Speakers

Michael J. MacCoss, Ph.D. (University of Washington): Introduction and event host

Brendan MacLean (MacCoss Lab, University of Washington): Status of the Skyline open-source software project 15 years after its inception [video]
The Skyline project started just after ASMS 2008 as a 2-year effort to bring better SRM/MRM software tools to the NCI-CPTAC Verification Working Group that could support the variety of mass spectrometers in use in participating laboratories. Nearly 15 years later, the Skyline project is a thriving proteomics community open-source collaboration supporting 6 mass spec instrument vendors, integrated with a wide variety of external software, with thousands of users worldwide and many thousands of instances started each week. (More info...)

Abigail Burrows Franco Ph.D., (University of Kentucky): Efficient generation of highly multiplexed serum biomarker panels using gas phase fractionation and DIA libraries [video]
Data Independent Acquisition (DIA) methods have become an attractive alternative to traditional Data Dependent Acquisition (DDA) methods for quantitative proteomics and biomarker identification. Here, we describe a novel DIA methodology for evaluating the equine proteome. Detectable peptides can serve as biomarkers for equine medicine to diagnose health conditions, monitor disease progression, and detect performance-enhancing drugs in anti-doping efforts. Typically, DDA-based spectrum libraries are required prior to DIA data analysis. (More info...)

Philip Remes Ph.D., (Thermo Fisher Scientific): A Skyline Tool for Creating Robust Large Scale Targeted MS/MS Assays [video]
Targeted MS/MS is the gold standard for quantitative quality in proteomics but is not widely utilized for large assays (1000’s of targets), because of the manual work involved in setting up the experiment, maintaining the retention time schedule, and analyzing the results. We created a Skyline External tool that automates the tedious parts and makes large scale targeted MS/MS a competitive option to Data Independent Acquisition (DIA) for some situations. (More info...)

Julia Robbins, (Talus Bio): How sweet it is: Leveraging the nuclear envelope glycome for the automated extraction of proteins from cell nuclei [video]
Protein localization within the subcellular environment influences their structure and function. One example is the transcription factor (TF) protein class, which commonly reside in the cytosol prior to being activated, typically by post-translational modification, and then translocating to the nucleus where they interact with DNA and other regulatory proteins to initiate transcription of genes. However, studying TFs is difficult because the process of isolating nuclei is a low-throughput, manual process, and existing bead-based approaches are not selective for nuclei. (More info...)

Stoyan Stoychev Ph.D., (Evosep and ReSyn Biosciences): Mag-Net: Bead based capture of membrane particles from plasma enables liquid biopsy measurements for >4,500 proteins [video]
The robust quantitative characterization of proteins from plasma is critical to the diagnosis of disease and therapeutic monitoring. Membrane-bound particles in plasma are composed of extracellular vesicles, exosomes, and apoptotic bodies and represent ~1-2% of the total protein composition. Analysis of this enriched membrane particle fraction by mass spectrometry is effectively a “liquid biopsy,” and significantly improves the dynamic range of the proteins measurable in plasma. (More info...)

Gary Siuzdak Ph.D., (The Scripps Research Institute): METLIN Ion Mobility: How to Analyze a Million Molecular Standards and Stay Sane [video]
The new METLIN Ion Mobility database has now been created having just completed the analysis of 30,000 molecular standards. METLIN Ion Mobility is an ongoing effort of the METLIN Tandem Mass Spectrometry database with over one million molecular standards analyzed, representing a challenging endeavor, especially when it needs to be accomplished at multiple collisional energies and in both positive and negative ionization modes. (More info...)

Lightning Talks

Ellen Casavant, Ph.D., (Genetech): AutoQC enables efficient and reproducible LC-MS/MS chromatography and instrumentation [video]
Mass spectrometry based proteomics is one approach to identifying and quantifying proteins from biological samples. In the Translational Medicine team at Genentech, discovery and targeted proteomics are performed on clinical samples to discover or quantify proteins relevant to therapeutic treatment or disease progression. To acquire high confidence data that can assist in therapeutic pipeline decision making, consistent evaluation of system suitability is imperative. (More info...)

Gunnar Dittmar Ph.D., (Luxembourg Institute of Health): Quantification of 782 Plasma Peptides by Multiplexed Targeted Proteomics [video]
Blood analysis is one of the foundations of clinical diagnostics. In recent years the analysis of proteins in blood samples by mass spectrometry has taken a jump forward in terms of sensitivity and the number of identified proteins. The recent development of parallel reaction monitoring with parallel accumulation and serial fragmentation (prm-PASEF) combines ion mobility as an additional separation dimension. This increases the proteome coverage while allowing the use of shorter chromatographic gradients. (More info...)

Jeroen Demmers Ph.D., (Erasmus MC Proteomics): Targeted mass spectrometry reveals that USP7 regulates the ncPRC1 Polycomb axis [video]
Ubiquitin-specific protease 7 (USP7) is a deubiquitylating enzyme that is involved in the regulation of multiple key cellular processes, including tumor suppression, transcription, epigenetics, the DNA damage response, and DNA replication. Whereas the role of USP7 in the p53 pathway is well established, a full picture of the USP7 regulatory network is lacking. For example, USP7 has been connected to the Polycomb system, but the molecular mechanism through which USP7 regulates Polycomb functions remains unclear. For debiquitinating enzymes, the regulatory mode of action is at the posttranslational level and, thus, proteomics tools are indispensable to study this. Here, we took an unbiased multi-omics approach with a strong targeted quantitative proteomics component to define the core USP7 network. (More info...)

Tom Lin Ph.D., (Washington University in St. Louis): An Unbiased Proteomics Method to Discover Posttranslational Arginylation Sites from Whole Proteomes [video]
Posttranslational arginylation installed on proteins by arginyltransferase (ATE1) is a critical modification for mammalian cellular homeostasis and development. Absence of this modification in ATE1 knockout mice was embryonically lethal with various signs of cardiovascular defects. Proteomic profiling of arginylation sites is extremely difficult since mass spectrometry cannot distinguish the same mass of translational and posttranslational arginine (+156 Da), and arginylated proteins go through Arg/N-degron pathway for ubiquitin-mediated degradation. Existing methods have proposed plausible arginylation sites on a handful of proteins (More info...)

Eduard Sabido Ph.D., (Center for Genomics Regulation and the University Pompeu Fabra): High-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry [video]
Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their dysregulation in humans has been linked to several diseases such as cancer, metabolic diseases or neurological disorder. Nowadays, liquid chromatography-tandem mass spectrometry is considered the gold standard method for the identification and quantification of these modifications due to its sensitivity and accuracy. However, the analysis of modified ribonucleosides by mass spectrometry is complex due to the presence of positional isomers. (More info...)

Ariana Shannon, (Ohio State University): Generating fit-for-purpose targeted assays from a catalog of pre-screened peptides using data-independent acquisition (DIA) based figures of merit [video]
The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) classifies proteomics studies in three tiers, where targeted assays are typically Tier-1 (clinical) or Tier-2 (non-clinical), and global studies are Tier-3. Tier-2 targeted proteomics assays using parallel reaction monitoring (PRM) are developed by assessing figures-of-merit (such as limit of quantification) with stable isotope labeled (SIL) peptides and refining or re-selecting those targets through iterative experiments. This process is expensive and time consuming as SIL peptides must be purchased prior to validation. (More info...)

Welcome

The Skyline Team is pleased to announce this year's big event, the Twelfth Annual Skyline User Group Meeting, which will be held in Houston, TX on Sunday afternoon before ASMS. We love seeing you all in-person -- so be sure to register and attend! We would like to thank the event sponsors (see below) for their generosity and interest in collaborating with the Skyline project on exciting new targeted and quantitative mass spectrometry techniques.  

--Brendan

When: Sunday, June 4, 2023
         12:00 - 1:00 pm : Lunch served
         1:00 - 2:30 pm : Presentations
         2:30 - 3:00 pm : Snacks and break-out discussions
         3:00 - 4:30 pm : Presentations

Where: Crystal Ballroom at the Rice 909 Texas Avenue, Houston, TX 77002 (map)

• From the Convention Center, head northeast on Avenida De Las Americas toward Mc Kinney
• Turn left onto Walker St
• Walk seven blocks and turn right onto Main Street
• Walk three blocks and turn left onto Texas Street
• Crystal Ballroom at the Rice (909 Texas Avenue) is on the right in 1/2 block

Here are transportation options in downtown Houston.

Scheduled Speakers

Michael J. MacCoss, Ph.D. (University of Washington): Introduction and event host

Brendan MacLean (MacCoss Lab, University of Washington): Status of the Skyline open-source software project 15 years after its inception
The Skyline project started just after ASMS 2008 as a 2-year effort to bring better SRM/MRM software tools to the NCI-CPTAC Verification Working Group that could support the variety of mass spectrometers in use in participating laboratories. Nearly 15 years later, the Skyline project is a thriving proteomics community open-source collaboration supporting 6 mass spec instrument vendors, integrated with a wide variety of external software, with thousands of users worldwide and many thousands of instances started each week. (More info...)

Abigail Burrows Franco Ph.D., (University of Kentucky): Efficient generation of highly multiplexed serum biomarker panels using gas phase fractionation and DIA libraries
Data Independent Acquisition (DIA) methods have become an attractive alternative to traditional Data Dependent Acquisition (DDA) methods for quantitative proteomics and biomarker identification. Here, we describe a novel DIA methodology for evaluating the equine proteome. Detectable peptides can serve as biomarkers for equine medicine to diagnose health conditions, monitor disease progression, and detect performance-enhancing drugs in anti-doping efforts. Typically, DDA-based spectrum libraries are required prior to DIA data analysis. (More info...)

Philip Remes Ph.D., (Thermo Fisher Scientific): A Skyline Tool for Creating Robust Large Scale Targeted MS/MS Assays
Targeted MS/MS is the gold standard for quantitative quality in proteomics but is not widely utilized for large assays (1000’s of targets), because of the manual work involved in setting up the experiment, maintaining the retention time schedule, and analyzing the results. We created a Skyline External tool that automates the tedious parts and makes large scale targeted MS/MS a competitive option to Data Independent Acquisition (DIA) for some situations. (More info...)

Julia Robbins, (Talus Bio): How sweet it is: Leveraging the nuclear envelope glycome for the automated extraction of proteins from cell nuclei
Protein localization within the subcellular environment influences their structure and function. One example is the transcription factor (TF) protein class, which commonly reside in the cytosol prior to being activated, typically by post-translational modification, and then translocating to the nucleus where they interact with DNA and other regulatory proteins to initiate transcription of genes. However, studying TFs is difficult because the process of isolating nuclei is a low-throughput, manual process, and existing bead-based approaches are not selective for nuclei. (More info...)

Stoyan Stoychev Ph.D., (Evosep and ReSyn Biosciences): Mag-Net: Bead based capture of membrane particles from plasma enables liquid biopsy measurements for >4,500 proteins
The robust quantitative characterization of proteins from plasma is critical to the diagnosis of disease and therapeutic monitoring. Membrane-bound particles in plasma are composed of extracellular vesicles, exosomes, and apoptotic bodies and represent ~1-2% of the total protein composition. Analysis of this enriched membrane particle fraction by mass spectrometry is effectively a “liquid biopsy,” and significantly improves the dynamic range of the proteins measurable in plasma. (More info...)

Gary Siuzdak Ph.D., (The Scripps Research Institute): METLIN Ion Mobility: How to Analyze a Million Molecular Standards and Stay Sane
The new METLIN Ion Mobility database has now been created having just completed the analysis of 30,000 molecular standards. METLIN Ion Mobility is an ongoing effort of the METLIN Tandem Mass Spectrometry database with over one million molecular standards analyzed, representing a challenging endeavor, especially when it needs to be accomplished at multiple collisional energies and in both positive and negative ionization modes. (More info...)

Lightning Talks

Ellen Casavant, Ph.D., (Genetech): AutoQC enables efficient and reproducible LC-MS/MS chromatography and instrumentation
Mass spectrometry based proteomics is one approach to identifying and quantifying proteins from biological samples. In the Translational Medicine team at Genentech, discovery and targeted proteomics are performed on clinical samples to discover or quantify proteins relevant to therapeutic treatment or disease progression. To acquire high confidence data that can assist in therapeutic pipeline decision making, consistent evaluation of system suitability is imperative. (More info...)

Gunnar Dittmar Ph.D., (Luxembourg Institute of Health): Quantification of 782 Plasma Peptides by Multiplexed Targeted Proteomics
Blood analysis is one of the foundations of clinical diagnostics. In recent years the analysis of proteins in blood samples by mass spectrometry has taken a jump forward in terms of sensitivity and the number of identified proteins. The recent development of parallel reaction monitoring with parallel accumulation and serial fragmentation (prm-PASEF) combines ion mobility as an additional separation dimension. This increases the proteome coverage while allowing the use of shorter chromatographic gradients. (More info...)

Jeroen Demmers Ph.D., (Erasmus MC Proteomics): Targeted mass spectrometry reveals that USP7 regulates the ncPRC1 Polycomb axis
Ubiquitin-specific protease 7 (USP7) is a deubiquitylating enzyme that is involved in the regulation of multiple key cellular processes, including tumor suppression, transcription, epigenetics, the DNA damage response, and DNA replication. Whereas the role of USP7 in the p53 pathway is well established, a full picture of the USP7 regulatory network is lacking. For example, USP7 has been connected to the Polycomb system, but the molecular mechanism through which USP7 regulates Polycomb functions remains unclear. For debiquitinating enzymes, the regulatory mode of action is at the posttranslational level and, thus, proteomics tools are indispensable to study this. Here, we took an unbiased multi-omics approach with a strong targeted quantitative proteomics component to define the core USP7 network. (More info...)

Tom Lin Ph.D., (Washington University in St. Louis): An Unbiased Proteomics Method to Discover Posttranslational Arginylation Sites from Whole Proteomes
Posttranslational arginylation installed on proteins by arginyltransferase (ATE1) is a critical modification for mammalian cellular homeostasis and development. Absence of this modification in ATE1 knockout mice was embryonically lethal with various signs of cardiovascular defects. Proteomic profiling of arginylation sites is extremely difficult since mass spectrometry cannot distinguish the same mass of translational and posttranslational arginine (+156 Da), and arginylated proteins go through Arg/N-degron pathway for ubiquitin-mediated degradation. Existing methods have proposed plausible arginylation sites on a handful of proteins (<20), most of which have not been further validated or functionally investigated. Therefore, protein arginylation remains an understudied field. (More info...)

Eduard Sabido Ph.D., (Center for Genomics Regulation and the University Pompeu Fabra): High-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry
Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their dysregulation in humans has been linked to several diseases such as cancer, metabolic diseases or neurological disorder. Nowadays, liquid chromatography-tandem mass spectrometry is considered the gold standard method for the identification and quantification of these modifications due to its sensitivity and accuracy. However, the analysis of modified ribonucleosides by mass spectrometry is complex due to the presence of positional isomers. (More info...)

Ariana Shannon, (Ohio State University): Generating fit-for-purpose targeted assays from a catalog of pre-screened peptides using data-independent acquisition (DIA) based figures of merit
The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) classifies proteomics studies in three tiers, where targeted assays are typically Tier-1 (clinical) or Tier-2 (non-clinical), and global studies are Tier-3. Tier-2 targeted proteomics assays using parallel reaction monitoring (PRM) are developed by assessing figures-of-merit (such as limit of quantification) with stable isotope labeled (SIL) peptides and refining or re-selecting those targets through iterative experiments. This process is expensive and time consuming as SIL peptides must be purchased prior to validation. (More info...)

Sponsors