Estimating protein isoform abundances with PAQu
{"A":[0],"single":[1],"gene":[2],"can":[3,65,207],"encode":[4],"multiple":[5,23],"versions":[6],"of":[7,17,25,57,70,105,186,190],"a":[8,47,51,88,122,137,180],"protein,":[9],"dubbed":[10],"isoforms,":[11],"with":[12,174],"varying":[13],"functionality.":[14],"Cellular":[15],"control":[16,177],"isoform":[18,106,169,189,212],"abundances":[19],"is":[20,28,50,112,200],"critical":[21],"for":[22,132,140],"aspects":[24],"biology":[26],"and":[27,74,99,135,158,176],"only":[29,67],"partially":[30],"regulated":[31],"by":[32],"transcript":[33,39,58],"levels.":[34],"While":[35],"long-read":[36],"sequencing":[37],"facilitates":[38],"quantification,":[40,128],"quantifying":[41],"the":[42,97,187],"resulting":[43],"protein":[44,156],"isoforms":[45,71,157],"on":[46],"large":[48],"scale":[49],"major":[52],"challenge,":[53],"complicating":[54],"biological":[55],"interpretation":[56],"alterations.":[59],"Standard":[60],"\\"bottom":[61],"up\\"":[62],"mass":[63],"spectrometry":[64],"assess":[66],"short":[68],"portions":[69],"called":[72],"peptides,":[73],"these":[75],"peptides":[76],"often":[77],"map":[78],"onto":[79],"more":[80],"than":[81],"one":[82],"isoform.":[83],"We":[84,162],"introduce":[85],"PAQu":[86,114,147,164,206],",":[87],"novel":[89],"Bayesian":[90],"method":[91],"that":[92,146,184,205],"leverages":[93],"multiomic":[94,130],"information":[95,131],"from":[96],"peptidome":[98],"transcriptome":[100],"to":[101,165],"provide":[102],"accurate":[103],"estimates":[104],"abundance":[107,170,213],"even":[108],"when":[109],"peptide":[110],"mapping":[111],"ambiguous.":[113],"offers":[115],"several":[116],"advantages":[117],"over":[118],"existing":[119],"methods":[120,151],"in":[121,152,168,196,211],"unified":[123],"framework.":[124],"It":[125],"provides":[126,136],"uncertainty":[127],"integrates":[129],"improved":[133],"accuracy,":[134],"rigorous":[138],"framework":[139],"hypothesis":[141,183],"testing.":[142],"Extensive":[143],"simulations":[144],"show":[145],"consistently":[148],"outperforms":[149],"competing":[150],"detecting":[153],"differentially":[154],"expressed":[155],"estimating":[159],"their":[160],"abundances.":[161],"use":[163],"investigate":[166],"differences":[167],"levels":[171,185,214],"between":[172],"people":[173],"schizophrenia":[175,197],"subjects,":[178],"confirming":[179],"long":[181],"held":[182],"C4A":[188],"Complement":[191],"Component":[192],"4":[193],"are":[194],"increased":[195],"while":[198],"C4B":[199],"not.":[201],"These":[202],"results":[203],"demonstrate":[204],"identify":[208],"significant":[209],"variations":[210],"not":[215],"previously":[216],"possible.":[217]}
Authors
- Matthew L. MacDonald (ORCID: https://orcid.org/0000-0002-2222-2996)
- Lambertus Klei (ORCID: https://orcid.org/0000-0003-4524-4968)
- Lorenzo Testa (ORCID: https://orcid.org/0000-0003-2782-4846)
- Kathryn Roeder (ORCID: https://orcid.org/0000-0002-8869-6254)
- David A. Lewis (ORCID: https://orcid.org/0000-0002-3225-6778)
- Anastasia Yocum
- Alesia Rengle
- Bernie Devlin
Institutions
- Scuola Superiore Sant'Anna (IT)
- University of Pittsburgh (US)
- Wagner College (US)
- Carnegie Mellon University (US)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2026-04-22
- DOI
- https://doi.org/10.64898/2026.04.20.719668
- Primary Topic
- Advanced Proteomics Techniques and Applications
- Type
- article
- Field-Weighted Citation Impact
- 0.00