Primary carnitine deficiency is an autosomal recessive disorder caused by loss-of-function variants in the SLC22A5 gene, which sits on chromosome 5q31.1 and encodes a protein called organic cation transporter 2, or OCTN2. This transporter is the gatekeeper of carnitine homeostasis: it pumps carnitine into cells across the plasma membrane and reabsorbs it in the renal proximal tubules, maintaining intracellular free carnitine concentrations 20 to 50 times higher than those outside the cell. When both copies of the gene are disabled, carnitine floods out of the body in urine and cells are starved of a molecule they desperately need to import long-chain fatty acids into mitochondria for beta-oxidation, the metabolic pathway that supplies energy during fasting and prolonged exertion.

The clinical consequences are stark. Roughly half of affected children develop hypoketotic hypoglycemia between 3 months and 2 years of age, a dangerous combination of low blood sugar and absent ketone bodies that can spiral into hepatic encephalopathy, lethargy, and hyperammonemia. The other half present between 2 and 4 years old with skeletal muscle weakness, poor exercise tolerance, cardiomyopathy, and arrhythmias. In severe cases, sudden death can occur, and multiple unexplained deaths among young adults in the Faroe Islands, where the disorder affects as many as 1 in 297 people, have been attributed to untreated primary carnitine deficiency. Yet the condition is also one of the most treatable inherited metabolic disorders known: early diagnosis and oral L-carnitine supplementation, typically at 50 to 100 milligrams per kilogram per day, can prevent irreversible damage entirely.

The screening pipeline described in the study relies on tandem mass spectrometry, or MS/MS, to measure free carnitine, abbreviated C0, in dried blood spots collected from newborns within 3 days of birth. Following Chinese expert consensus, the team used a cutoff of 10 micromoles per liter. Of the 439,486 newborns screened over ten years, 1,518, or 0.35 percent, fell below that threshold on the initial test. Nearly all of them, 1,517 infants, were recalled for re-screening, and 154 showed persistently low C0 levels. Of the 152 who completed full diagnostic evaluation, 20 received a clinically relevant diagnosis, a diagnostic yield of 13.16 percent. Seventeen were diagnosed with primary carnitine deficiency, yielding a screening-detected prevalence in Yancheng of 1 in 25,852, while three cases traced back to maternal carnitine deficiency transmitted through the placenta rather than an inherited defect in the infant.

The numbers reveal the central challenge of screening for this disease. Carnitine crosses the placenta freely during pregnancy, and neonatal levels are strongly shaped by maternal factors, so a normal mother can partially buffer a genuinely affected newborn, keeping the infant’s C0 above the minimum value on day 3. Physiological carnitine decline during pregnancy, premature sample collection, insufficient intake from exclusive breastfeeding, prematurity, low birth weight, and cesarean section all inflate the false-positive rate. The statistical analysis made this tension visible: the PCD group’s median C0 fell from 7.33 micromoles per liter at initial screening to 4.98 at re-screening, a significant drop, while the false-positive group’s median barely moved from 8.45 to 8.22, a non-significant change. The maternal deficiency group, unusually, rose from 4.33 to 4.98. But the ranges overlapped across all three groups, which means C0 measurements alone cannot settle a diagnosis.

That is where genetics entered the picture. The team sequenced the exons and flanking intronic regions of SLC22A5 in recalled newborns using the DNBSEQ-T7 platform at an average depth of at least 200-fold, then validated every variant by Sanger sequencing and classified pathogenicity under American College of Medical Genetics and Genomics guidelines. Fifteen of the 17 PCD infants carried two pathogenic variants, four of them homozygous, giving molecular confirmation of the biochemical picture. Across these patients, 32 variants spanning 10 distinct sites were identified, all in exonic regions, and missense changes dominated. One variant stood out: c.1400C>G, which swaps a serine for a cysteine at position 467 of the OCTN2 protein, accounted for 13 of the 32 variants, or 40.63 percent, making it the clear hotspot in this region of Jiangsu Province.

The hotspot finding carries real practical weight, because SLC22A5 variant spectra differ sharply across ethnic groups and regions. The common variant in Italy is c.505C>T; in the United States it is c.136C>T; and c.1400C>G ranks among the most frequent in Japan and has not been reported in non-East Asian populations. Large-scale Chinese studies have flagged c.1400C>G, c.51C>G, and c.760C>T as common, but with regional variation. In Yancheng, c.1400C>G towered over the second most frequent variant, c.51C>G at 21.88 percent, while c.760C>T appeared only once. Knowing which variants dominate locally allows laboratories to build faster, cheaper targeted molecular probes rather than sequencing the entire gene for every recalled infant.

The study also confronted the limits of genetic testing head-on. Two of the 17 PCD infants carried only one detectable variant, yet their C0 levels stayed below 10 micromoles per liter across three consecutive measurements with adequate feeding, their mothers had normal carnitine levels, and no secondary cause could be found, supporting a clinical diagnosis of PCD. This is not unusual: sequencing that covers only coding regions and 10 base pairs of flanking intronic sequence cannot detect variants in regulatory or deep intronic regions, nor methylation changes. Previous research found pathogenic variants in only 84 percent of alleles among people with impaired fibroblast carnitine transport, and in one large series only 56.4 percent of suspected PCD individuals carried biallelic variants. The authors therefore insist that diagnosis must rest on combined biochemical and genetic evaluation rather than either alone.

Follow-up, ranging from 18 months to 10 years, showed the payoff of early detection. None of the diagnosed children experienced acute metabolic decompensation, and all but one showed normal intellectual, motor, and growth development; the exception had poor exercise tolerance. Four families chose not to medicate their asymptomatic children but committed to avoiding fasting, infection, and prolonged strenuous exercise, the classic triggers of metabolic crisis. Among the three maternal deficiency cases, two mothers were themselves found to carry the c.1400C>G variant in homozygous form and were diagnosed with PCD, underscoring how newborn screening can cascade into diagnoses in asymptomatic adults who remain at risk of sudden cardiac death.

Perhaps the most forward-looking result came from a single recurrence-risk family. Their previous child carried two heterozygous SLC22A5 variants, c.865C>T, a premature stop codon, and c.1400C>G, inherited from the mother and father respectively. Sanger sequencing of amniotic fluid DNA in the next pregnancy revealed only the maternal variant, meaning the fetus had an extremely low probability of disease given the autosomal recessive inheritance and the parents’ normal phenotypes. The couple continued the pregnancy, and the newborn’s screening C0 fell within the normal range with normal follow-up. The authors are careful to frame this as a case illustration rather than general evidence, but it demonstrates that SLC22A5 testing can anchor prenatal diagnosis and informed reproductive counseling for families who already know the fear of this disease, offering certainty at a moment when it matters most.

Subject of Research: Newborn screening and prenatal genetic diagnosis of primary carnitine deficiency caused by SLC22A5 variants

Article Title: Newborn Screening of Primary Carnitine Deficiency and Prenatal Genetic Diagnosis for a Recurrence‐Risk Family

Article References: Sun, H., Zheng, J., Zhou, C., Chen, H., Zhang, L., Li, X., Bao, D., Yang, F., & Liu, J. (2026). Newborn Screening of Primary Carnitine Deficiency and Prenatal Genetic Diagnosis for a Recurrence‐Risk Family. Molecular Genetics & Genomic Medicine, 14(10), Article e70316. https://doi.org/10.1002/mgg3.70316

Image Credits: AI Generated

DOI: 10.1002/mgg3.70316

Keywords: primary carnitine deficiency, newborn screening, SLC22A5, OCTN2, tandem mass spectrometry, prenatal diagnosis, genetic testing, carnitine transporter, hypoketotic hypoglycemia, L-carnitine supplementation, autosomal recessive inheritance, China

A new study from researchers at the Korea Food Research Institute, published in Food Science and Biotechnology, offers one of the most detailed answers yet for aging bodies. Led by Yu Ra Lee and corresponding author Yoonsook Kim, the team used targeted tandem mass spectrometry to track CML and CEL across five compartments in aged mice: blood plasma, kidney, liver, brain, and ileum, the final segment of the small intestine where most nutrient absorption occurs. The results reveal a strikingly uneven landscape, with dietary CML driving dramatic accumulations in some tissues while leaving others seemingly untouched, and with blood levels telling only a partial story about what is happening deep inside organs.

The experimental design was straightforward but technically demanding. Aged mice received a diet supplemented with CML, allowing the researchers to follow the fate of a single, well-defined dietary glycation product rather than the complex cocktail found in heat-processed foods. A second group received FPS-ZM1, a synthetic compound that blocks the receptor for advanced glycation end products, known as RAGE, a cell-surface protein that binds AGEs and triggers inflammatory signaling. By comparing these groups against controls, the researchers could disentangle how much of the tissue burden came from the diet itself and how blocking the AGE receptor might alter the picture.

The mass spectrometry approach deserves attention because quantifying AGEs is notoriously difficult. CML and CEL are small, chemically similar modifications of lysine, and tissues contain a bewildering array of proteins that may carry them. Targeted tandem mass spectrometry, often abbreviated LC-MS/MS when coupled to liquid chromatography, works by first separating the compounds chromatographically and then fragmenting them in the instrument, monitoring specific parent-to-fragment ion transitions that act like molecular fingerprints. This selective monitoring, typically run in multiple reaction monitoring mode, allows the method to distinguish CML from the sea of other molecules in a tissue digest and to quantify it against stable isotope-labeled internal standards, delivering accuracy that older colorimetric or antibody-based assays could not match.

What the numbers showed was remarkable. Compared with control animals, mice fed dietary CML accumulated 3.78 times more CML in their kidneys and a striking 10.26 times more in the ileum. CEL, which was not directly supplemented but can form downstream from related carbonyl chemistry, also rose significantly, increasing 2.33-fold in kidney and 1.69-fold in ileum. The ileum result is perhaps the most intuitive: as the site of absorption, the intestinal wall sees the highest concentration of anything arriving from the gut lumen, and the new data confirm that dietary CML does not simply pass through but accumulates in the tissue itself. The kidney, meanwhile, is a known hotspot for AGE deposition in aging and diabetes, and these findings reinforce its status as a primary sink for glycation products.

Just as telling were the tissues where the signal was weaker. The liver and brain did not show the same dramatic fold-changes, suggesting that tissue-selective barriers and metabolism shape the distribution of dietary AGEs. The blood-brain barrier, which tightly regulates what enters the central nervous system, may filter out a substantial share of circulating glycation products, though the receptor RAGE is known to mediate transport of certain ligands across that barrier under some conditions. The liver, as the body’s principal detoxification organ, may clear or process absorbed AGEs efficiently. Whatever the mechanisms, the study makes clear that a dietary bolus of CML does not blanket the body uniformly; it concentrates where physiology allows.

The correlation analysis added a layer of nuance with real clinical implications. Plasma CML levels correlated positively with CML levels in the brain, with a Spearman coefficient of 0.574 and a p-value of 0.002, and with the ileum, at a coefficient of 0.414 and p equal to 0.036. In other words, a blood draw gave a statistically meaningful window into glycation burden in at least two organs. But plasma CEL told a different story entirely, showing no significant correlations with any tissue measured. For researchers and clinicians who rely on circulating AGE markers as proxies for whole-body or organ-specific burden, this is a caution: the reliability of a blood marker depends on which AGE you are measuring and which tissue you care about.

The FPS-ZM1 arm of the experiment pointed toward a possible intervention strategy. Mice that received the RAGE antagonist showed lower AGE levels in selected tissues compared with animals that did not. RAGE is not merely a passive binding protein; when engaged by AGEs, it activates inflammatory and oxidative stress pathways that have been implicated in diabetic complications, kidney disease, cardiovascular damage, and neurodegeneration. Blocking the receptor has previously been shown in other mouse models to reduce amyloid-beta-related brain pathology, and the new findings suggest that RAGE signaling may also influence how glycation products distribute and persist in aging tissue. The authors describe the association carefully, and the study was not designed as a therapeutic trial, but the pattern supports the idea that the AGE-RAGE axis is a meaningful lever in age-related tissue accumulation.

Why does this matter for human health? The modern Western diet, rich in heat-processed and industrially prepared foods, delivers a substantial daily load of preformed AGEs, and epidemiological and mechanistic studies have linked high dietary AGE intake to obesity, early renal pathology, and chronic inflammation. Prior work with isotopically labeled dietary CML in mice demonstrated that a fraction of orally administered CML is absorbed and distributed to organs, but questions remained about how aging changes that distribution and whether blood measurements could stand in for tissue measurements. The new study addresses both gaps in aged animals, showing that the aging kidney and gut are particularly receptive to dietary CML and that plasma markers must be interpreted with tissue context in mind.

There are, of course, limits to how far mouse data can be extrapolated. The study used a purified CML supplement rather than the heterogeneous AGE mixture found in actual foods, and the doses, metabolism, and lifespan of laboratory mice differ from those of humans. The researchers also note that endogenous AGE formation, driven by oxidative stress and reactive carbonyls such as methylglyoxal and glyoxal, proceeds alongside dietary intake and can complicate attribution. Still, by applying a rigorously validated targeted mass spectrometry method across five biological compartments in aged animals, the Korean team has produced a map of where dietary glycation products actually go, and that map argues for caution in reading blood tests, continued scrutiny of AGE-rich diets, and sustained interest in RAGE as a target for protecting aging organs from the slow chemical wear of glycation.

Subject of Research: Tissue-selective accumulation of dietary advanced glycation end products in aged mice

Article Title: Tissue-selective accumulation of carboxymethyllysine and carboxyethyllysine after dietary carboxymethyllysine exposure in aged mice revealed by targeted tandem mass spectrometry

Article References: Lee, Y. R., Cho, S., Ha, S. K., Ahn, J., Kim, D., Choi, I., & Kim, Y. (2026). Tissue-selective accumulation of carboxymethyllysine and carboxyethyllysine after dietary carboxymethyllysine exposure in aged mice revealed by targeted tandem mass spectrometry. Food Science and Biotechnology. https://doi.org/10.1007/s10068-026-02332-4

Image Credits: AI Generated

DOI: 10.1007/s10068-026-02332-4

Keywords: advanced glycation end products, carboxymethyllysine, carboxyethyllysine, tandem mass spectrometry, aging, kidney, ileum, RAGE, dietary AGEs, plasma biomarkers, glycation, mice study

The study, published in BMC Pediatrics, was led by a team at the Women and Children’s Medical Center of Shenzhen Maternity and Child Healthcare Hospital affiliated with Southern Medical University. The investigators started with an unusually complete dataset: 2,652 deaths of children under five years of age recorded in Shenzhen between January 2016 and December 2023. From this mortality cohort, they applied prespecified, record-based cause-of-death exclusions and removed deaths occurring within 72 hours of birth, reasoning that very early neonatal deaths typically involve distinct clinical circumstances and are less likely to reflect undiagnosed metabolic disease. That filtering left 1,982 children eligible for metabolic investigation.

The critical resource was the archived dried blood spots, the small cards of filter paper collected from nearly every newborn in China as part of routine screening programs. These spots preserve a biochemical snapshot of the infant’s blood in the first days of life. Dried blood spots were available for 652 of the eligible children, and the team analyzed each one for 43 metabolites using tandem mass spectrometry, a technique that can precisely quantify tiny amounts of amino acids, acylcarnitines, and other small molecules in a single rapid run. The screening panel was designed to flag 48 different conditions, using both individual metabolite concentrations and prespecified metabolite ratios, since ratios often discriminate true disease from benign variation more reliably than any single value.

Tandem mass spectrometry works by ionizing the compounds extracted from the blood spot and then sorting them by their mass-to-charge ratio in two sequential stages, which allows the instrument to distinguish closely related molecules such as the various acylcarnitines that accumulate when fatty acid oxidation is impaired. When a fatty acid oxidation enzyme is deficient, the body cannot efficiently break down fats for energy, and specific intermediate acylcarnitines build up in the blood in characteristic patterns. Elevated concentrations of these markers, or abnormal ratios between them, serve as biochemical fingerprints of the underlying enzymatic block. In this cohort, 50 of the 652 tested children were flagged as positive by the MS/MS panel, a striking yield given that none of them had received a metabolic diagnosis before death.

To determine whether these biochemical signals reflected genuine disease, the researchers turned to whole-exome sequencing, a next-generation sequencing approach that reads the protein-coding regions of all roughly 20,000 human genes. Because most known inborn errors of metabolism are caused by variants in genes encoding enzymes, transporters, or cofactor proteins, the exome captures the great majority of the relevant disease space. The team sequenced all 50 MS/MS-positive cases and interpreted the variants according to American College of Medical Genetics and Genomics and Association for Molecular Pathology criteria, the standard framework for classifying sequence variants as pathogenic, benign, or uncertain.

The molecular work delivered definitive answers in 13 of the 50 cases, or 26 percent. Twelve of these were inborn errors of metabolism, and one child turned out to have Smith-Magenis syndrome, a genomic disorder caused by a deletion on chromosome 17 that is not a metabolic disease at all but which had produced a misleading biochemical signal. One additional case was classified as probable ornithine transcarbamylase deficiency, a urea cycle disorder that can cause lethal hyperammonemia but which often eludes both standard screening and postmortem testing. Among the definitively diagnosed metabolic cases, the spectrum included fatty acid oxidation disorders, which emerged as the dominant category, consistent with the known tendency of these conditions to present as sudden, catastrophic illness in a previously healthy child, sometimes triggered by fasting or infection.

The diagnostic categories named in the study’s abbreviations read like a catalogue of rare but devastating pediatric disease: very-long-chain acyl-CoA dehydrogenase deficiency, carnitine-acylcarnitine translocase deficiency, systemic primary carnitine deficiency, multiple acyl-CoA dehydrogenation deficiency, methylmalonic acidemia, pyruvate dehydrogenase deficiency, ethylmalonic encephalopathy, and mucolipidosis II or III alpha/beta. Each of these conditions has a distinct biochemical signature and a distinct genetic cause, and each is potentially detectable, and in some cases treatable, if identified in time. The fact that they surfaced only after death underscores the central argument of the paper: expanded newborn screening is not universally implemented, and where it is absent or incomplete, lethal metabolic disease can pass through the health system entirely unrecognized.

One of the most clinically informative findings emerged from the comparison between the 13 definitively diagnosed cases and the 37 MS/MS-positive cases that lacked a definitive molecular diagnosis. The diagnosed children had significantly lower rates of low birth weight, 31 percent versus 84 percent; preterm birth, 15 percent versus 78 percent; and obstetric complications, 46 percent versus 78 percent, with P values below 0.001 for the first two comparisons and 0.040 for the third. In other words, the children whose deaths were ultimately explained by inherited metabolic disease were far more likely to have been born at term with normal birth weight and uncomplicated pregnancies. This pattern suggests that a metabolic cause of death should rise higher on the differential diagnosis when a seemingly healthy, full-term baby deteriorates or dies without an alternative explanation, whereas MS/MS abnormalities in preterm or low-birth-weight infants may more often reflect the physiological turbulence of prematurity rather than true inherited disease.

The study also examined how well the biochemical and genetic evidence agreed with each other, a question of real practical importance because discordant findings complicate diagnosis and family counseling. Among the 13 definitively diagnosed cases, clear metabolite-genotype concordance was observed in nine, or 69.2 percent, meaning the biochemical pattern and the pathogenic variants pointed to the same disease. Partial concordance was seen in two cases and non-concordance in two. These discordant cases illustrate a well-known limitation of newborn screening panels: metabolite levels can be influenced by age, feeding, liver function, and prematurity, and a positive screen is not a diagnosis. The authors argue that this is precisely where sequencing adds decisive value, establishing molecular diagnoses and clarifying atypical, nonspecific, or biochemically confusing findings that MS/MS alone cannot resolve.

The implications reach well beyond Shenzhen. The study provides direct evidence that retrospective analysis of archived dried blood spots can convert unexplained pediatric deaths into explained ones, offering families a diagnosis, clarifying recurrence risk for future pregnancies, and identifying relatives who may carry the same condition. Just as importantly, it strengthens the case for broader access to expanded MS/MS newborn screening worldwide, since every undiagnosed case in this cohort represents a child whose condition was, in principle, detectable at birth. The authors advocate a risk-stratified approach to genomic testing, reserving whole-exome sequencing for cases that remain clinically or biochemically unresolved after screening. As sequencing costs continue to fall and blood spot archives grow, the combination of metabolomics and genomics may become a standard tool not only for diagnosing living children but for understanding why some of the most vulnerable never survive their first years.

Subject of Research: Detection of undiagnosed inborn errors of metabolism in unexplained early childhood deaths using newborn dried blood spot screening and whole-exome sequencing

Article Title: Inborn errors of metabolism in unexplained early childhood deaths: a retrospective cohort study combining MS/MS and WES

Article References: Zhou, L., Yang, X., Wu, D., Zhang, L., Tu, X., Zhan, Z., Xie, S., Xu, Y., Liu, C., Wu, B., & Liu, W. (2026). Inborn errors of metabolism in unexplained early childhood deaths: a retrospective cohort study combining MS/MS and WES. BMC Pediatrics. https://doi.org/10.1186/s12887-026-07740-3

Image Credits: AI Generated

DOI: 10.1186/s12887-026-07740-3

Keywords: inborn errors of metabolism, newborn screening, tandem mass spectrometry, whole-exome sequencing, dried blood spots, early childhood mortality, fatty acid oxidation disorders, pediatrics, metabolomics, genetic diagnosis, urea cycle disorders, Shenzhen

Spectral library searching is one of the most sensitive strategies available for peptide identification. Rather than comparing an experimental tandem mass spectrum against theoretically predicted fragments, a library search compares the query spectrum against a curated collection of previously observed, empirically validated spectra. Because real spectra capture the idiosyncrasies of fragmentation behavior, ion intensities and instrument-specific artifacts, library-based matches are typically more reliable and more sensitive than theoretical database searches. This advantage, however, comes with a limitation: the library only contains spectra for the peptide forms that were catalogued when it was built. If a peptide in the sample carries a modification that was not represented in the library, the corresponding spectrum will be absent and the peptide will go unidentified.

Open modification search was developed precisely to close that gap. Instead of restricting the search to a narrow window of precursor mass differences, an open search tolerates arbitrarily large mass shifts between the query precursor and candidate library entries, allowing a modified query spectrum to be matched against the unmodified spectrum of the same peptide sequence, with the mass difference then interpreted as the modification. The strategy has proven effective for discovering unexpected post-translational modifications, but it introduces a subtle and problematic side effect. When a modification is attached to a peptide, it does not only shift the precursor mass; it can also shift the masses of the fragment ions that contain the modified residue. Those fragment-ion shifts distort the spectral similarity calculations at the heart of library matching, degrading alignment between the query and library spectra and causing true matches to score poorly against incorrect candidates.

The authors of the new study identified this failure mode as the central weakness of existing open spectral library search methods. During the candidate retrieval stage, in which the search engine must decide which library spectra deserve detailed scoring, conventional approaches do not adequately account for modification-induced fragment-ion shifts. The consequence is that genuinely modified peptides may never even reach the scoring stage, because their distorted spectra fail to rank the correct library entry among the top candidates. The problem is especially acute for peptides carrying modifications near the C-terminus, where a large fraction of fragment ions in typical fragmentation modes include the modified site and are therefore displaced by the mass shift. For these species, conventional candidate retrieval is particularly susceptible to losing the true match in the noise.

POMS tackles this weakness by changing how candidate spectra are represented and compared. The framework integrates complementary spectral representations with sequence-derived theoretical fragment features, producing a composite description of each library spectrum that is robust to the displacement of fragment ions caused by a modification. Because the theoretical features are derived from the peptide sequence itself, they provide a stable anchor for alignment even when the experimental spectrum’s observed fragments have been shifted by an unanticipated mass. This dual-representation strategy compensates for the modification-induced shifts during alignment, improves the correspondence between query and library spectra, and increases robustness to variability in the position of the modification site along the peptide backbone.

To assess the practical impact of these design choices, the researchers benchmarked POMS on large-scale human tandem mass spectrometry datasets, including data derived from human embryonic kidney cells. The results were striking. During the open search phase, POMS yielded up to approximately eight percent more peptide identifications than conventional candidate retrieval methods, a substantial gain in a field where every additional identification represents hard-won biological information. Cross-validation against independent database search engines, a standard approach for verifying that newly reported matches are credible rather than artifacts of a particular algorithm, demonstrated a greater than five percent increase in consistent peptide identifications, indicating that the additional matches reported by POMS are corroborated by orthogonal search strategies.

The gains were most pronounced for the peptide classes that conventional methods struggle with most. POMS substantially improved the identification of peptides carrying C-terminal modifications, exactly the category for which modification-induced fragment-ion shifts are most disruptive to conventional candidate retrieval. This matters because many biologically important modification events occur at or near peptide termini, and their systematic under-detection can skew downstream biological interpretation. By recovering these difficult cases, POMS expands the visible inventory of the proteome and reduces a form of detection bias that has been embedded in open search workflows.

An important consideration for any computational tool intended for large-scale proteomics is whether its added sensitivity comes at an unacceptable computational cost. The authors emphasize that POMS incorporates modification-aware candidate retrieval while preserving computational efficiency, making it a practical option for the very large datasets that characterize modern proteomics experiments. The framework is designed to slot into existing spectral library search workflows rather than requiring laboratories to rebuild their pipelines from scratch, lowering the barrier to adoption. In addition, the software exploits approximate nearest neighbor techniques to manage the scale of library searching, ensuring that the richer spectral representations do not translate into prohibitive search times.

For the broader proteomics community, the implications extend beyond a simple sensitivity bump. Post-translational modifications govern nearly every aspect of protein function, from enzyme activation and signal transduction to protein degradation and disease states, and mass spectrometry remains the dominant technology for mapping them at scale. Open modification search has been a transformative idea, but its full potential has been throttled by the candidate-retrieval bottleneck that POMS directly addresses. By making the earliest and most consequential step of the search modification-aware, the framework increases both the sensitivity and the reliability of modification-tolerant searching, offering researchers a sharper lens for PTM discovery in contexts ranging from basic cell biology to biomarker research.

The tool is publicly available to the research community under a CC BY-NC-SA 4.0 license through the GitHub repository maintained by the Korea Basic Science Institute, allowing laboratories to evaluate it against their own data and integrate it into their analysis pipelines. The work was supported by the Korea Basic Science Institute and by grants from the National Research Foundation of Korea funded by the Korean Ministry of Science and ICT, reflecting a sustained national investment in proteome informatics. As spectral libraries continue to grow and instruments generate ever-larger volumes of tandem mass spectra, methods such as POMS that combine domain-aware algorithm design with practical efficiency are likely to define the next generation of peptide identification tools, helping researchers extract more complete and more accurate pictures of the modified proteome from the data they already collect.

Subject of Research: Modification-aware open spectral library search for identification of post-translationally modified peptides in tandem mass spectrometry

Article Title: POMS enhances open spectral library search for identification of modified peptides

Article References: Seo, Y., Paek, E., & Na, S. (2026). POMS enhances open spectral library search for identification of modified peptides. BMC Bioinformatics. https://doi.org/10.1186/s12859-026-06672-0

Image Credits: AI Generated

DOI: 10.1186/s12859-026-06672-0

Keywords: proteomics, tandem mass spectrometry, post-translational modifications, open modification search, spectral library search, peptide identification, modified peptides, fragment-ion shifts, candidate retrieval, proteome informatics, POMS, BMC Bioinformatics

Mass spectrometry-based amyloid typing has earned a reputation as the gold standard for identifying the amyloidogenic protein in tissue deposits. By shredding laser-microdissected amyloid plaques into peptides and reading their mass spectra, laboratories can distinguish among more than thirty amyloid types with a specificity that immunohistochemistry and immunofluorescence simply cannot match. Yet the technique has remained confined largely to a handful of reference laboratories because it depends on nanoflow liquid chromatography, in which solvents are pushed through capillaries with inner diameters measured in tens of micrometers. Nanoflow systems deliver exquisite sensitivity, but they come with steep up-front costs, demanding maintenance, long column equilibration times, and a level of operational complexity that deters routine clinical adoption.

The Stanford team, led by Morgan W. Mann and Fangjun Chen with senior authors Megan L. Troxell and Ruben Y. Luo, set out to re-engineer the workflow so that it could run on the high-flow liquid chromatography systems already humming away in hospital laboratories. Their solution rests on two complementary innovations: a sample preparation method called suspension trapping, known commercially as S-Trap, and an acquisition strategy known as data-independent acquisition, or DIA. Together, these techniques allow the analysis of microdissected amyloid plaques using conventional-flow chromatography coupled to tandem mass spectrometry, without sacrificing the diagnostic accuracy that clinicians rely upon.

Suspension trapping is the quieter revolution of the two. In traditional proteomics sample preparation, proteins extracted from tiny tissue fragments must be digested into peptides through a series of solution exchanges, buffer removals, and cleanups that consume time and lose precious material at every step. The S-Trap approach instead traps proteins on a quartz filter matrix as they precipitate out of an acidic methanol-containing buffer. Digestion enzymes then pass through the trap, generating peptides that are eluted in a single, efficient step. The method is fast, robust, and minimizes sample loss, which matters enormously when the starting material consists of a few thousand cells harvested by laser capture microdissection from a formalin-fixed paraffin-embedded tissue section.

Data-independent acquisition addresses the other half of the problem. In classical data-dependent acquisition, the mass spectrometer selects the most intense ions in each scan for fragmentation, a stochastic process that can miss low-abundance peptides and produces data that are tedious to align across runs. DIA, by contrast, fragments all ions within successive wide mass windows, systematically recording fragment spectra for essentially everything in the sample. The resulting data are reconstructed computationally against spectral libraries, yielding consistent and quantitative peptide identifications. Because DIA tolerates the higher flow rates, wider chromatographic peaks, and greater sample loads of high-flow chromatography, it made the leap away from nanoflow feasible rather than merely aspirational.

To translate raw proteomic data into a diagnosis, the researchers also developed a custom selection heuristic that sifts through the hundreds of proteins detected in each plaque and identifies the most likely amyloidogenic culprit. Amyloid deposits are not pure; they sweep up serum proteins, immunoglobulin fragments, and extracellular matrix components as they form. Distinguishing the genuine amyloidogenic protein from innocent bystanders requires weighing total protein abundance, the presence of type-specific signature peptides, and the biological plausibility of each candidate. The heuristic automates this judgment, reducing an expert curation task that could take hours into a reproducible computational step suitable for a busy clinical workflow.

The performance data are striking. Working with laser capture microdissected plaques from 47 patient samples, 10 from cardiac biopsies and 37 from renal biopsies, the team split the material into a training set of 25 samples and an independent testing set of 22. The high-flow LC-DIA-MS/MS method identified the amyloidogenic protein in approximately 96 percent of plaques in both sets, a success rate comparable to established nanoflow approaches. The two inaccuracies observed across the cohort both traced to difficulties in identifying immunoglobulin lambda proteins, once in a specimen obtained after treatment had altered the composition of the deposits and once in a plaque containing two distinct amyloid types simultaneously. These edge cases, the authors note, define the boundaries of the method rather than undermining its general utility.

Reducing the sample preparation workflow to under eight hours carries practical significance beyond convenience. Amyloidosis is increasingly recognized as an urgent diagnosis; cardiac involvement can progress rapidly, and new therapies such as transthyretin stabilizers and silencing agents work best when started early. Every hour shaved from the analytical pipeline shortens the time between biopsy and answer. Equally important, the shift to high-flow chromatography means the method can run on instruments of the kind already deployed for clinical chemistry assays, drug monitoring, and newborn screening in hospital laboratories. That compatibility could transform amyloid typing from a rarefied referral test into an accessible diagnostic performed locally, at lower cost and with faster turnaround.

The study, published in Clinical Proteomics, was conducted on remnant patient specimens under approved institutional review board protocols and funded through the Stanford University Department of Pathology’s Test Development Program, underscoring its explicitly clinical orientation. The authors acknowledge one commercial entanglement: a collaborative research relationship between one investigator and Thermo Fisher Scientific, which provided technical support. While the method will still require validation in other laboratories and across broader panels of amyloid types, the combination of suspension trapping, data-independent acquisition, and high-flow chromatography represents a credible path toward democratizing molecular amyloid typing, offering patients everywhere the prospect of a faster, more precise answer to the question their treatment ultimately depends on.

Subject of Research: A high-flow liquid chromatography-tandem mass spectrometry method for typing amyloidosis in clinical laboratories

Article Title: Suspension trapping and data-independent acquisition enable high-flow liquid chromatography-tandem mass spectrometry-based amyloidosis typing in clinical laboratories

Article References: Mann, M. W., Chen, F., Zhu, C., Lu, C., Liang, B., Kambham, N., Troxell, M. L., & Luo, R. Y. (2026). Suspension trapping and data-independent acquisition enable high-flow liquid chromatography-tandem mass spectrometry-based amyloidosis typing in clinical laboratories. Clinical Proteomics. https://doi.org/10.1186/s12014-026-09628-x

Image Credits: AI Generated

DOI: 10.1186/s12014-026-09628-x

Keywords: amyloidosis, mass spectrometry, proteomics, data-independent acquisition, suspension trapping, liquid chromatography, clinical diagnostics, laser capture microdissection, AL amyloidosis, ATTR amyloidosis, tandem mass spectrometry, clinical proteomics