A reference collection for shotgun (bottom-up) proteomics as we practice it at the UWPR

These pages collect the reference material we use and share at the UWPR, following the bottom-up proteomics workflow from sample preparation and digestion through acquisition strategies and data analysis. You will find background reading in the knowledgebase, step-by-step bench protocols, part lists for the consumables our systems use, and the safety documents that govern work in our lab. The MS Laboratories & Cores section shares our hardware designs and reference material with other laboratories and core facilities.

Knowledgebase: Shotgun Proteomics

Protein identification and quantification strategies: DDA, DIA, targeted acquisition (SRM, PRM), and stable isotope labeling.

 Sample Preparation

Protein extraction, separation, and enrichment.

 Protein Digestion & Peptide Fractionation

Cleaving proteins into peptides for LC-MS: MS-compatible detergents, digestion kits and enzymes, chemical cleavage, peptide fractionation and enrichment, and peptide cleanup.

 Protocols & Methods

Step-by-step bench protocols for sample preparation, digestion, peptide fractionation, and column preparation.

 Data Analysis

References and local tool guides for LC-MS data analysis.

 Reagents & Consumables

Part lists, standards, and consumables used on the UWPR systems.

 MS Laboratories & Cores

Hardware designs and reference material from the UWPR: the NSI source, the column-packing pressure cell, and common background ions.

 Safety

UWPR safety guidelines, chemical SOPs, and UW EH&S resources.