Key papers in Spectroscopy
Pofolia’s corpus holds 70 papers from the Spectroscopy subfield (2012–2025). The list below starts with the most cited.
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”.
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
Fast step heterodyne light-induced thermoelastic spectroscopy gas sensing based on a quartz tuning fork with high-frequency of 100 kHz
Opto-Electronic Advances · 2025 · Q1 · SJR 3.00 · FWCI 29.10 · 62 citations · Open access
A novel gas sensor utilizes a high-frequency quartz tuning fork (~100 kHz) to achieve a tenfold faster response time, enabling measurement cycles as short as 33 ms, a significant improvement over standard sensors.
An ultra-highly sensitive LITES sensor based on multi-pass cell with ultra-dense spot pattern designed by multi-objective algorithm
PhotoniX · 2025 · Q1 · SJR 3.00 · FWCI 26.76 · 57 citations · Open access
Researchers developed an ultra-highly sensitive Light-Induced Thermoelastic Spectroscopy (LITES) sensor using a novel multi-pass cell (MPC) with an ultra-dense spot pattern, achieving a minimum detection limit (MDL) of 4.78 ppb for acetylene.
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.
iProX in 2021: connecting proteomics data sharing with big data
Nucleic Acids Research · 2021 · Q1 · SJR 8.00 · FWCI 69.37 · 1,115 citations · Open access
The integrated proteome resource iProX launched a big data platform in 2021, enabling PB-level storage and second-level query latency for proteomics datasets.
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.
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