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COVID-19 update, March 20, 2020:

While regular SUMS laboratory operations are still on hold in compliance with the shelter in place order, contact SUMS for assistance with approved essential research projects.  SUMS aims to be ready to support the campus research restart under physical distancing guidelines.  Meetings and seminars will continue to be held via Zoom.  Email us at spectrometry@stanford.eduMore info

Events

SUMS Seminar Series
Online Thursdays, noon-1 pm

see below for seminar info and registration 

Note: In response to COVID-19 concerns, the seminars are going online;
Please register for individual seminars to get Zoom connection info

Thursday May 28 - SUMS Seminar Series

Mass spec bloopers!

The lighter side of mass spec.  A collection of the weird and the wonderful -- we couldn't make this stuff up if we tried!

Hear from our intrepid crew:

  • Birgit Schilling, Buck Institute
  • David Quilici, University of Nevada, Reno
  • Brett Phinney, University of California, Davis
  • Kimberly Lee, Cell Signaling Technology
  • Toni Koller, Massachusetts Institute of Technology
  • Allis Chien, Stanford University


Zoom meeting, noon-1 pm
Register here

June 1-12, 2020 - ASMS

Join the ASMS Reboot online!

https://asms.org/conferences/asms-2020-reboot/

Thursday June 18 - SUMS Seminar Series

ASMS review: recap the reboot!

What caught your eye at ASMS?  What are your take-homes?  Which presentations would you recommend to others?  Join us to recap the reboot -- compare notes, share highlights, and discuss developments of interest.


Zoom meeting, noon-1 pm
Register here

Thursday June 25, 2020 - SUMS Seminar Series

Fundamentals: Bioanalytical LC/MS method validation -- fit for purpose

With the increasing importance of research reproducibility and requirements of peer-reviewed scientific journals, the reliability of bioanalytical data and the value of method validation cannot be underestimated.  Unreliable results are subject to misinterpretation and can lead to project failure.  At the same time, extensive method validation is a complicated and time-consuming process and is not to be undertaken lightly.  This seminar will provide an overview of validation guidelines, requirements, approaches, workflow, and data analysis.  Case studies will illustrate the fit-for-purpose concept -- suiting the level of validation to the intended purpose of the study.  Please bring your questions and suggestions.

Ludmila Alexandrova, PhD
Zoom webinar, noon-1 pm
Register here


Webinars Available On-Demand

Thursday May 21, 2020 - SUMS Seminar Series

Fundamentals: Applications of LC/MS in small molecule drug discovery

Liquid chromatography-mass spectrometry (LC/MS) is a proven technique of choice for many assays implemented during the various stages of drug discovery and development. Join us for an overview of LC/MS applications in the drug discovery process with emphasis on metabolism and pharmacokinetic studies. We will share real-world project examples with focus on selection of suitable LC/MS instrumentation, method development approaches, sample preparation, data analysis and interpretation.

Ludmila Alexandrova, PhD
Zoom webinar, noon-1 pm
Watch recorded webinar

Thursday May 14 - SUMS Seminar Series

Breakout discussion topics:

  • Implementing new technologies & techniques
    What new areas are looming on your horizon?  Think and talk through approaches to selecting, testing and onboarding new methods in a core lab environment.
     
  • Folk wisdom: sample prep, instrument operations, data analysis
    The devil is in the (unpublished) details!  Share best practices for the various stages of a mass spec experiment, both in and out of the lab.
     
  • Research restart in the COVID-19 era
    During the unfolding COVID-19 situation, universities including Stanford have ceased non-essential research activities. As we prepare to return to the lab, this forum will be an opportunity to discuss changed workflows, new laboratory safety measures, and phased research restart strategies.
     

Bring your questions, share your experiences, and learn from each other in the hosted breakout discussions; then rejoin everyone in the main meeting room for a report back on key points from each of the discussions.  Note: the breakout room discussions will not be recorded; the summary reports to the recombined group will be recorded and made available here.

Speakers: you, and many others!
Zoom meeting, noon-1 pm
View recorded discussion summary

Thursday May 7, 2020 - SUMS Seminar Series

Fundamentals: Native mass spectrometry & relevant techniques

Beryl Xia, PhD
Zoom webinar, noon-1 pm
View recorded webinar
Download .pdf of slides

 

Interested in using mass spectrometry as a tool for structural biology? Curious about emerging  approaches for protein research? This seminar will provide a broad overview of native mass spectrometry and its applications, and touch on both popular and non-commercial emerging techniques relevant to native mass spectrometry. Topics include charge detection mass spectrometry (CDMS), ion mobility spectrometry (IMS), hydrogen-deuterium exchange (HDX), and more.

Thursday April 30, 2020 - SUMS Seminar Series

Fundamentals: Peptide quantitation strategies

Fang Liu, PhD; Beryl Xia, PhD
Zoom webinar, noon-1 pm
View recorded webinar
Download .pdf of slides

 

A deeper dive into quantitation techniques specifically for peptides, including selected reaction monitoring (SRM), parallel reaction monitoring (PRM), TOMAHAQ, SureQuant, and more.

Thursday April 23, 2020 - SUMS Seminar Series

Fundamentals: Measuring concentrations of small molecules using mass spectrometry - theory and practice, part II

Karolina Krasinska, MS
Zoom webinar, noon-1 pm
View recorded webinar
Download .pdf of slides


Part II, with emphasis on the practice: How can I measure concentrations of specific molecules in my sample? What are the possible approaches and how do I determine which one is best for my application?  What do I need to consider when planning such a project? This seminar will answer these questions and more, explaining mass spectrometry-based targeted quantitation from the ground up.  Learn about common pitfalls and strategies to navigate around them. Gain practical tips on data analysis and what your data can and can’t tell you. Bring your questions, learn from your fellow researchers’ questions, and come away with a solid grounding in this core analytical technique.

Thursday April 16, 2020 - SUMS Seminar Series

Fundamentals: New proteomic approaches and essential data handling tips

Kratika Singhal, MS; Rowan Matney, BA
Zoom webinar, noon-1 pm
View recorded webinar
Download .pdf of slides

 

Get the inside scoop on both ends of proteomic workflows: from sample prep approaches for experiments like TMTPro-16plex, phosphoproteomics and SureQuant, to what to do with your data once the results are in.

Thursday April 9, 2020 - SUMS Seminar Series

Fundamentals: Intact protein mass spectrometry - tips and best practices

Theresa McLaughlin, MS
Zoom webinar, noon-1 pm
View recorded webinar

Download .pdf of slides

Mass spectrometry is a powerful tool for analyzing intact proteins.  This seminar will focus on recommendations and practical considerations for success.  Which instruments should you use? How much sample is required? What buffer components can be tolerated?  Which modifications can be detected? How is the data analyzed? We will answer these questions and cover details of the ESI-LC/MS methods used at SUMS for intact protein MW determination.

Thursday April 2, 2020 - SUMS Seminar Series

Fundamentals: Measuring concentrations of small molecules using mass spectrometry - theory and practice, Part I

Karolina Krasinska, MS
Zoom webinar, noon-1 pm
View recorded webinar

Download .pdf of slides

How can I measure concentrations of specific molecules in my sample? Can I use a mass spectrometer to analyze my samples of interest?  What mass spectrometers are best suited for this purpose? What are the possible approaches and how do I determine which one is best for my application?  What do I need to consider when planning such a project? This seminar will answer these questions and more, explaining mass spectrometry-based targeted quantitation from the ground up.  Learn about common pitfalls and strategies to navigate around them. Gain practical tips on data analysis and what your data can and can’t tell you. Bring your questions, learn from your fellow researchers’ questions, and come away with a solid grounding in this core analytical technique.

Thursday March 26, 2020 - SUMS Seminar Series

Fundamentals: Quantitation strategies in mass spectrometry-based proteomics

Fang Liu, PhD
Zoom webinar, noon-1 pm
View recorded webinar
Download .pdf of slides

This seminar will cover the most commonly used methods for mass spectrometry‐based quantification in proteomic applications. Quantification can be performed using either unlabeled or labeled approaches. Advantages and disadvantages, including quantification accuracy and reproducibility, will be discussed for each type of approach. This is a great opportunity for scientists who are new to mass spectrometry to learn about options available in qualitative and quantitative proteomics, and which method to choose for their research applications.

Sponsor: PharmaFluidics

Mythbusters at SUMS

Episode 135: Hidden Nasties, air date 12/16/09

Mythbusters Episode 135

Event Archive

Thursday March 12, 2020 - SUMS Seminar Series

Analyzing the volatilome via Secondary Electro-Spray Ionization (SESI): Technical development and its application to breath and microbial VOCs

Dr. Guillermo Vidal-de-Miguel, CEO, Fossil Ion Technology
Prof. Jiangjiang Zhu, Ohio State University

Thursday Free Lunch Seminar, noon-1 pm
Bass Biology 122

Sponsor: Diagnose Early Inc.

The metabolome is very dynamic, with many molecules being continuously absorbed, synthesized, and degraded in response to the environment and other endogenous stimuli. Its volatile fraction (the volatilome) is available non-invasively, but relevant metabolites tend to be very diluted. Secondary Electro-Spray Ionization (SESI) enables the real-time analysis of biologically relevant metabolites with very low vapor pressures at minute concentrations. This enabled applications like breath analysis for biomarker discovery, pharmacokinetic profiling, and micro-organism monitoring. This presentation will be divided into two: the technical development of SESI and its application to breath analysis, and the detection and monitoring of microbial VOCs for human health studies. A Super SESI instrument will be available in the laboratory for demonstration.

Thursday February 27, 2020 - SUMS Seminar Series

Capillary Electrophoresis coupled to Mass Spectrometry: Is the combination of exceptional speed, resolution and identification the holy grail of molecule characterization and monitoring?

Bill McCrea, MS
Thursday Free Lunch Seminar, noon-1 pm
Bass Biology 122

Capillary electrophoresis has been a trusted and highly valued technology for many years due to the exceptional speed and resolution of the separations.  Unfortunately, the electrolytes and additives that make it so effective have traditionally limited CE to optical detection methods requiring additional analyses to determine absolute identification.  The development of microfluidic ZipChip technology has resulted in highly efficient separations of both large and small molecules using ESI compatible background electrolytes.  The combination of high-resolution CE separations and high-resolution mass spectrometric detection provides absolute identification with extremely fast runtimes for a variety of molecules in a wide range of matrices.  Add into the equation nano-scale flow rates and nanoliter sample consumption -- is this the holy grail of analytical workflows?

Bill McCrea received his MS in Synthetic Chemistry from Montana State University and spent over 15 years in the biotech and pharmaceutical industries developing oncology drugs.  During this time, It became clear that advanced technologies and instrumentation were the secret to improved efficiencies and getting more effective drugs to humans faster.  Helping researchers on the front line of drug research, discovery and development get the most useful tools to overcome challenges and impact their research has become an obsession.

Sponsor: 908 Devices

February 19, 2020 - SUMS Seminar Series

High Resolution Ion Mobility Spectrometry and IMSn from Monosaccharides to Protein Complexes

Andy Baker, PhD
Wednesday Free Lunch Seminar, noon-1 pm
Bass Biology 121

Over the past two decades ion mobility (IM) coupled with mass spectrometry (MS) has evolved into an enabling analytical technique widely utilized in research areas ranging from small molecule structural elucidation to the detailed analysis of large protein complexes. A novel circular mobility separator allows scalable pathlength and enables very high (500+) resolution IMS experiments.  In addition to the high mobility resolution, a number of novel experiments, including pre- and post mobility- fragmentation and IMSn experiments can be used to investigate ion structures. Selected examples of these experiments will be presented using model systems including nucleotides, sugars, proteins and small molecule imaging.

Andy Baker received his Ph.D in Analytical Chemistry from Indiana University working with Milos Novotny at the interface between problems of biochemical significance, high resolution chromatographic techniques, and mass spectrometric techniques. He is currently a Consulting MS Applications Scientist at Waters focusing on LC/MS/MS and LC/IMS/MS techniques for the characterization of target components from complex mixtures in both targeted and untargeted (‘OMIC) workflows.

Sponsor: Waters

January 22, 2020 - SUMS Seminar Series

LC/MS Analysis with Protein Metrics - The Basic, Best Practices, and Tips-n-Tricks

Speakers: Claire Bramwell, PhD; Maria Basanta-Sanchez, PhD; Marshall Bern, PhD; Eric Carlson, PhD
Wednesday Free Lunch Seminar, noon-1 pm
Bass Biology 121

Does your research rely on LC/MS analysis?  Do you spend long hours on data analysis?   Protein Metrics offers a broad set of solutions for post-data acquisition analysis covering a wide range of use cases and workflows.   Come learn about various basics and some best practices for your proteomics MS/MS searches, analyses of cross-linking, detailed PTMs, ways of doing reporting, or simply some Tips-N-Tricks.   Bring your data and we'll spend some time answering questions and helping you learn how to analyze your data better.

Sponsor: Protein Metrics

December 11, 2019 - SUMS Seminar Series

Mass Spec Fundamentals: what you didn’t know you needed to know

Speaker: Ryan Leib, PhD
Wednesday Free Lunch Seminar, noon-1 pm
Bass Biology 121

This seminar will cover the basic foundations of ion generation, manipulation, and detection in a typical LC/MS experiment, and why it matters to your research.  This is a great jumping on point for scientists new to mass spectrometery who are excited to learn a bit about the underlying physical processes that make these experiments possible.

This is the first in a series of Fundamentals seminars; future presentations will cover otehr critical topics like experimental design, data analysis, and statistical modeling approaches to mass spectrometry results.

Sponsor: ThermoFisher Scientific

November 13, 2019 - SUMS Seminar Series

SpatialOMx offers highest cellular sensitivity and specificity for molecular analysis of tissue

Shannon Cornett, PhD - Imaging/MRMS Applications Manager, Bruker Daltonics
Wednesday Free Lunch Seminar, noon-1 pm
Bass Biology 121

Abstract: LC-MS analyses of tissue homogenates identify a wide range of compounds extracted from all cell phenotypes in the homogenate.  Often, however, signals originating from discrete cells cannot be distinguished from signals from other cell phenotypes in the tissue.  MALDI Imaging is a molecular mapping tool which captures molecular signals directly from tissue and has been shown to differentiate cell phenotype even when histological analysis is indeterminate.  Combined, the two techniques enable a SpatialOMx approach to studying molecular changes in tissue.  Learn how timsTOF fleX with its dual ESI/MALDI ion source powers MALDI guided SpatialOMx to offer the most specific molecular insight into cellular processes.

Sponsor: Bruker

October 30, 2019 - SUMS Seminar Series

Atmospheric Ion Mobility Spectrometry - Applications for Macromolecular Analysis
Dr. Henry Benner - CEO, IonDx
 

Wednesday Free Lunch Seminar, noon-1 pm
Bass Biology 121

Abstract: Regulatory agencies require biotech organizations to perform detailed structural analysis of their biotherapeutics. This involves primary, secondary, tertiary and quaternary structural assessment. The majority of higher order structural analytics rely on indirect biophysical techniques because x-ray crystallography is not easily implemented in biotherapeutic workflows. A well-recognized technical challenge is to screen and fingerprint protein structures more rapidly. In this seminar we will provide background information on atmospheric pressure ion mobility spectrometry (IMS), an emerging analytical technology attempting to address this concern. We will showcase historical applications as well as recent research work on various classes of proteins, including monoclonal antibodies. We hope that this scientific webinar will introduce the audience to IMS and provide a forum for discussing potential applications for studying various protein-protein interactions, protein-nucleic acid structures and other exciting modalities.

Sponsor: IonDX

2019 Stanford University Mass Spectrometry Research Applications Symposium (SUMS-RAS)

October 10, 2019
Arrillaga Alumni Center
Details

2018 Stanford University Mass Spectrometry Research Applications Symposium (SUMS-RAS)

October 4, 2018
Arrillaga Alumni Center
Details

2017 Stanford University Mass Spectrometry Research Applications Symposium (SUMS-RAS)

October 26, 2017
Arrillaga Alumni Center
Details

2016 Stanford University Mass Spectrometry Research Applications Symposium (SUMS-RAS)

October 6, 2016
Arrillaga Alumni Center
Details

2015 Stanford University Mass Spectrometry Research Applications Symposium (SUMS-RAS)

October 29, 2015
Arrillaga Alumni Center
Details

2014 Stanford Mass Spectrometry Users' Meeting

October 7, 2014
Arrillaga Alumni Center
Details

2013 Stanford Mass Spectrometry Users' Meeting

October 29, 2013
Arrillaga Alumni Center
Details

2012 Stanford Mass Spectrometry Users' Meeting

October 23, 2012
Arrillaga Alumni Center
Details

2011 Stanford Mass Spectrometry Users' Meeting

September 26, 2011
Arrillaga Alumni Center
Details

2010 Stanford Mass Spectrometry Users' Meeting

September 2, 2010
Braun auditorium
Details

2009 Stanford Mass Spectrometry Users' Meeting

September 3, 2009
Braun auditorium
Details

2008 Stanford Mass Spectrometry Users' Meeting

August 21, 2008
Clark Center (Bio-X) auditorium
Details

Practical Aspects of Long Column Capillary Chromatography

April 1, 2007
ABRF 2007, Tampa, FL
New Objective Users' Meeting
download.pdf

2006 Stanford Mass Spectrometry Users' Meeting

September 7, 2006
Clark Center (Bio-X) auditorium
Details

Proteomic Investigations usng a Double-vented Tetraphasic Continuous Column Approach to MudPIT Analysis (abstract)

September 10, 2006
Oral Session: The Essential Role of On-line Separations for Mass Spectrometry Based Proteomics
American Chemical Society, Fall 2006, San Francisco, CA
download.pdf

Advances in Mass Spectrometry Workflows for Proteomics - Identification, Characterization, Biomarker Discovery and Validation

May 17, 2006
Stanford University, Stanford, CA
Presented by Applied Biosystems
Details

Waters Technology Forum

May 9, 2006
Stanford University, Stanford, CA
Presented by Waters Corporation
Details

Biological Applications of Q-Tof Mass Spectrometry in an Academic Core Facility

April 25, 2006
Q-Tof Users' Meeting, Monterey, CA
Hosted by Waters Corporation
download.pdfMeeting details

Benefits and Practical Aspects of Long Column Chromatography

March 8, 2006
Web seminar
Hosted by Eksigent Technologies
 

Cleaning up MudPIT: Triphasic Traps & Long Columns

February 13, 2006
ABRF 2006, Long Beach, CA
Eksigent Users' Meeting
download.pdf

2005 Stanford Mass Spectrometry Users' Meeting

September 1, 2005
Stanford University, Stanford, CA
Sponsored by Thermo Electron Corporation
Details

Vented Column Technology Applied to Proteomic MudPIT Analysis on Long Capillary Columns

June 9, 2005
ASMS 2005, San Antonio, TX
download.pdf

Automated Direct Monitoring of H/D Exchange Reactions for Mapping Conformational Landscapes of Proteins

June 5, 2005
ASMS 2005, San Antonio, TX
Advion Users' Meeting
download.pdf

An Evaluation of Extended Length Reverse Phase Capillary Columns for Simple LC/MS Peptide Mapping and for Complex Proteomic Separations

May 26, 2004
ASMS 2004, Nashville, TN
download.pdf

Mass Spectrometry & Stanford Chemistry

November 21, 2003
Stanford Dept. of Chemistry
download.pdf