Spectroscopy papers
Pofolia’s corpus holds 84 papers from Spectroscopy (2012–2026), each with a short summary. Below, the 20 most-cited, then the most recently added.
At a glance
- Most cited: GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers (2015, 27,148 citations).
- The 20 papers listed have 115,981 citations between them.
- 18 of the 20 with a known journal quartile appeared in a Q1 journal.
- 12 have a free full text (open access).
- Most frequent journals: Nucleic Acids Research, Journal of Quantitative Spectroscopy and Radiative Transfer, Molecular & Cellular Proteomics.
- Published between 2012 and 2022.
Most cited
Ranked by citation count. Because citations accumulate over time, this list naturally leans towards work published a few years ago; for where the field is now, see “recently added”. How to read the signals
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
SoftwareX · 2015 · Q2 · 27,148 citations · Open access
GROMACS version 5 achieves new performance heights in molecular simulations by implementing multi-level parallelization algorithms across SIMD, multithreading, CPU-GPU acceleration, domain decomposition, and ensemble-level parallelism.
Tissue-based map of the human proteome
Science · 2015 · Q1 · SJR 10.00 · FWCI 374.62 · 16,073 citations
Researchers have created a comprehensive map of the human tissue proteome, detailing protein presence and localization across 32 tissues and organs using an integrated omics approach.
The HITRAN2016 molecular spectroscopic database
Journal of Quantitative Spectroscopy and Radiative Transfer · 2017 · Q1 · FWCI 292.66 · 7,955 citations
The HITRAN2020 database, a comprehensive compilation of molecular spectroscopic parameters, has been significantly updated with new experimental and theoretical data, enhancing accuracy for atmospheric absorbers and expanding spectral coverage.
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Journal of Chemical Theory and Computation · 2013 · Q1 · SJR 1.00 · FWCI 61.99 · 7,622 citations
Two complementary, freely available software packages, PTRAJ and its successor CPPTRAJ, are introduced for processing and analyzing molecular dynamics trajectory data.
The PRIDE database and related tools and resources in 2019: improving support for quantification data
Nucleic Acids Research · 2018 · Q1 · SJR 8.00 · FWCI 493.21 · 7,443 citations · Open access
The PRIDE database, a major repository for mass spectrometry-based proteomics data, has been significantly upgraded with a new architecture and improved support for quantitative data via the mzTab format.
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
Nucleic Acids Research · 2021 · Q1 · SJR 8.00 · FWCI 518.31 · 6,779 citations · Open access
The PRIDE database, a major repository for mass spectrometry proteomics data, has significantly expanded its resources and infrastructure since 2019. It now processes around 500 datasets monthly and offers direct access to mass spectra via the PRIDE Spectra Archive.
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ
Molecular & Cellular Proteomics · 2014 · Q1 · SJR 2.00 · FWCI 98.97 · 5,556 citations · Open access
A new method called MaxLFQ enables accurate and robust label-free protein quantification across entire proteomes by maximizing the use of available MS signals and employing a novel normalization strategy.
The ORCA quantum chemistry program package
The Journal of Chemical Physics · 2020 · Q1 · FWCI 187.33 · 5,072 citations · Open access
The ORCA program package is a comprehensive, general-purpose software for theoretical research across chemistry and related fields, featuring a wide array of computational methods and unique implementations.
2016 update of the PRIDE database and its related tools
Nucleic Acids Research · 2015 · Q1 · SJR 8.00 · FWCI 263.12 · 3,668 citations · Open access
The PRIDE Archive, a leading mass spectrometry proteomics data repository, has been redeveloped with a new storage backend, submission system, and web interface, supporting key data standards and seeing a significant increase in data submissions.
Independent gradient model based on Hirshfeld partition: A new method for visual study of interactions in chemical systems
Journal of Computational Chemistry · 2022 · Q1 · SJR 1.00 · FWCI 274.81 · 3,599 citations
A new method, IGMH, improves upon the existing Independent Gradient Model (IGM) for visualizing chemical interactions by using Hirshfeld partitioning of electron density, leading to clearer and more accurate graphical representations.
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations
Nucleic Acids Research · 2014 · Q1 · SJR 8.00 · FWCI 57.85 · 3,484 citations · Open access
The PhosphoSitePlus knowledgebase now includes over 330,000 mammalian post-translational modifications (PTMs), with over 95% derived from mass spectrometry data that has been reanalyzed for improved reliability.
A subcellular map of the human proteome
Science · 2017 · Q1 · SJR 10.00 · FWCI 121.88 · 3,004 citations
Researchers have created the Cell Atlas, a comprehensive image-based map detailing the subcellular location of 12,003 human proteins across 30 cellular structures, significantly advancing our understanding of cellular architecture.
Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis
Molecular & Cellular Proteomics · 2012 · Q1 · SJR 2.00 · FWCI 66.21 · 3,001 citations · Open access
A novel strategy uses fragment ion spectral libraries to mine data-independent acquisition (DIA) mass spectrometry data, enabling consistent and accurate quantification of peptides across large proteomes.
Fluorescent Sensors for Measuring Metal Ions in Living Systems
Chemical Reviews · 2014 · Q1 · SJR 16.00 · FWCI 94.93 · 2,440 citations · Open access
This review synthesizes the latest advancements in fluorescent sensors designed to detect and quantify metal ions within living biological systems.
The InterPro protein families and domains database: 20 years on
Nucleic Acids Research · 2020 · Q1 · SJR 8.00 · FWCI 147.80 · 2,420 citations
The InterPro database, a comprehensive resource for protein classification, has reached its 20th year of operation, marked by significant updates to its content and associated software.
The HITRAN2020 molecular spectroscopic database
Journal of Quantitative Spectroscopy and Radiative Transfer · 2021 · Q1 · FWCI 139.61 · 2,387 citations
The HITRAN2020 database, a major update to the standard for molecular spectroscopic parameters, now includes new molecules, isotopologues, and vibrational bands, significantly extending spectral coverage and completeness.
Automated exploration of the low-energy chemical space with fast quantum chemical methods
Physical Chemistry Chemical Physics · 2020 · Q2 · FWCI 97.61 · 2,342 citations
A new computational scheme uses fast semiempirical quantum chemistry (GFn-xTB) and meta-dynamics to efficiently explore the low-energy chemical space of large molecules, generating thermodynamic ensembles of conformers.
iProX: an integrated proteome resource
Nucleic Acids Research · 2018 · Q1 · SJR 8.00 · FWCI 60.50 · 2,038 citations · Open access
iProX is a new public platform developed to facilitate worldwide access and sharing of raw proteome data, analysis results, and metadata from mass spectrometry-based experiments.
Fluorescent chemosensors: the past, present and future
Chemical Society Reviews · 2017 · Q1 · SJR 11.00 · FWCI 82.99 · 1,978 citations · Open access
This review traces the 150-year history of fluorescent chemosensors, highlighting key developments and their broad applications in biology, physiology, pharmacology, and environmental sciences.
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
Nucleic Acids Research · 2012 · Q1 · SJR 8.00 · FWCI 114.22 · 1,972 citations · Open access
The PRIDE database, a major repository for mass spectrometry-based proteomics data, has been updated with new statistics on its content and descriptions of its submission and analysis tools.
Recently added
Ultrahigh resolution 19F and 31P NMR spectroscopy
Communications Chemistry · 2026 · Q1 · SJR 1.00
A new ultra-broadband, ultrahigh resolution NMR experiment enables pure shift spectra for fluorine and phosphorus, overcoming bandwidth limitations of existing methods.
3D-printed polymeric cryogel for tetracycline adsorption
Journal of Cleaner Production · 2026 · Q1 · SJR 2.00
A 3D-printed cryogel made from gelatin, carboxymethylcellulose, and sodium alginate, crosslinked with Fe3+, achieved a maximum experimental tetracycline adsorption capacity of 336.45 mg/g, with a theoretical maximum of 445.61 mg/g.
Hidden Morphological Features in Organically Synthesized Porous Carbon Revealed through Analysis of Contradictory NMR Spectra
ACS Omega · 2026 · Q1
A dense, interpenetrated morphology of sp and sp3 carbon explains contradictory solid-state NMR spectra in Organically Synthesized Porous Carbon (OSPC) anode materials, while porosity arises from a newly uncovered open framework structure.
Balancing thermal insulation and mechanical performance in aerogel insulating mortar through synergistic cement-HPMC regulation
Construction and Building Materials · 2026 · Q1 · SJR 2.00
Optimized aerogel insulating mortar (AIM) with 5.293g cement and 8.0g HPMC achieves a dry density of 211.8 kg/m³, thermal conductivity of 60.2 mW/(m·K), and compressive strength of ~0.50 MPa, further reduced to 48.56 mW/(m·K) after pathway regulation.
Development of a Translational Assay for Identification and Quantitation of Orthologous Proteins to Aid Drug Development in Preclinical Models
Journal of Proteome Research · 2026 · Q1 · SJR 1.00
A new mass spectrometry-based assay can identify and quantify conserved proteins across species, demonstrated using ataxin-2 (ATXN2) and showing consistent protein downregulation with miRNA treatment in preclinical models.
Machine learning-based rescoring with MS²Rescore boosts peptide identification and taxonomic specificity in metaproteomics
Environmental Microbiome · 2026 · Q1 · SJR 1.00
MS²Rescore, a machine learning tool, significantly increases peptide identification rates (outperforming Sage) and lowers false discovery rates to 0.1% in metaproteomics, especially in complex environments like soil.
Relating transcriptomics to protein abundance reveals self‐driven versus interactor‐driven proteins
Protein Science · 2026 · Q1 · SJR 3.00
A new statistical model classifies genes into 'self-driven' (protein abundance linked to own transcript) and 'interactor-driven' (protein abundance linked to partners' transcripts), with the latter having longer mRNA half-lives.
In situ learning-based spin engineering of pulsed dynamic nuclear polarization
Science Advances · 2026 · Q1 · SJR 4.00 · FWCI 2.06 · 1 citations
Researchers developed an in situ method using Bayesian machine learning and random walk procedures to design pulsed dynamic nuclear polarization (DNP) sequences directly on spin systems.
Journals in this field
The journals that publish most of this field’s papers. Quartile (Q1–Q4), SJR and h-index are from SCImago Journal Rank; “in this field” is how many of the journal’s pooled papers belong here. What is a Q1 journal? · What is the h-index?
| Journal | Quartile | SJR | h-index | In this field | Summaries |
|---|---|---|---|---|---|
| Nucleic Acids Research | Q1 | 8.00 | 714 | 11 | 43 |
| Chemical Reviews | Q1 | 16.00 | 905 | 7 | 124 |
| Chemical Society Reviews | Q1 | 11.00 | 709 | 7 | 90 |
| Molecular and Cellular Proteomics | Q1 | 2.00 | 219 | 5 | 5 |
| Journal of Chemical Theory and Computation | Q1 | 1.00 | 248 | 5 | 14 |
| Analytical Chemistry | Q1 | 1.00 | 390 | 4 | 16 |
| Science | Q1 | 10.00 | 1433 | 3 | 268 |
| Accounts of Chemical Research | Q1 | 5.00 | 495 | 2 | 19 |
Every journal in Spectroscopy (Q1–Q4) →
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