High-performance serum metabolite characterization by NPELDI-MS. (A) Illustration of NPELDI-MS. The Upper digital image shows the MS chips after microarray printing, and the Bottom image was recorded during NPELDI-MS. (Scale bar, 5 mm.) (B and C) Elemental mappings of the nanoparticle-analyte (His in B and BSA in C) hybrids are shown with O in yellow, Fe in purple, and C in green, respectively. The insert images were high-angle annular dark-field images of nanoparticle-analyte hybrids. (Scale bars, 200 nm.) (D) The similarity scores between 1,000 nL of pristine serum and its dilutions by 10-to 1,000-fold using 100 to 1 nL of pristine serum. The error bars were calculated as SD of five repeated experiments. (E and F) Intensities of five molecular peaks (gray line for [Ala + Na] + at an m/z of 112.04, red line for [Lys + Na] + at an m/z of 169.09, blue line for [Arg + Na] + at an m/z of 197.19, green line for [Glc + Na] + at an m/z of 203.05, and purple line for [Suc + Na] + at an m/z of 365.11) for intrachip (ten replicates per sample) in E and interchip (five chips for 5 d, one chip per day) detection in F, respectively. (G and H) CV distribution of intensities for the apparent molecular peaks in ten serum samples (five HDs denoted as HD1 to HD5 and five BrCa patients denoted as BrCa1 to BrCa5) for intrachip (ten replicates per sample) in G and interchip detection (five chips for 5 d, one chip per day) in H, respectively.

High-performance serum metabolite characterization by NPELDI-MS. (A) Illustration of NPELDI-MS. The Upper digital image shows the MS chips after microarray printing, and the Bottom image was recorded during NPELDI-MS. (Scale bar, 5 mm.) (B and C) Elemental mappings of the nanoparticle-analyte (His in B and BSA in C) hybrids are shown with O in yellow, Fe in purple, and C in green, respectively. The insert images were high-angle annular dark-field images of nanoparticle-analyte hybrids. (Scale bars, 200 nm.) (D) The similarity scores between 1,000 nL of pristine serum and its dilutions by 10-to 1,000-fold using 100 to 1 nL of pristine serum. The error bars were calculated as SD of five repeated experiments. (E and F) Intensities of five molecular peaks (gray line for [Ala + Na] + at an m/z of 112.04, red line for [Lys + Na] + at an m/z of 169.09, blue line for [Arg + Na] + at an m/z of 197.19, green line for [Glc + Na] + at an m/z of 203.05, and purple line for [Suc + Na] + at an m/z of 365.11) for intrachip (ten replicates per sample) in E and interchip (five chips for 5 d, one chip per day) detection in F, respectively. (G and H) CV distribution of intensities for the apparent molecular peaks in ten serum samples (five HDs denoted as HD1 to HD5 and five BrCa patients denoted as BrCa1 to BrCa5) for intrachip (ten replicates per sample) in G and interchip detection (five chips for 5 d, one chip per day) in H, respectively.

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Significance Breast cancer (BrCa) is the most common cancer worldwide, and high-performance metabolic analysis is emerging in diagnosis and prognosis of BrCa. Here, we used nanoparticle-enhanced laser desorption/ionization mass spectrometry to record serum metabolic fingerprints of BrCa in seconds, achieving high reproducibility and low consumption...

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... Serum Metabolite Characterization by NPELDI-MS. To improve the analytical speed, sample consumption, and reproducibility of LDI-MS, we conducted highperformance serum metabolic fingerprinting by NPELDI-MS (Fig. 1A). The ferric nanoparticles were prepared using a modified low-cost solve-thermal method (Materials and Methods), showing the designed surface roughness structure as an ideal matrix for NPELDI-MS. Due to the size-selective trapping and affinity-based cationization of metabolites by the surface nanostructures of nanoparticles (SI ...
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... (Fig. 1A). The ferric nanoparticles were prepared using a modified low-cost solve-thermal method (Materials and Methods), showing the designed surface roughness structure as an ideal matrix for NPELDI-MS. Due to the size-selective trapping and affinity-based cationization of metabolites by the surface nanostructures of nanoparticles (SI Appendix, Fig. S1), NPELDI-MS allowed direct detection of metabolites from the interference of proteins and salts in serum (SI Appendix, Fig. S2) with minimum sample treatment at high speed (∼30 s per sample). To validate the size-selective trapping of nanoparticles, histamine (His) and bovine serum albumin (BSA), as representatives for metabolites (MW ...
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... were mixed with nanoparticles to form nanoparticle-analyte hybrids. Consequently, the elemental mapping analysis of the nanoparticle-analyte hybrids showed a significantly higher molecular size-selective trapping rate (defined as the ratio of carbon signal intensity on the nanoparticles to the background) for His than for BSA (P < 0.001; Fig. 1 B and C and SI Appendix, Table S1). Importantly, the NPELDI-MS process afforded fast analytical speed with 2 s per sample (with 2,000 laser shots at a pulse frequency of 1,000 Hz; Materials and Methods), which could be coupled with on-chip microarray (384 samples per chip) to achieve automatic large-scale sample screening (Fig. ...
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... BSA (P < 0.001; Fig. 1 B and C and SI Appendix, Table S1). Importantly, the NPELDI-MS process afforded fast analytical speed with 2 s per sample (with 2,000 laser shots at a pulse frequency of 1,000 Hz; Materials and Methods), which could be coupled with on-chip microarray (384 samples per chip) to achieve automatic large-scale sample screening (Fig. ...
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... note, we calculated the cosine similarity score of apparent molecular peaks (with average intensity of >500) between native serum and its dilutions using 1 to 100 nL of serum to identify the minimum sample volume for detection. We obtained qualified similarity scores above 0.771 using 10 to 100 nL of serum (Fig. 1D) due to the efficient absorption and transfer of laser energy for enhanced detection sensitivity by two to six orders (compared with organic matrices; SI Appendix, Fig. S3 and Table S2). Specifically, 108 apparent molecular peaks of metabolites were observed, likely owing to the high sensitivity of NPELDI-MS, which helped to form a ...
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... Subsequently, we validated these seven metabolites as L-glyceric acid (GA), nicotinamide (NAM), His, uracil (Ura), thymine (Thy), 3,4-dihydroxybenzylamine (DB), and dehydrophenylalanine (DP) (24,25), respectively, through accurate MS using Fourier transform ion cyclotron resonance (FT-ICR)-MS or MS/MS using time-of-flight (TOF)-MS (SI Appendix, Fig. S10 and Table S10). Among them, His, Ura, Thy, DB, and DP were down-regulated (P < 0.05), while GA and NAM were up-regulated (P < 0.001) in BrCa compartments compared with in BBD and HD compartments (Fig. ...
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... studies (5,12,(44)(45)(46)(47). To determine the minimum sample number to conduct machine learning, we used a power analysis of ten samples (five/five BrCa/non-BrCa compartments) as a pilot study and obtained a power of > 0.8 with the sample number of 200 (100/100 BrCa/non-BrCa compartments) at a false discovery rate of 0.10 (SI Appendix, Fig. S11), validating that the machine learning results were at a sufficient confidence ...

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... Amino acid metabolites, including tryptophan and its associated pathway metabolites, arginine, proline, histidine, 5-oxoproline, kynurenine, nicotinate, and nicotinamide, have been suggested as potential early diagnostic biomarkers for breast cancer [9][10][11][12][13][14][15][16][17]. The catabolism of tryptophan, an essential amino acid, is associated with the immune system, and tryptophan has been studied in the context of cancer [15]. ...
... Several studies have suggested the potential of nicotinic acid and nicotinamide as biomarkers for breast cancer diagnosis. Huang, et al. [12] reported that serum levels of nicotinic acid and nicotinamide were significantly higher in patients with breast cancer than in individuals with benign breast disease or healthy controls. However, Zhang, et al. [17] reported a significant decrease in serum nicotinamide levels in breast cancer. ...
... Regarding nucleic acid metabolism, increased plasma hypoxanthine and decreased serum uracil levels have been reported [12,14,41]. Hypoxanthine is related to purine metabolism. ...
... Gamma = 'scale' uses a heuristic based on the number of features, ensuring an optimal range for γ. Class weight was set to 'balanced' to compensate for any imbalance in the dataset [33,34]. The grid search aimed to balance model complexity and margin separation between the cancer and control groups. ...
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Breast cancer remains a major public health concern, and early detection is crucial for improving survival rates. Metabolomics offers the potential to develop non-invasive screening and diagnostic tools based on metabolic biomarkers. However, the inherent complexity of metabolomic datasets and the high dimensionality of biomarkers complicates the identification of diagnostically relevant features, with multiple studies demonstrating limited consensus on the specific metabolites involved. Unlike previous studies that rely on singular feature selection techniques such as Partial Least Square (PLS) or LASSO regression, this research combines supervised and unsupervised machine learning methods with random sampling strategies, offering a more robust and interpretable approach to feature selection. This study aimed to identify a parsimonious and robust set of biomarkers for breast cancer diagnosis using metabolomics data. Plasma samples from 185 breast cancer patients and 53 controls (from the Cooperative Human Tissue Network, USA) were analyzed. This study also overcomes the common issue of dataset imbalance by using propensity score matching (PSM), which ensures reliable comparisons between cancer and control groups. We employed Univariate Naïve Bayes, L2-regularized Support Vector Classifier (SVC), Principal Component Analysis (PCA), and feature engineering techniques to refine and select the most informative features. Our best-performing feature set comprised 11 biomarkers, including 9 metabolites (SM(OH) C22:2, SM C18:0, C0, C3OH, C14:2OH, C16:2OH, LysoPC a C18:1, PC aa C36:0 and Asparagine), a metabolite ratio (Kynurenine-to-Tryptophan), and 1 demographic variable (Age), achieving an area under the ROC curve (AUC) of 98%. These results demonstrate the potential for a robust, cost-effective, and non-invasive breast cancer screening and diagnostic tool, offering significant clinical value for early detection and personalized patient management.
... 6,7 Recent metabolomic analyses of various cancers, including lung, liver, colorectal, bladder, breast, and endometrial malignancies, have described biomarkers derived from samples including tissues, blood, urine, and saliva. [8][9][10][11][12][13][14] For patients with cervical cancer, predictive, diagnostic, and prognostic biomarkers have been reported in urine, blood, cervical canal lavage fluid, and tissues. [15][16][17][18][19][20][21][22] Despite the clear value of exploring metabolomics-based biomarkers in cervical cancer, there is a paucity of cervical mucus-derived ancillary biomarkers that would help to differentiate between various premalignant lesions and invasive cancer. ...
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Approximately 660,000 women are diagnosed with cervical cancer annually. Current screening options such as cytology or human papillomavirus testing have limitations, creating a need to identify more effective ancillary biomarkers for triage. Here, we evaluated whether metabolomic analysis of cervical mucus metabolism could be used to identify biomarkers of cervical intraepithelial neoplasia (CIN) and cervical cancer. The case–control group consisted of 181 CIN, 69 squamous cell carcinoma (SCC) patients, and 48 healthy controls in the primary cohort. We undertook metabolomic analyses using ultra‐HPLC–tandem mass spectrometry. Univariate and multivariate analyses were carried out to profile metabolite characteristics, and receiver operating characteristic (ROC) analysis identified biomarker candidates. Five metabolites conferred the highest discriminatory power for SCC: oxidized glutathione (GSSG) (area under the ROC curve, 0.924; 95% confidence interval, 0.877–0.971), malic acid (0.914, 0.859–0.968), kynurenine (0.884, 0.823–0.945), GSSG/glutathione (GSH) (0.936, 0.892–0.979), and kynurenine/tryptophan (0.909, 0.856–0.961). Malic acid was the best marker for detection of CIN2 or worse (0.858, 0.793–0.922) and was a clinically useful metabolite. We confirmed the reproducibility of the results by validation cohort. Additionally, metabolomic analyses revealed eight pathways strongly associated with cervical neoplasia. Of these, only the tricarboxylic acid cycle was strongly associated with all CINs and cancer, indicating active energy production. Aberrant arginine metabolism by decreasing arginine and increasing citrulline might reduce tumor immunity. Changes in cysteine‐methionine and GSH pathways might drive the initiation and progression of cervical cancer. These results suggest that metabolic analysis can identify ancillary biomarkers and could improve our understanding of the pathophysiological mechanisms underlying cervical neoplasia.
... SMF machine learning is an efficient readout to differentiate non-BrCa from BrCa. 21 In this study, magnesium, aluminum, and lanthanum ternary hydroxides are loaded on zeolite to prepare a MALZ (Mg-Al-La-zeolite) composite and used to enrich phosphorylated metabolites. After parameter optimizations, the comprehensive analysis of phosphorylated metabolites in liver cancer serum samples is carried out via liquid chromatography−mass spectrometry (LC−MS). ...
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... 14 Peripheral blood tumor biomarkers are readily accessible biomarkers and their roles in cancer prevention and treatment, such as plasma metabolic fingerprinting, have been extensively explored. 15,16 Researchers have explored the clinical significance of platelet-to-lymphocyte ratio (PLR) for the prediction of prognosis in bladder cancer patients, and the prognostic value of IL-6 has been evaluated in other tumors. 17,18 However, no studies have explored the prognostic value of the combination of PLR and IL-6 in bladder cancer. ...
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... While, Gajda-Walczak et al. [257] utilise surface plasmon resonance and quartz crystal microbalance with energy dissipation tests for the detection of BRCA1 mutations. Additionally, Huang et al. [258] introduce nanoparticle-enhanced laser desorption/ionisation MS for the detection of metabolite markers in BC. These advancements showcase a diverse range of technologies poised to enhance our understanding, detection and diagnosis of BC. 1D SDS-PAGE, one-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis; 2-DE, two-dimensional gel electrophoresis; 2D-DIGE, two-dimensional difference gel electrophoresis; BC, breast cancer; ELISA, enzyme-linked immunosorbent assay; ELLA, sandwich enzyme-linked lectin assay; ICAT, isotope-coded affinity tag; LC-MS/MS, liquid chromatography-tandem mass spectrometry; MALDI-TOF/MS, matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry; MRM-MS, multiple reaction monitoring mass spectrometry; TNBC, triple-negative breast cancer; WB, Western blotting. ...
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... Higher levels of glutamate in breast cancer patients suggest it plays an important role in fatty acids overproduction [41,42]. Histidine association with BC has been corroborated by Huang et al [43]. Additionally, this team of researchers applied a neural network model on a panel of seven saliva biomarkers to predict the probability of being diagnosed as BrCa-positive breast cancer and attained an AUC of 86.5. ...
... Additionally, this team of researchers applied a neural network model on a panel of seven saliva biomarkers to predict the probability of being diagnosed as BrCa-positive breast cancer and attained an AUC of 86.5. The 7-metabolite panel consists of L-glyceric acid, nicotinamide, histamine, uracil, thymine, 3,4-dihydroxybenzyl amine and dehydro phenylalanine [43]. ...
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