MacCoss Lab Documentation Index

UPDATE: The internal documents site has been moved to https://sites.google.com/a/uw.edu/maccoss-lab. Please look there for up-to-date documents.

This page provides links to lab protocols, software documentation, and tutorials.

Skyline-daily. This is a link to the day-by-day updates of Skyline, the MacCoss Lab software for SRM/MRM method-building and data analysis.

Background reading

More suggested papers can be found on the MacCoss lab home page.
• Review of mass-spectrometry based proteomics (a good place to start).
• An older review of peptide mass spectrometry.
• The 2-d ion trap.
• Review of shotgun proteomics.
• Yeast proteome analysis. An example of shotgun proteomics.
• Overview of quantitative methods
• Quantification using 15-N labelling.
• RelEx software for measuring quantitative differences.
• Mass spec analysis of membrane proteins.
• The original SEQUEST paper.
• Distributed SEQUEST for use on the cluster.
• Normalized SEQUEST score.
• DTASelect. (see below for documentation).
• File formats: MS1, MS2, and SQT.
• An introduction to the support vector machine (SVM).

Lab protocols

• E. coli growth and digestion.
• French press lysis.
• Western blots.
• Worm bleaching (hypochlorote wash).
• Digestion of insoluble protein fractions.
• Digestion with RapiGest (general protein digestion protocol).
• Red blood cell ghost prep.
• Sucrose floating of worms.
• TAP tag protocols.
• Worm growth.
• Acetone precipitation
• Freezing worms
• TCA precipitation
• Fractionation by sucrose gradient
• Cleaning the LTQ mass spectrometer.
• Methanol-chloroform precipitation.

Lab meeting presentations

Past group meeting presentations can be found here

Instrument usage log

• To log instrument usage, go to the form here.
• To view the instrument log, go to here.

Software documentation

All programs available to MacCoss lab members and collaborators are summarized in this table including links to documentation.

Tutorials

• Instructions on how to password protect your web pages
• Information about the mailing list for the lab, including how to subscribe and unsubscribe.
• Calendar tutorial for using the lab calendar for the meeting schedule and instrument sign-up.
• How to run hermie for peptide identifications.
• How to set up your ssh keys on a new computer account (proteome or sage). This is necessary for running SEQUEST searches with or without hermie.
• Instructions for recording new additions to the worm strain archive
• A short tutorial on how to run contrast to compare DTASelect results among multiple experiments.