Introduction to Mass Spectrometry

Mass spectrometry is an analytical technique that provides direct information about the analyte. When applied to proteomics, we can get amino acid sequence information of the peptides in our sample and use data processing tools to map the peptide sequences back to their source proteins.  

In the Sheynkman lab, we perform LC-MS analysis using an Orbitrap Eclipse mass spectrometer for a variety of proteomics projects. Applications include: global “discovery” proteomics, large-scale targeted identification of isoform-specific peptides using the long-read proteogenomics (LRP) pipeline, and affinity-purification mass spectrometry (AP-MS) to interrogate isoform-specific protein binding partners. 

We rely heavily on the bioinformatic output of sample-specific long-read RNA sequencing (lrRNA-seq) to obtain sample-matched protein databases. These databases are used during the protein inference steps of LC-MS analysis. The full suite of potential protein isoforms in our sample is derived from the lrRNA-seq data and subsequent LRP pipeline analysis. The resulting sample-matched protein database is a crucial ingredient for confirming the protein expression of novel protein isoforms.

How do I get started? 

Read about the MS research we are currently pursuing: interactomics and novel MS technologies for proteoform detection.

Here are some links to review papers for mass spec and proteomics. Also, check out the series of fun YouTube videos from Dr. Alan Doucette! 

An Introduction to Mass Spectrometry-Based Proteomics (2023)

A Quantitative Proteome Map of the Human Body (2020)

A draft map of the human proteome (2014)

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0 (2019)

Lessons in de novo peptide sequencing by tandem mass spectrometry (2013)

Mass spectrometry for proteomics (2008)

Instrumentation at the Leading Edge of Proteomics (2024)

Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics? (2022)

Dr. Alan Doucette has a series of FUN and educational videos with fantastic introductory lessons in mass spec and proteomics:

“Short Chemistry” YouTube channel