Recommended Literature

Original work:

Vadadokhau et al. (2026). Preventing Proteomics Data Tombs Through Collective Responsibility and Community Engagement. Scientific Data, 13 (1):287. DOI: 10.1038/s41597-026-06614-8

Main insights:

Nowadays, public proteomics repositories hold a lot of mass spectrometry data, which, despite being open access, are almost not reusable. Referred to as "Data tombs," the issues with these datasets mainly arise from vague or inconsistent reporting, missing spectral libraries or  sequence databases, insufficient replicates and software restrictions. This article urges the creation of a minimum re-analysis package, which should be included along each new entry into public proteomics  repositories. The content of this package is based on the limitations observed among 6 peer-reviewed articles and notably encourages the use of open file formats, the creation of community standards, quality control summaries, complete instead of partial spectral libraries and more accurate code reporting.

Original work:

Doncheva et al. (2025). Understanding Data Analysis Steps in Mass-Spectrometry-Based Proteomics Is Key to Transparent Reporting. Journal of Proteome Research, 24 (10), 4965-4976. DOI: 10.1021/acs.jproteome.5c00287

Main insights:

Highlight common errors and oversights done while reporting mass spectrometry data analysis procedures. Incomplete or inaccurate descriptions of analytical workflows can limit reproducibility and prevent the scientific community from fully assessing a study’s potential. This article points out good practices and discusses why the community should put efforts into more transparently reporting data analysis workflows.

Original work:

Daly et al. (2025). An Optimized SP3 Sample Processing Workflow for In-Depth and Reproducible Phosphoproteomics. Journal of Proteome Research, 24 (8), 4300-4308. DOI: 10.1021/acs.jproteome.5c00220

Main insights:

Comparative study of the different cell lysis procedures, protein processing methods and phospho-site enrichment strategies available in the scientific literature. This work introduces an optimized sample processing workflow for phosphoproteomics by obtaining roughly 1.6-; 6- and 36-fold increases in singly, doubly and triply phosphorylated peptides, respectively, compared to previous studies.

Original work:

Nickerson and Doucette (2020). Rapid and Quantitative Protein Precipitation for Proteome Analysis by Mass Spectrometry. Journal of Proteome research, 19 (5), 2035-2042. DOI: 10.1021/acs.jproteome.9b00867

Main insights:

Development of a quick and unbiased method (in regard to molecular weight, isoelectric point and hydrophobicity) to precipitate proteins in a complex mixture. While maximizing protein recovery, this method can be used to concentrate a diluted lysate or to change solvents.

Original work:

Hughes et al. (2019). Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nature protocols, 14:68-85. DOI: 10.1038/s41596-018-0082-x

Main insights:

Development of the SP3 beads technology that allows unbiased and robust protein purification prior proteomic analysis. SP3 beads are routinely used at the BMS Core Facility to process samples for mass spectrometry.

Have you ever wondered what the mass spectrometer responsible for your data acquisition is made of? These videos will show you the inside of the Orbitrap Fusion Lumos, the QTrap 5500 and the QExactive; the main instruments used at the BMS Core Facility.

Each video below offers a cross-sectional view of the selected instrument and animates the peptide processing workflow within the machine. Punctual annotations on crucial steps are also available.