PXD061696

PXD061696 is an original dataset announced via ProteomeXchange.

Title	Recombinant Protein Spectral Library (rPSL) DIA-MS Method Improves Identification and Quantification of Low-Abundance Cancer-Associated and Kynurenine Pathway Proteins
Description	Data-independent acquisition mass spectrometry (DIA-MS) is a powerful tool for quantitative proteomics, but a well-constructed reference spectral library is crucial to optimize DIA analysis, particularly for low-abundance proteins. In this study, we evaluate the efficacy of a recombinant protein spectral library (rPSL), generated from tryptic digestion of 42 human recombinant proteins, in enhancing the detection and quantification of lower-abundance cancer-associated proteins. Additionally, we generated a combined sample-specific biological-rPSL by integrating the rPSL with a spectral library derived from pooled biological samples. We compared the performance of these libraries for DIA data extraction with standard methods, including sample-specific biological spectral library and library-free DIA methods. Our specific focus was on quantifying cancer-associated proteins, including key enzymes involved in kynurenine pathway, across patient-derived tissues and cell lines. Both rPSL and biological-rPSL DIA approaches provided significantly improved coverage of lower- abundance proteins, enhancing sensitivity and more consistent protein quantification across matched tumour and adjacent noncancerous tissues from breast and colorectal cancer patients and in cancer cell lines. Overall, our study demonstrates that rPSL and biological-rPSL coupled with DIA-MS workflows, can address the limitations of both biological library-based and library-free DIA methods, offering a robust approach for quantifying low-abundance cancer-associated proteins in complex biological samples.
HostingRepository	PRIDE
AnnounceDate	2025-05-15
AnnouncementXML	Submission_2025-05-15_05:43:36.594.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shivani Krishnamurthy
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-11 06:31:15	ID requested
⏵ 1	2025-05-15 05:43:37	announced

10.1038/s42004-025-01531-0;

Krishnamurthy S, Gunasegaran B, Paul-Heng M, Mohamedali A, P Klare W, Pang CNI, Gluch L, Shin JS, Chan C, Baker MS, Ahn SB, Heng B, Recombinant Protein Spectral Library (rPSL) DIA-MS method improves identification and quantification of low-abundance cancer-associated and kynurenine pathway proteins. Commun Chem, 8(1):141(2025) [pubmed]

submitter keyword: Snap frozen tissues, rPSL, DIA-MS, Cancer- Associated Proteins, Cell Lysates, Kynurenine Pathway Proteins, Recombinant Protein Spectral Library

Seong Beom Ahn
contact affiliation	Macquarie Medical School
contact email	charlie.ahn@mq.edu.au
lab head
Shivani Krishnamurthy
contact affiliation	Macquarie University
contact email	shivani.krishnamurthy@hdr.mq.edu.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD061696
     1. Label: PRIDE project
     2. Name: Recombinant Protein Spectral Library (rPSL) DIA-MS Method Improves Identification and Quantification of Low-Abundance Cancer-Associated and Kynurenine Pathway Proteins