What Solid-Phase Peptide Extraction got wrong, from 12 theses

Tried and failed

nanomaterial solid-phase extraction for peptide enrichment applied to S-palmitoylated peptide profiling in cell lysates. Outcome: no signal. Reason: yielded almost no identifiable target peptides and zero hits in open search mode

Novel proteomics approaches to study S-acylation in biomolecular condensate regulation and disease · Imperial · PhD

Considered and rejected

Considered and rejected: Solid phase extraction / sample prep for mass spectrometry without any reducing agents was rejected due to resulting in very low peptide detection

Non-Lysine Acyl Modifications and Their Effects on Cellular Function · Duke · Doctorate

Tried and failed

direct peptide extraction without enrichment applied to endogenous low-abundance tissue peptides. Outcome: no signal. Reason: endogenous peptide concentrations were below detection limits without targeted enrichment prior to mass spectrometry

Characterisation of the Apelin Receptor and its Endogenous Ligands, Apelin and Elabela/Toddler in the Cardio-Renal System · Cambridge · PhD

Lost to a baseline

Direct peptide monomer copolymerization yielded only 60% recovery of peptide monomer post-purification compared to near 100% conjugation efficiency in post-functionalization.

Engineering Intravenous Therapies for Trauma · University of Washington · PhD

Considered and rejected

Considered and rejected: Post-purification chemical conjugation via terminal cysteine or sortase transpeptidation (sortagging) of synthetic phosphorylated peptides was rejected due to complex multi-step purification and poor yields.

A materials-based approach for localized delivery of cancer immunotherapy · MIT · PhD

Considered and rejected

Considered and rejected: Rejected standard solution-phase multi-labeling for fluorosequencing due to sample losses during multiple purification cycles

Methods and technology development for bulk and single-molecule proteomics · UT Austin · PhD

Tried and failed

solid-phase peptide synthesis and chromatographic purification applied to hydrophobic dipeptide repeat proteins. Reason: extreme insolubility and aggregation prevented purification despite successful chemical synthesis

The Discovery and Chemical Synthesis of Peptides and Proteins that Cross Biological Barriers · MIT · PhD

Tried and failed

reversed-phase HPLC peptide purification applied to recombinantly expressed short amyloidogenic peptides. Outcome: no signal. Reason: cleaved peptide could not be detected or recovered from the chromatographic separation

Advances in Instrumentation for Dynamic Nuclear Polarization & Magic-Angle Spinning NMR · MIT · PhD

Tried and failed

adding salt to surfactant extraction buffer applied to protein extraction from FFPE tissue. Outcome: worse than baseline. Reason: substantially reduced peptide recovery efficiency

Enabling Sensitive and Robust Characterization of Protein Therapeutics and Biomarkers in Biomatrices Through Novel LC-MS-Based Strategies · University at Buffalo · PhD

Tried and failed

direct on-bead proteolytic digestion applied to streptavidin affinity purification eluates. Reason: poorly reproducible recovery and high background contamination from released streptavidin peptides

DISSECTING THE FUNCTION AND INTERACTOME OF PLEKHS1 IN PROSTATE TUMORIGENESIS · Cambridge · PhD

Considered and rejected

Considered and rejected: Rejected DEAE-C anion exchange chromatography for peptide purification due to substantial loss of peptide recovery, replacing it with cold 1:1 Et2O:hexane precipitation before HPLC.

Biosynthetic and Chemical Investigation of Lipid II-Binding Antimicrobials. · Duke · PhD

Considered and rejected

Considered and rejected: Rejected Protein A chromatography as the primary method for large-scale Pep12-Fc purification due to its slow required flow rate, choosing ammonium sulfate precipitation instead

Inhibition of Essential Protein-Protein Interactions in Plasmodium and SARS-CoV-2 · Johns Hopkins · Master's

Left open

Remeasure extraction efficiency by extracting a diluted multianalyte standard using solid-phase extraction and LC-MS. Blocker: Requires access to a wet laboratory, multianalyte chemical standards, SPE cartridges, and a triple quadrupole LC-MS instrument

Tracking antibiotic pollution in urban waterways using solid-phase extraction and triple quadrupole LCMS · UT Austin

Left open

Extend the SMART peptide purification method to complex peptide mixtures and pilot large-scale chromatography manufacturing runs. Blocker: Requires a wet chemistry lab, preparative chromatography equipment, and peptide synthesis/purification materials.

Fundamentals of peptide adsorption in reversed-phase liquid chromatography · Imperial · PhD

Left open

Develop a solid-phase aniline derivatization protocol to combine chemical derivatization and extraction into a single step for dissolved organic matter analysis. Blocker: Requires a wet chemistry laboratory, solid-phase extraction materials, and UHPLC-ESI-MS/MS instrumentation.

Molecular characterization of microbial interactions with labile dissolved organic matter · MIT · PhD

Left open

Optimize protein purification conditions for SLC25A51 to yield sufficient protein for proteoliposome reconstitution and structural microscopy. Blocker: Requires a wet biochemistry lab, physical reagents, and specialized structural microscopy equipment

Labeled nicotinamide adenine dinucleotide reveals the mechanism of mitochondrial NAD⁺ replenishment · UT Austin · PhD

Left open

Develop and evaluate multiple extraction methods to capture cationic and zwitterionic PFAS and organofluorines in serum. Blocker: Requires a wet chemistry laboratory, human serum samples, extraction chemicals, and analytical instruments (CIC, LC-MS/MS).

Characterization of per- and polyfluoroalkyl substances in human serum: novel methods for assessing exposure · Boston University · PhD

Left open

Compare the analytical performance of the QuEChERS extraction method against solid-phase extraction (SPE) for wastewater surveillance samples. Blocker: Requires a wet chemistry laboratory, chemical reagents, wastewater samples, and analytical instruments (e.g., LC-MS).

Applications of Wastewater Surveillance in a Small-Scale Wastewater System · Dalhousie · Master's

Left open

Develop molecularly imprinted polymer solid-phase extraction (MIP-SPE) methods to enrich polyphosphonates for compound-specific isotope analysis at low microgram-per-liter concentrations. Blocker: Requires chemical synthesis of molecularly imprinted polymers and physical wet-lab analytical equipment (LC-IRMS)

Manganese–driven oxidation of aminopolyphosphonates studied by compound–specific carbon isotope analysis · Tübingen · PhD

Left open

Develop an extraction and secondary chromatographic method using polar sorbents or anion exchange resins to retain short-chain PFAS analytes. Blocker: Requires an analytical chemistry wet lab, chromatography equipment, and chemical standards.

Evaluating "Forever Chemicals" from Soup to Nuts: Sample Preparation, Targeted Analysis, and Suspect Screening for the Characterization of Per- and Polyfluoroalkyl Substances (PFAS · University at Buffalo · PhD

Left open

Measure anion exchange sorbent affinity for phosphorothioate oligonucleotides, phosphorylated peptides, lipids, and proteins using coated planar nitinol extraction devices. Blocker: Requires a wet chemistry lab, functionalized nitinol substrates, sorbents, and analytical instruments (e.g., LC-MS, fluorescence spectrometers).

Improving bioanalytical methods for nucleic acids with chemically tuned separations · Iowa State · PhD