A proteomics reading list: open-access papers worth your time

How to use this list

Each entry is a primary paper or a tutorial that settled a method, introduced a tool or changed how a step is planned. We have kept to work that a reader can verify: every entry is linked to its PubMed record and DOI, and papers with free full text are marked. The short note under each heading says why it matters at the bench, not what the abstract says.

Sample preparation: from protein to peptide

Filter-aided sample preparation made SDS lysis compatible with LC-MS; suspension trapping replaced the ultrafiltration membrane with a depth filter and cut processing to under an hour; SP3 moved the same job onto magnetic beads for very low input and automation. Read these four together and the trade-offs in our digestion comparison become obvious.

Papers

1. Wiśniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods 2009;6:359-362. PubMed · DOI
2. Zougman A, Selby PJ, Banks RE. Suspension trapping (STrap) sample preparation method for bottom-up proteomics analysis. Proteomics 2014;14:1006. PubMed · DOI
3. HaileMariam M et al. S-Trap, an ultrafast sample-preparation approach for shotgun proteomics. J Proteome Res 2018;17:2917-2924. PubMed · DOI
4. Hughes CS et al. Ultrasensitive proteome analysis using paramagnetic bead technology. Mol Syst Biol 2014;10:757. Open access PubMed · DOI · Full text (PMC)
5. Hughes et al. Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nat Protoc 2019. PubMed · DOI

Acquisition: DDA, DIA and the newest analysers

Gillet and colleagues defined SWATH-type DIA; the Ludwig tutorial is the clearest open explanation of how it works; Bruderer introduced the Spectronaut approach; Guzman showed what narrow-window DIA achieves on the Orbitrap Astral. For isobaric labelling, Ting's MS3 paper explains the ratio-compression problem that SPS-MS3 on Tribrid instruments was built to solve.

Papers

1. Gillet et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 2012. Open access PubMed · DOI · Full text (PMC)
2. Ludwig et al. Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. Mol Syst Biol 2018. Open access PubMed · DOI · Full text (PMC)
3. Bruderer et al. Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues. Mol Cell Proteomics 2015. Open access PubMed · DOI · Full text (PMC)
4. Guzman et al. Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition. Nat Biotechnol 2024. Open access PubMed · DOI · Full text (PMC)
5. Ting et al. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods 2011. Open access PubMed · DOI · Full text (PMC)

Data analysis

DIA-NN brought neural-network scoring and predicted libraries to DIA; MaxDIA and MSFragger-DIA extended the two most widely used free DDA platforms to DIA data. If your group runs only one of these, the others are worth knowing for the day a reviewer asks for an independent reanalysis.

Papers

1. Demichev V et al. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat Methods 2020;17:41-44. Open access PubMed · DOI · Full text (PMC)
2. Sinitcyn et al. MaxDIA enables library-based and library-free data-independent acquisition proteomics. Nat Biotechnol 2021. Open access PubMed · DOI · Full text (PMC)
3. Yu et al. Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform. Nat Commun 2023. Open access PubMed · DOI · Full text (PMC)

Plasma and biofluids

Anderson and Anderson's survey is still the reference for why plasma is hard; Geyer's review argues for profiling whole cohorts rather than hunting single markers; Blume and Ferdosi describe the nanoparticle-corona approach to dynamic-range compression that underpins modern deep plasma proteomics.

Papers

1. Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 2002;1:845-867. Open access PubMed · DOI
2. Geyer et al. Revisiting biomarker discovery by plasma proteomics. Mol Syst Biol 2017. Open access PubMed · DOI · Full text (PMC)
3. Blume JE et al. Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona. Nat Commun 2020;11:3662. Open access PubMed · DOI · Full text (PMC)
4. Ferdosi et al. Engineered nanoparticles enable deep proteomics studies at scale by leveraging tunable nano-bio interactions. Proc Natl Acad Sci U S A 2022. Open access PubMed · DOI · Full text (PMC)

Phosphoproteomics

EasyPhos is the benchmark plate-format TiO₂ workflow; the FAIMS study quantifies what gas-phase fractionation adds to single-shot phosphoproteomes; Ochoa's atlas is the reminder that detection is not the same as understanding.

Papers

1. Humphrey et al. High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform. Nat Protoc 2018. PubMed · DOI
2. Muehlbauer LK et al. Global phosphoproteome analysis using high-field asymmetric waveform ion mobility spectrometry on a hybrid Orbitrap mass spectrometer. Anal Chem 2020;92:15959-15967. Open access PubMed · DOI · Full text (PMC)
3. Ochoa et al. The functional landscape of the human phosphoproteome. Nat Biotechnol 2019. Open access PubMed · DOI · Full text (PMC)

Tissue and single cells

Coscia's FFPE workflow shows that archival blocks can be profiled at cohort scale; Brunner's single-cell study established what ultra-sensitive LC-MS can quantify from one cell; Gatto's recommendations are what a reviewer will expect from a single-cell proteomics manuscript.

Papers

1. Coscia F et al. A streamlined mass spectrometry-based proteomics workflow for large-scale FFPE tissue analysis. J Pathol 2020;251:100-112. Open access PubMed · DOI
2. Brunner AD et al. Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation. Mol Syst Biol 2022;18:e10798. Open access PubMed · DOI · Full text (PMC)
3. Gatto et al. Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nat Methods 2023. Open access PubMed · DOI · Full text (PMC)

Transcript versus protein

Before integrating RNA-seq with proteomics, read Buccitelli and Selbach on why transcript and protein abundance correlate only moderately, and what that means for the conclusions a multi-omics study can draw. Our integration guide builds on it.

Papers

1. Buccitelli & Selbach. mRNAs, proteins and the emerging principles of gene expression control. Nat Rev Genet 2020. PubMed · DOI

Citations verified against PubMed records on 2 November 2026; “Open access” marks papers whose full text is freely available via PubMed Central or the journal.

Missing a paper you think belongs here? Tell us, the list is revised as the field moves.

Written by the omicslink proteomics team. Reviewed November 2026.