Nature Methods offers a unique interdisciplinary forum for the publication of novel methods. Nature Methods focuses on the life sciences, combining practical, technique-driven subject matter with rigorous peer-review standards to ensure that readers are consistently presented with only the most valuable and highest quality methodological research. The journal offers its readers primary research papers as well as an array of opinions, reviews and short journalistic pieces to provide busy researchers with a broad, yet easily absorbed perspective of important methodological developments in the life sciences. http://feeds.nature.com/nmeth/rss/current Nature Publishing Group en © 2026 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Nature Methods © 2026 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. permissions@nature.com https://www.nature.com/uploads/product/nmeth/rss.gif http://feeds.nature.com/nmeth/rss/current https://www.nature.com/articles/s41592-026-03268-7 Nature Methods, Published online: 16 October 2026; doi:10.1038/s41592-026-03268-7

This Review summarizes recent developments in fluorescent protein technology, including the engineering of fluorescent biosensors.]]> Anneliese M. M. GestSohum MehtaJin Zhang doi:10.1038/s41592-026-03268-7 Nature Methods, Published online: 2026-10-16; | doi:10.1038/s41592-026-03268-7 2026-10-16 Nature Methods 10.1038/s41592-026-03268-7 https://www.nature.com/articles/s41592-026-03268-7 https://www.nature.com/articles/s41592-026-03264-x Nature Methods, Published online: 16 October 2026; doi:10.1038/s41592-026-03264-x

AmpliconSuite is a toolkit that enables the analysis of focal amplifications from cancer whole-genome sequencing data.]]> Jens LuebeckTed LiefeldIvy Tsz-Lo WongEdwin HuangForrest KimBhargavi DameracharlaMichael ChanRohil AhujaKyra FetterDhruv KhatriKaiyuan ZhuThorin TaborDaniel SchreyerGino PrasadAditi GnanasekarSiavash Raeisi DehkordiSimone SpandauMichał AdamaszekRishaan KenkreTushar AgasheDevika TorviMădălina Giurgiu-KraljičSoyeon KimHoon KimPeter BaileyRoel G. W. VerhaakViraj DeshpandeMichael ReichPaul S. MischelJill P. MesirovVineet Bafna doi:10.1038/s41592-026-03264-x Nature Methods, Published online: 2026-10-16; | doi:10.1038/s41592-026-03264-x 2026-10-16 Nature Methods 10.1038/s41592-026-03264-x https://www.nature.com/articles/s41592-026-03264-x https://www.nature.com/articles/s41592-026-03266-9 Nature Methods, Published online: 14 October 2026; doi:10.1038/s41592-026-03266-9

Addressing sex-related variation might seem like an experimental or data analysis time-sink. It’s not.]]> Vivien Marx doi:10.1038/s41592-026-03266-9 Nature Methods, Published online: 2026-10-14; | doi:10.1038/s41592-026-03266-9 2026-10-14 Nature Methods 10.1038/s41592-026-03266-9 https://www.nature.com/articles/s41592-026-03266-9 https://www.nature.com/articles/s41592-026-03249-w Nature Methods, Published online: 14 October 2026; doi:10.1038/s41592-026-03249-w

LoL-align is a probabilistic, distance-based protein structure alignment algorithm that iteratively optimizes a local log-odds score, achieving higher sensitivity for remote homologs and better alignment quality than available methods.]]> Lasse ReifenrathMichel van KempenGyuri KimSoo Hyun KimMohammadreza RadnezhadCameron L. M. GilchristMilot MirditaMartin SteineggerJohannes Söding doi:10.1038/s41592-026-03249-w Nature Methods, Published online: 2026-10-14; | doi:10.1038/s41592-026-03249-w 2026-10-14 Nature Methods 10.1038/s41592-026-03249-w https://www.nature.com/articles/s41592-026-03249-w https://www.nature.com/articles/s41592-026-03247-y Nature Methods, Published online: 14 October 2026; doi:10.1038/s41592-026-03247-y

This Article presents MassNet, a large-scale AI-ready corpus of 1.5 billion MS/MS spectra spanning 35 species, paired with a standardized storage format called Mass Spectrometry DDA Tensor (MSDT). Built on this resource, XuanjiNovo is a nonautoregressive transformer for de novo peptide sequencing that substantially outperforms previous methods.]]> Jun AXiang ZhangXiaofan ZhangJiaqi WeiTe ZhangYamin DengPu LiuZongxiang NieYiwen YuYi ChenNanqing DongZhiqiang GaoSiqi SunTiannan Guo doi:10.1038/s41592-026-03247-y Nature Methods, Published online: 2026-10-14; | doi:10.1038/s41592-026-03247-y 2026-10-14 Nature Methods 10.1038/s41592-026-03247-y https://www.nature.com/articles/s41592-026-03247-y https://www.nature.com/articles/s41592-026-03276-7 Nature Methods, Published online: 13 October 2026; doi:10.1038/s41592-026-03276-7

How biologists can make the most of supplementary materials for impact.]]> Andreas BueckleMatthias StahlKelly KrauseTorsten MöllerHelena Klara Jambor doi:10.1038/s41592-026-03276-7 Nature Methods, Published online: 2026-10-13; | doi:10.1038/s41592-026-03276-7 2026-10-13 Nature Methods 10.1038/s41592-026-03276-7 https://www.nature.com/articles/s41592-026-03276-7 https://www.nature.com/articles/s41592-026-03255-y Nature Methods, Published online: 13 October 2026; doi:10.1038/s41592-026-03255-y

A small, photoswitchable and genetically encodable protein operating in the near-infrared window is reported for photoacoustic tomography applications.]]> Olena S. OliinykYirui XuJinhuan LuoKateryna O. TokarchukKyrylo Yu. ManoilovJosie van de KlashorstMatthew P. EyringMu-en WangMing ChenPengfei SongJohn W. HickeyJunjie YaoVladislav V. Verkhusha doi:10.1038/s41592-026-03255-y Nature Methods, Published online: 2026-10-13; | doi:10.1038/s41592-026-03255-y 2026-10-13 Nature Methods 10.1038/s41592-026-03255-y https://www.nature.com/articles/s41592-026-03255-y https://www.nature.com/articles/s41592-026-03267-8 Nature Methods, Published online: 12 October 2026; doi:10.1038/s41592-026-03267-8

These early career scientists in Europe share challenges and advice about finding the ‘right’ lab and lab–life blend.]]> Vivien Marx doi:10.1038/s41592-026-03267-8 Nature Methods, Published online: 2026-10-12; | doi:10.1038/s41592-026-03267-8 2026-10-12 Nature Methods 10.1038/s41592-026-03267-8 https://www.nature.com/articles/s41592-026-03267-8