Protocols, Software & Example Dataset

Title Description References
Regulations to use MS instrumentation and submit samples This document describes the current regulations to utilize the mass spectrometers in the MSF as well as submit samples for each instrument Text
Storks deliver babies (p=0.008) Many of the results we produce have some form of evaluation of their significance. This article provide a very important basis to understand what a p-value truly is.
Abstract: "This article shows that a highly statistically significant correlation exists between stork populations and human birth rates across Europe. While storks may not deliver babies, unthinking interpretation of correlation and p-values can certainly deliver unreliable conclusions."
Matthews, R., 2000. Storks deliver babies (p= 0.008). Teaching Statistics, 22(2), pp.36-38.


Title Description
Advion training material This link provide access to the training material for the Advion ExpressIon system, including videos, presentations and manuals.




Title Description References
FASP - Label free

FASP - TMT Labelling
This protocol describes a procedure for proteomics sample prep using medium to high amount of starting material (10-100 µg, indicatively). It utilizes membrane filter cartridges to perform all steps and yield a high quality peptide mixture from a variety of sample types. The protocol describes the procedure for formalin fixed paraffin embedded tissue samples, but it can be adapted to any type of protein sample. This method is compatible with detergents and other chemicals that are not normally recommended for MS analysis. The method has been validated for label free as well as TMT labelling. Wiśniewski, Jacek R., et al. "Universal sample preparation method for proteome analysis." Nature methods 6.5 (2009): 359-362.
In-gel digestion This protocol is intended for protein ID experiments, and it is a good standard procedure for most in-gel digestion experiments. Shevchenko, Andrej, et al. "In-gel digestion for mass spectrometric characterization of proteins and proteomes." Nature protocols 1.6 (2006): 2856.
Advanced in-gel digestion This page was created by the University of Washington Proteomics Resource (UWPR) and contains protocols for both standard as well as quantitative in-gel digestion sample preparation. In addition, it contains a list of useful staining kits compatible with mass spectrometry, as well as other resources to optimize in-gel digestion.
Shevchenko et al. Anal. Chem. 68, pp. 850-858, 1996

Wong, S. C., Grimley, C., Padua, A., Bourell, J. H., and Henzel, W. J. (1993) Peptide Mapping of 2-D Gel Proteins by Capillary HPLC. Tech. In Prot. Chem. IV, 371-378
Single-Tube Solid Phase-enhanced Sample Preparation (SP3) This protocol utilizes magnetic microparticles that have been functionalized with COOH moieties. The microparticles can capture proteins (and anything with a primary amine group), and the magnetic property allows to separate the solvent (and the chemicals/contaminants) from the protein during the sample preparation. It can handle very low protein amounts down to few ng.  This method is compatible with detergents and other chemicals that are not normally recommended for MS analysis.
Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J. Ultrasensitive proteome analysis using paramagnetic bead technology. Molecular Systems Biology. 2014; 10(10):1-10.

Hughes, Christopher S., et al. "Single-pot, solid-phase-enhanced sample preparation for proteomics experiments." Nature protocols 14.1 (2019): 68-85.
Q-Exactive training material This link opens up our Box folder with all the training material relevant to the Q-Exactive platform for proteomics. The training includes powerpoint presentations and video recordings of the on-line training performed by Thermo Scientific
MSF proteomics seminar:  Bottom up proteomics gel bands and simple proteins mixtures This material in this shared folder includes a presentation given by the MSF on 04/28/2023 which encompass the general approach to prepare, run and and analyze a simple proteoin mixture or a gel-band



Title Description References
MALDI Booking Instruction This document explains how to access our MALDI booking system.  
Polyalanine calibration dataset This dataset provides an example of how a polyalanine calibration should look like, both in positive as well as in negative mode. This is currently the standard calibration mix for the LSU MSF MALDI in the 500-5000 Da range Gruendling, Till, et al.  Rapid Communications in Mass Spectrometry 30.6 (2016): 681-683.
Bruker Guide to MALDI Sample Preparation This document is provided by Bruker, the manufacturer of the LSU MSF UltrafleXtreme MALDI instrument. It provides a useful starting point to select a proper matrix for your sample and create the appropriate solution.  
MALDI Target Cleaning This document is provided by Bruker, the manufacturer of the LSU MSF UltrafleXtreme MALDI instrument. It provides guidance for cleaning MALDI targets.  
Matrix Airbrush deposition guide This document provides a cleaning procedure for the airbrush available in the MSF as well as three publications to guide the use to a proper brushing deposition fo the matrix. Warren, Alexander D., David J. Mitchell, and Paul J. Gates. "Methodologies for the airbrush application of MALDI matrices." European Journal of Mass Spectrometry 24.1 (2018): 89-95.

Gemperline, Erin, Stephanie Rawson, and Lingjun Li. "Optimization and comparison of multiple MALDI matrix application methods for small molecule mass spectrometric imaging." Analytical chemistry 86.20 (2014): 10030-10035.

Li, Bin, et al. "A one-step matrix application method for MALDI mass spectrometry imaging of bacterial colony biofilms." Journal of Mass Spectrometry 51.11 (2016): 1030-1035.
HTX 3+ sprayer training  This document was created by Taylar Bell (Murray group) as an initial guide to the use of the HTX sprayer, which allows for automatic and reproducible deposition of MALDI matrix on almost any surface  
Bruker rapifleX training material This link point to a Box folder with traiing material related to the Bruker rapifleX MALDI TOF/TOF system. The material cover several aspect of the MALDI data acquisition process.  


Title Description References
ESI Sample Preparation instructions This document provides basic guidelines about the preparation of a sample for ESI TOF analysis. The procedures detailed are especially useful when submitting a sample for exact mass determination, such as a synthesis product.  

Title Description References
mMass A simple but powerful spectrum visualization and manipulation tool. Niedermeyer, Timo HJ, and Martin Strohalm. "mMass as a software tool for the annotation of cyclic peptide tandem mass spectra." PloS one 7.9 (2012): e44913.
Molecular Weight Calculator A PNNL application that helps calculating masses as well as perform accurate prediction of parameters such as isotopic patterns.  
openMS An open source LC-MS and LC-MS/MS data management and processing. It can also be used for visualization of single spectra. Lange, E., et al. "OPENMS; a generic open source framework for chromatography/MS-based proteomics." Molecular & Cellular Proteomics. Vol. 4. 
Proteomics and Imaging Tools Application written in C# that encloses several apps used during analysis with Waters mass spectrometers and Bruker MALDI instrument. Wang, Kelin, et al. "MALDI imaging directed laser ablation tissue microsampling for data independent acquisition proteomics." Journal of Mass Spectrometry 55.4 (2020): e4475.
MZmine 2 MZmine 2 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data. T. Pluskal, S. Castillo, A. Villar-Briones, M. Orešič, MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data, BMC Bioinformatics 11:395 (2010). PMID: 20650010
Bruker Data Analysis Viewer This software is the same software used to visualize and process data obtained with the Bruker amaZon ion trap mass spectrometer in the MSF facility. After installation, the software can be used as a data viewer (no processing will be available). Download of the software requires registration on the Bruker website.  
Thermo Software download page This link will bring you to the download page for Thermo Scientific software. You will need to create an accountin order to access the demo software as well as free software such as FreeStyle, which allows you to open all the raw data obtained with the Q-Exactive, or Proteome Discoverer, which allows you to see the results of our database searches. You may have to download the Foundantion program, which is located in the "Other releases" section. You can download any version of FreeStyle, while our version of Proteome Discoverer is the 2.4 SP1  
Instruction to install Proteome Discoverer 2.4 This documents provides details instructions to install Proteome Discoverer 2.4 on your computer.