PXD057211

PXD057211 is an original dataset announced via ProteomeXchange.

Title	Data-driven rescoring meets identification transfer in multi-batch isobaric labeling experiments: the best of both worlds (ProSIMSIt)
Description	Multi-batch isobaric labeling experiments are frequently applied for clinical and pharmaceutical studies of large sample cohorts. To tackle the critical issue of missing values in such studies, we introduce the ProSIMSIt pipeline. It combines the advantages of tandem mass spectrum clustering via SIMSI-Transfer and data-driven rescoring via Prosit and Oktoberfest. We demonstrate that these two tools are complementary and mutually beneficial. On large-scale cancer cohort data, ProSIMSIt increased the number of peptide spectrum matches (PSMs) by 40% on both global and phosphoproteome datasets. Furthermore, on data from proteome-wide drug-response profiling of post-translational modifications (decryptM), our pipeline substantially increased drug-PTM relations and unveils previously unseen downstream effects of drug target inhibition. ProSIMSIt is available as an open-source Python package with a simple command line interface that allows easy application to MaxQuant result files.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_04:22:41.675.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Firas Hamood
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive HF; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-25 12:32:51	ID requested
⏵ 1	2025-05-07 04:22:43	announced

Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czeka, ń, ski A, J, ę, dryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Feny, ö D, Agarwal A, Anurag M, Avtonomov D, Birger C, Birrer MJ, Boca SM, Bocik WE, Borate U, Borucki M, Burke MC, Cai S, Calinawan A, Carr SA, Carter S, Castro P, Cerda S, Chaikin M, Chan DW, Chan D, Charamut A, Chen F, Chen J, Chen L, Chen LS, Chesla D, Chheda MG, Chinnaiyan AM, Chowdhury S, Cieslik MP, Clark DJ, Cottingham S, Culpepper H, Day J, De Young S, Demir E, Dhanasekaran SM, Dhir R, Domagalski MJ, Dottino P, Druker B, Duffy E, Dyer M, Edwards NJ, Edwards R, Elburn K, Field JB, Francis A, Gabriel S, Geffen Y, Geiszler D, Gillette MA, Godwin AK, Grady P, Hannick L, Hariharan P, Hilsenbeck S, Hindenach B, Hoadley KA, Hong R, Hostetter G, Hsieh JJ, Hu Y, Ittmann MM, Jaehnig E, Jewell SD, Ji J, Jones CD, Karabon R, Ketchum KA, Khan M, Kim BJ, Krek A, Krubit T, Kumar-Sinha C, Leprevost FD, Lewis M, Li QK, Li Y, Liu H, Lubinski J, Ma W, Madan R, Malc E, Malovannaya A, Mareedu S, Markey SP, Marrero-Oliveras A, Martignetti J, McDermott J, McGarvey PB, McGee J, Mieczkowski P, Modugno F, Montgomery R, Newton CJ, Omenn GS, Paulovich AG, Perou AM, Petralia F, Piehowski P, Polonskaya L, Qi L, Richey S, Robinson K, Roche N, Rohrer DC, Schadt EE, Schnaubelt M, Shi Y, Skelly T, Sokoll LJ, Song X, Stein SE, Suh J, Tan D, Tansil D, Teo GC, Thangudu RR, Tognon C, Traer E, Tyner J, Um KS, Valley DR, Vatanian N, Vats P, Velvulou U, Vernon M, Wang LB, Wang Y, Webster A, Westbrook T, Wheeler D, Whiteaker JR, Wilson GD, Zakhartsev Y, Zelt R, Zhang H, Zhang Y, Zhang Z, Zhao G, Proteogenomic Characterization of Endometrial Carcinoma. Cell, 180(4):729-748.e26(2020) [pubmed]

10.1126/science.ade3925;

Zecha J, Bayer FP, Wiechmann S, Woortman J, Berner N, M, ü, ller J, Schneider A, Kramer K, Abril-Gil M, Hopf T, Reichart L, Chen L, Hansen FM, Lechner S, Samaras P, Eckert S, Lautenbacher L, Reinecke M, Hamood F, Prokofeva P, Vornholz L, Falcomat, à C, Dorsch M, Schr, ö, der A, Venhuizen A, Wilhelm S, M, é, dard G, Stoehr G, Ruland J, Gr, ü, ner BM, Saur D, Buchner M, Ruprecht B, Hahne H, The M, Wilhelm M, Kuster B, Decrypting drug actions and protein modifications by dose- and time-resolved proteomics. Science, 380(6640):93-101(2023) [pubmed]

10.1021/acs.jproteome.4c00967;

10.1016/j.cell.2020.01.026;

Hamood F, Gabriel W, Pfeiffer P, Kuster B, Wilhelm M, The M, ProSIMSIt: The Best of Both Worlds in Data-Driven Rescoring and Identification Transfer. J Proteome Res, 24(4):2173-2180(2025) [pubmed]

submitter keyword: Prediction,Missing Values, Isobaric Labelling, SIMSI-Transfer, Oktoberfest, MaxQuant

Bernhard Kuster
contact affiliation	Chair of Proteomics and Bioanalytics, Technical University of Munich, Bavaria, Germany
contact email	kuster@tum.de
lab head
Firas Hamood
contact affiliation	Technical University of Munich (TUM)
contact email	firas.hamood@tum.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057211

PRIDE project URI

• PRIDE
  1. PXD057211
     1. Label: PRIDE project
     2. Name: Data-driven rescoring meets identification transfer in multi-batch isobaric labeling experiments: the best of both worlds (ProSIMSIt)