{"doi":"10.1101/2021.03.08.434385","title":"High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe","abstract":"Abstract The dia-PASEF technology exploits ion mobility separation for high-sensitivity analysis of complex proteomes. Here, we demonstrate neural network-based processing of the ion mobility data, which we implement in the DIA-NN software suite. Using spectral libraries generated with the MSFragger-based FragPipe computational platform, the DIA-NN analysis of dia-PASEF raw data increases the proteomic depth by up to 69% compared to the originally published dia-PASEF workflow. For example, we quantify over 5200 proteins from 10ng of HeLa peptides separated with a 95-minute nanoflow gradient, and over 5000 proteins from 200ng using a 4.8-minute separation with an Evosep One system. In complex samples, featuring a mix of human and yeast lysates, the workflow detects over 11700 proteins in single runs acquired with a 100-minute nanoflow gradient, while demonstrating quantitative precision. Hence, the combination of FragPipe and DIA-NN provides a simple-to-use software platform for dia-PASEF data analysis, yielding significant gains in high-sensitivity proteomics.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":213066,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":40,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9429,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":230152,"name":"Fengchao Yu","orcid":"0000-0002-7695-3698","position":1,"is_corresponding":false},{"id":230154,"name":"Guo Ci Teo","orcid":"0000-0003-3212-4051","position":2,"is_corresponding":false},{"id":804317,"name":"Łukasz Szyrwiel","orcid":"0000-0003-1983-2950","position":3,"is_corresponding":false},{"id":279384,"name":"George Rosenberger","orcid":"0000-0002-1655-6789","position":4,"is_corresponding":false},{"id":698911,"name":"Jens Decker","orcid":null,"position":5,"is_corresponding":false},{"id":804926,"name":"Stephanie Kaspar‐Schoenefeld","orcid":null,"position":6,"is_corresponding":false},{"id":804318,"name":"Kathryn S. Lilley","orcid":"0000-0003-0594-6543","position":7,"is_corresponding":false},{"id":434222,"name":"Michael Mülleder","orcid":"0000-0001-9792-3861","position":8,"is_corresponding":false},{"id":51780,"name":"Alexey I. Nesvizhskii","orcid":"0000-0002-2806-7819","position":9,"is_corresponding":false},{"id":28498,"name":"Markus Ralser","orcid":"0000-0001-9535-7413","position":10,"is_corresponding":false},{"id":804316,"name":"Vadim Demichev","orcid":"0000-0002-2424-9412","position":0,"is_corresponding":true}],"reference_count":31,"raw_metadata":null,"created_at":"2026-07-18T23:52:31.378994Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}