Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Low-Abundance Serum Protein Biomarker Candidates for HCC in Patients with Liver Cirrhosis

ABSTRACT: In this study, we employed both untargeted and targeted analysis of low abundance serum proteins to identify potential biomarkers for HCC. We employed a two-phase proteomics approach to identify low abundance serum proteins as potential biomarkers for HCC.The first phase involved DDA-based untargeted proteomics analysis of serum samples from HCC cases and patients with CIRR. Label-free quantification (LFQ) was performed to identify statistically significantly differentially expressed proteins. In the second phase, a targeted proteomics analysis was conducted using PRM on the same cohort of samples targeting proteins selected in the untargeted study along with AFP and other previously reported biomarker candidates.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Serum

DISEASE(S): Adult Hepatocellular Carcinoma,Liver Cirrhosis

SUBMITTER: Habtom Ressom

LAB HEAD: Habtom Ressom

PROVIDER: PXD061721 | Pride | 2026-06-15

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	PRM_Sample_01.raw	Raw
	PRM_Sample_02.raw	Raw
	PRM_Sample_03.raw	Raw
	PRM_Sample_04.raw	Raw
	PRM_Sample_05.raw	Raw

Items per page:

1 - 5 of 90

Publications

Low-Abundance Serum Protein Biomarker Candidates for HCC in Patients with Liver Cirrhosis.

Sajid Muhammad Salman MS Varghese Rency S RS Kroemer Alexander A Ressom Habtom W HW

Journal of proteome research 20250609 7

Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality worldwide, often presenting diagnostic challenges in patients with underlying liver cirrhosis (CIRR). In this study, we employed both untargeted and targeted analysis of low-abundance serum proteins to identify potential biomarkers for HCC. In the untargeted study, we identified 15 proteins that exhibited statistically significant differential expression in HCC vs CIRR. In the targeted study, we confirmed differen ...[more]

PMID: 40490917

Similar Datasets

Quantification of calcyclin and heat shock protein 90 in sera from women with and without preeclampsia by mass spectrometry

Project description:Maternal serum levels of calcyclin and heat shock protein 90 were compared throughout pregnancy from the first trimester till term among women with preeclampsia (PE) and age-matched normotensive pregnant controls (C). Serum samples from two different studies, a nested case-control study embedded in the Rotterdam periconception cohort and the Lepra Study both conducted at the Erasmus MC in Rotterdam. They were collected in the first, second and third trimester of pregnancy in 43 patients with preeclampsia, consisting of 20 early-onset and 23 late-onset preeclampsia, and 46 normotensive pregnant controls. A serum based 2D LC-MS assay on Parallel Reaction Monitoring mode using a high resolution tribrid mass spectrometer was used to quantify both calcyclin and heat shock protein 90.

2018-11-21 | PXD009025 | Pride

Unveiling Endogenous Serum Peptides as Potential Biomarkers for Hepatocellular Carcinoma in Patients with Liver Cirrhosis

Project description:In this study, we used a comprehensive approach involving endogenous peptidome along with bioinformatics analysis, to identify and evaluate potential biomarkers for HCC. Serum samples from 40 subjects, comprising 20 HCC cases and 20 patients with liver cirrhosis (CIRR), were analyzed. Among 2568 endogenous peptides, 68 showed significant differential expression between the HCC vs. CIRR. Further analysis revealed three endogenous peptides (VMHEALHNHYTQKSLSLSPG, NRFTQKSLSLSPG, and SARQSTLDKEL) that showed far better performance compared to AFP in terms of area under the receiver operating characteristic curve (AUC), showcasing their potential as biomarkers for HCC. Additionally, endogenous peptide IAVEWESNGQPENNYKT that belongs to precursor protein Immunoglobulin heavy constant gamma 4, was detected in 100% of the HCC group and completely absent in all samples of the CIRR group, suggesting a promising diagnostic biomarker. Gene ontology and pathway analysis revealed the potential involvement of these dysregulated peptides in HCC.

2025-05-06 | PXD051029 | Pride

Proteomic signature of host response to SARS-CoV-2 infection in the nasopharynx

Project description:Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2 infection has become a global health pandemic. COVID-19 severity ranges from asymptomatic infection to severe multi-organ disease. Although the inflammatory response has been implicated in the pathogenesis of COVID-19, the exact nature of dysregulation in signaling pathways has not yet been elucidated underscoring the need for further molecular characterization of SARS-CoV-2 infection in humans. Here, we characterize the host response directly at the point of viral entry through analysis of nasopharyngeal swabs. Multiplexed high resolution mass spectrometry-based proteomic analysis of confirmed COVID-19 cases and negative controls identified 7,682 proteins and revealed significant upregulation of interferon-mediated antiviral signaling in addition to multiple other proteins that are not interferon-stimulated genes (ISGs) or well-characterized during viral infections. Downregulation of several proteasomal subunits, E3 ubiquitin ligases, and components of protein synthesis machinery was significant upon SARS-CoV-2 infection. Targeted proteomics to measure abundance levels of MX1, ISG15, Stat1, RIG-I and CXCL10, permitted differentiation of COVID-19 positive from negative cases. Phosphoproteomic analysis revealed increased phosphorylation of several proteins with known antiviral properties and as well as several proteins including CEP131, CFAP57 and xxxx that have not previously been implicated in the context of viral (or coronavirus) infections. Additionally, decreased phosphorylation levels of AKT and PKC, which have been shown to play varying role in different viral infections, were observed in infected individuals relative to controls. These data provide novel insights that add depth to our understanding of SARS-CoV-2 infection in the upper airway and help characterize a signature for this viral infection.

2021-08-09 | PXD022889 | Pride

Targeted experiment to validate genetic deletion in KO cells

Project description:Validation of genetic deletion by targeted proteomics

2023-03-04 | PXD032220 | Pride

Development of LC-FAIMS-MS and its application to lipidomics study of Acinetobacter baumannii infection

Project description:Here we present the development and application of LC-FAIMS-MS/MS based platform for untargeted lipidomics. The combination of normal phase liquid chromatography (NPLC), which can separate different types of phospholipids based on their head groups, and high-resolution MS (HRMS) offers a powerful qualitative and quantitative workflow for serum lipid profiling.We exploited this NPLC-FAIMS-HRMS to analyze the serum lipid profiles in mice infected intranasally with Acinetobacter baumannii, and developed an MS/MS matching tool to identify the detected lipids.

2025-05-07 | PXD055224 | Pride

Neurodegeneration and humoral response proteins in cerebrospinal fluid associate with pediatric-onset multiple sclerosis -- Validation

Project description:The pathogenesis of multiple sclerosis (MS) remains to be elucidated. Pediatric-onset MS (POMS) represents the earliest stage of the disease. CSF proteins in POMS may therefore provide causal information. Therefore, the aim of the current study was to analyze CSF proteins in children with an initial CNS acquired demyelinating syndrome (ADS) and to make a comparison between POMS and monophasic ADS (mADS). Patients were selected from two prospective pediatric ADS studies. Liquid chromatography-mass spectrometry was performed in a Dutch discovery cohort (POMS n=28; mADS n=39). Parallel reaction monitoring-mass spectrometry was performed on selected proteins more abundant in POMS with ≥ 8 unique peptides in a combined Dutch and Canadian validation cohort (POMS n=48; mADS n=106).

2022-09-30 | PXD031022 | Pride

Comparison of targeted mass spectrometry techniques with an immunoassay: a case study for HSP90 alpha, part 1

Project description:We developed 2D-LC-MS/MS-based SRM and PRM assays to measure HSP90 alpha in serum and compared the results to a commercially available immunoassay (ELISA). Serum samples were trypsin-digested and fractionated by SCX chromatography prior to SRM and PRM measurements. PRM data obtained by high-resolution mass spectrometry correlated better with ELISA measurements than SRM data measured on a triple quadrupole mass spectrometer. While all three methods (SRM, PRM, ELISA) were able to quantify HSP90 alpha in serum at the ng/mL level, the use of PRM on a high-resolution mass spectrometer reduced variation. To rule out that the observed differences in SRM and PRM are due to different mass spectrometry systems, the SCX fractions were measured on the same high-resolution instrument (Orbitrap) in the ion trap mode (IT-PRM); such measurements showed that intense co-eluting signals were present in the SRM method, but these interfering peaks were eliminated in the high-resolution PRM mode. Thus, this report shows that it is possible to measure ng/mL levels of HSP90 alpha in a reproducible, selective and sensitive way using PRM. This opens up the possibility to quantify low levels of multiple proteins in complex samples based on a fractionation strategy on tryptic peptides followed by SRM and PRM.

2018-07-05 | PXD006618 | Pride

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes

Project description:Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with key host proteins and processes.

2022-01-20 | PXD025817 | Pride

Exercise-Associated Microbial Metabolites Prevent Skeletal Muscle Atrophy in Adult Mice

Project description:We previously reported that skeletal muscle adaptation to regular exercise requires a healthy gut microbiome, contributing to growing evidence that some exercise benefits are mediated by microbiome-derived metabolites. Here, to identify such exercise-associated microbial metabolites, we transfer cecal contents from exercise-trained donor mice into exercise-naïve recipient mice undergoing unilateral hindlimb immobilization. Recipients of cecal material from exercise-trained donors exhibit less muscle atrophy compared with those receiving transfers from sedentary donors. Untargeted metabolomics reveal metabolites enriched in cecal content, serum, and muscle of recipients from exercise-trained donors, consistent with microbial origin. Oral administration of two such metabolites (pipecolic acid and succinate) attenuates muscle atrophy and preserves muscle function in exercise-naïve mice, potentially by enhancing cellular energy status and translational capacity. These findings further define the gut microbiome-skeletal muscle axis and provide evidence that exercise-associated microbial metabolites serve as a novel class of exercise mimetics for treating conditions responsive to physical activity.

2026-05-27 | PXD077599 | Pride

Genome-wide analysis of gene expression in human iPSCs and NSCs engineered by safe-harbor TALEN-mediated gene targeting

Project description:Human iPSCs and NSCs were engineered by AAVS1 and/or C13 safe-harbor TALENs which mediated targeted integration of various reporter genes at single or dual safe-harbor loci. Multiple clones of targeted human iPSCs were used to compare with parental untargeted NCRM5 iPSCs. Polyclonal targeted human NSCs were used to compare with their parental untargeted NCRM1NSCs or H9NSCs. Total RNA obtained from targeted human iPSCs or NSCs compared to untargeted control iPSCs or NSCs.

2014-09-01 | E-GEOD-55975 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data