008},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.5918999910354614},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5181999802589417},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.505299985408783},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.4948999881744385},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.40459999442100525},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.3797999918460846},{"id":"https://openalex.org/C31827203","wikidata":"https://www.wikidata.org/wiki/Q874296","display_name":"Tandem mass spectrometry","level":3,"score":0.3617999851703644},{"id":"https://openalex.org/C86153913","wikidata":"https://www.wikidata.org/wiki/Q7682439","display_name":"Tandem mass tag","level":5,"score":0.3490000069141388},{"id":"https://openalex.org/C2986587452","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical analysis","level":2,"score":0.3472999930381775},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.3301999866962433},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33000001311302185},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.3133000135421753},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29580000042915344},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2865999937057495},{"id":"https://openalex.org/C3020001037","wikidata":"https://www.wikidata.org/wiki/Q836575","display_name":"Quality assessment","level":3,"score":0.2547000050544739},{"id":"https://openalex.org/C112979427","wikidata":"https://www.wikidata.org/wiki/Q4949102","display_name":"Bottom-up proteomics","level":5,"score":0.2524000108242035}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.11.750886","doi":"https://doi.org/10.64898/2026.09.11.750886","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.11.750886","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/13/2026.09.11.750886.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.11.750886","doi":"https://doi.org/10.64898/2026.09.11.750886","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.11.750886","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/13/2026.09.11.750886.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7212525352.pdf","grobid_xml":"https://content.openalex.org/works/W7212525352.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W4382022265","https://openalex.org/W4393004135","https://openalex.org/W4408403697","https://openalex.org/W4411463597","https://openalex.org/W4414413670","https://openalex.org/W7119509296","https://openalex.org/W7125495601","https://openalex.org/W7130654629","https://openalex.org/W7147364498","https://openalex.org/W7223175165"],"related_works":["https://openalex.org/W4323980276","https://openalex.org/W4385462917","https://openalex.org/W4392615577","https://openalex.org/W3109132606","https://openalex.org/W4285392955","https://openalex.org/W4386156770","https://openalex.org/W2075326868","https://openalex.org/W370944199","https://openalex.org/W265464850","https://openalex.org/W7147364498"],"abstract_inverted_index":{"Abstract":[0],"Mass":[1],"spectrometry":[2],"(MS)-based":[3],"proteomics":[4],"now":[5],"routinely":[6],"profiles":[7],"proteomes":[8],"at":[9],"scale,":[10],"but":[11],"extracting":[12],"biological":[13],"insight":[14],"and":[15,46,55,68],"integrating":[16,60],"complementary":[17],"modalities":[18],"remains":[19],"challenging.":[20],"Here,":[21],"we":[22],"present":[23],"AlphaPeptTools,":[24],"a":[25],"Python":[26],"package":[27],"for":[28,49],"the":[29,36,41,62],"analysis":[30,57],"of":[31,40],"MS-proteomics":[32],"data":[33,38],"built":[34],"on":[35],"AnnData":[37],"structure":[39],"scverse.":[42],"AlphaPeptTools":[43],"implements":[44],"scalable":[45],"modular":[47],"strategies":[48],"MS-data":[50],"ingestion,":[51],"quality":[52],"control,":[53],"preprocessing,":[54],"statistical":[56],"while":[58],"seamlessly":[59],"with":[61],"scverse":[63],"ecosystem,":[64],"unlocking":[65],"multi-level,":[66],"spatial,":[67],"multimodal":[69],"analyses.":[70],"Code":[71],"Availability:":[72],"https://github.com/MannLabs/AlphaPeptTools.git":[73]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-15T00:00:00"}
