PXD037656

PXD037656 is an original dataset announced via ProteomeXchange.

Title	Mass spectrometry-based proteomics workflows in cancer research: the relevance of choosing the right steps. Mass Spec Methods
Description	The qualitative and quantitative description of proteome changes that condition cancer development can be achieved by liquid chromatography-mass spectrometry (LC-MS). LC-MS-based proteomics strategies are carried out according to predesigned workflows that comprise of several steps such as sample selection, sample processing including labelling, MS acquisition methods, statistical treatment and bioinformatics to understand the biological meaning of the findings and set predictive classifiers. As the choice of best options might not be straightforward, we will herein review and assess past and current proteomics approaches for the discovery of new cancer biomarkers. While some aspects of the workflows might be subjected to sample type and size, we recommend, based on our experience and on others, the use of bead-based sample preparation followed by data-independent acquisition (DIA) with label-free quantification methodologies or data-dependent acquisition (DDA) with tandem mass tags (TMT) quantification for broad proteome and phosphoproteome characterizations. Moreover, we will review major bioinformatics tools to interpret and visualize proteomics results and suggest most popular machine learning techniques for the selection of predictive biomarkers. Finally, we would like the reader of this manuscript to reflect on the approximation of proteomics strategies to clinical diagnosis and prognosis by discussing current barriers and proposals to circumvent them
HostingRepository	PRIDE
AnnounceDate	2026-02-16
AnnouncementXML	Submission_2026-02-16_11:51:16.858.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Paula Carrillo Rodríguez
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-24 00:58:02	ID requested
⏵ 1	2026-02-16 11:51:17	announced

10.3390/CANCERS15020555;

submitter keyword: mass spectrometry

proteomics

sample preparation

data-dependent acquisition (DDA)

data-independent acquisition (DIA)

workflows, data analysis

bioinformatics

María del Carmen Hernández Valladares
contact affiliation	1. Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway 2 Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain 3 Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
contact email	mariahv@ugr.es
lab head
Paula Carrillo Rodríguez
contact affiliation	Vall d'Hebron Institute of Oncolgoy
contact email	paulacrdgz@gmail.com
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/2026/02/PXD037656

PRIDE project URI

• PRIDE
  1. PXD037656
     1. Label: PRIDE project
     2. Name: Mass spectrometry-based proteomics workflows in cancer research: the relevance of choosing the right steps. Mass Spec Methods