PXD062853-1

PXD062853 is an original dataset announced via ProteomeXchange.

Title	Order 37630 - Juan Francisco Tamez Fernandez 2025-01-31
Description	Dear Juan Francisco, Dear Pablo we finished analyzing your latest order. In short, the data looks great! Your neg. controls behave as expected and cluster tightly. The probe (JT-195) enriches for a lot of prey proteins. Many are shared with the cysteinome control. Replicates are very similar. Kind regards, Tobias *** Always reply to workflow results by using the order comments function in b-fabric! Please do NOT send emails to proteomics@ or individual people involved in workflow processing (order coach). *** 1 Downloading results packaged in a b-fabric workunits [https://fgcz-bfabric.uzh.ch/wiki/tiki-index.php?page=WorkunitDownload] 2 General data processing logic LC-MS raw data => Dia-NN => proLFQ/SAINTexpress => Interaction proteomics report |-> ScaffoldDIA 3 Workunit guidance 3.1 Dia-NN The main output of Dia-NN is called _report.tsv and is a precursor-centric table in long format. It describes chromatographic features mapped to peptides. This file can be loaded in downstream processing tools like DIAgui [https://github.com/mgerault/DIAgui] or amica [https://github.com/tbaccata/amica] or a spread sheet calculator. For direct exploration of Dia-NN output we recommend using the so called matrix files named _report._matrix.tsv These files summarize the main report for pr (precursor), pg (protein group), or gg (gene group) level by the maxLFQ algorithm in matrix-like tables (feature x sample). Be aware that maxLFQ estimates are tailored towards comparisons between experimental conditions (also called horizontal comparisions). They should not be used for rank sorting proteins, as estimator for the abs. amount of proteins. For this special estimators like topN or iBAQ should be used (available in DIAgui) [https://github.com/vdemichev/DiaNN] 3.2 SAINTexpress The main interaction scoring results are summarized in the interaction proteomics report. This report is named SaintExpressReport*_.html and can be viewed in any web browser. All numbers shown in the report are extracted from the SAINTexpress output which is available as DIANN__data.xlsx. The list tab summarizes all bait-prey pairs scored by the ML model for the different comparisons. We judge preys by co-filtering in effect size (FoldChange) and significance dimension (BFDR). Suitable cutoffs are very experiment/data dependent, especially in the effect size dimension. We tend to use BFDR <5% and FC >1 as initial thresholds. Refiltering according to known interactions is always a good approach to arrive at meaningful candidate lists. The ORA_Bait__.txt files can be used to upload candidate lists to web tools like String-DB [https://string-db.org] for network/enrichment analysis. They are always filtered according to parameters shown in the interaction proteomics report. [https://saint-apms.sourceforge.net/Main.html] 3.3 ScaffoldDIA The main output of protein identification and quantification performed by Dia-NN is also available as ScaffoldDIA formatted file (_result.sdia). ScaffoldDIA allows to browse LC-MS datasets using a GUI. The ScaffoldDIA app can be downloaded free of charge from [https://www.proteomesoftware.com/products/scaffold-dia] and runs on all mayor (OS) platforms. Be aware that Dia-NN matrix files might be different to ScaffoldDIA outputs, since ScaffoldDIA takes the Dia-NN main report (which describes chromatographic features mapped to peptides) and recalculates protein inference, reestimate protein quantifies. The output in the app also heavily depends on the set filter options. We do NOT recommend using ScaffoldDIA exports for statistical downstream processing, but only for interactive explorative analysis.
HostingRepository	PRIDE
AnnounceDate	2025-09-22
AnnouncementXML	Submission_2025-09-21_16:10:16.114.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tobias Kockmann
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-11 07:12:49	ID requested
⏵ 1	2025-09-21 16:10:17	announced

10.1021/jacs.5c07109;

Tamez-Fern, á, ndez JF, Steven CF, Nguyen J, Rivera-Fuentes P, Potent Inducers of Paraptosis through Electronic Tuning of Hemicyanine Electrophiles. J Am Chem Soc, 147(36):32571-32579(2025) [pubmed]

submitter keyword: probe

Rivera Fuentes
contact affiliation	Faculty of Science (MNF), Department of Chemistry, University of Zurich (UZH)
contact email	pablo.riverafuentes@uzh.ch
lab head
Tobias Kockmann
contact affiliation	Functional Genomics Center Zurich
contact email	tobias.kockmann@fgcz.ethz.ch
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/2025/09/PXD062853

PRIDE project URI

• PRIDE
  1. PXD062853
     1. Label: PRIDE project
     2. Name: Order 37630 - Juan Francisco Tamez Fernandez 2025-01-31