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S2-4_Champion_ASMS2025_Skyline_T01.pdf

Skyline Quantification of N-terminal Acetylation Peptidoforms Preserves Protein Abundance in Bottom-up Proteomics. Matthew M. Champion Skyline User Meeting ASMS 2025 Tuberculosis (TB) is the deadliest infectious disease in human history • Causes 1.2M deaths annually • Would be the deadliest pandemic if classified as one1 • Caused by Mycobacterium tuberculosis (M. tb) • A variety of non-tuberculosis...

Event Information

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...

09-Roux-Dalvai.pdf

Comparative analysis of library-based and library-free DIA strategies using Skyline software Florence ROUX-DALVAI Skyline User Group Meeting ASMS 2022, Minneapolis Skyline UGM – ASMS - 2022.06.05Florence Roux-Dalvai CHU de Québec – Université Laval 2 Discovery Proteomics Database search Trypsin digestion Protein sample LC-MSMS analysis BioRender.com Skyline UGM – ASMS - 2022.06.05...

Questions and Answers

Q: The ion mobility prediction tab appears to select the ion mobility value from the most intense scan. Is there a way to pick the most discriminatory ion mobility value in the same way (i.e. ion mobility value with the greatest difference in intensity between the best and second best peak)? Ans: The option you suggest is not currently available. The algorithm expects a targeted, clean sample prep...

7 - Dubois.pdf

Laura G. Dubois Duke Proteomics and Metabolomics Core Facility Expanding Skyline’s Capabilities to Small Molecule Data Analysis Goals and Objectives • Growth of Skyline utilization in our lab • How to create a Skyline document for small molecule applications • Exemplar small molecule workflows • Skyline – future additions and features to aid metabolomics community Skyline...

6 - Birgit.pdf

Platform Independent and Label-free Quantitation of Protein Acetylation and Phosphorylation using MS1 Extracted Ion Chromatograms in Skyline OH OPO3H- NH3 + HNCOCH3 kinases phosphatase acetyl transferases deacetylases Birgit Schilling Buck Institute for Research on Aging Workshop ASMS 2012 Mitochondrial Sirtuins and Metabolic Regulation • Type 2 Diabetes • Metabolic syndromes...

ImportingAssayLibraries-2_6.pdf

1 Skyline Importing Assay Libraries With some other SRM and DIA tools an extended transition list format called an “assay library” has become popular. The assay library format adds relative ion abundance, extracted from spectral libraries, and iRT (normalized retention time) information to other common transition list information (e.g. protein name, peptide sequence, precursor m/z and...

4-MeenaChoi.pdf

Sta$s$cal  Analysis  with  MSstats2   Meena  Choi   Purdue  University   2013.3.10   1  US  HUPO  2013  :  Sta.s.cal  Methods  for  Quan.ta.ve  Proteomics   Overview   1.  R  packages  :  MSstats2  and  SRMstats   2.  Default  analysis  of  a  label-­‐based  SRM  experiment  (Human   Plasma  :  Ovarian  Cancer)  ...

2015-MSACL-Thompson.pdf

Skyline for small molecules: a flexible tool for cross-platform LC-MS/MS method creation and data analysis for metabolomics. J. Will Thompson1, Brian Pratt2, Max Horowitz-Gelb2, Laura G. Dubois1, Lisa St.John-Williams1, Giuseppe Astarita3, M. Arthur Moseley1, Michael MacCoss2, and Brendan MacLean2 1Duke Proteomics and Metabolomics Core, Center for Genomic and Computational Biology, School of Medicine,...

1-6-Kennedy.pdf

Leveraging Skyline to develop and analyze data from a targeted mass spectrometry assay for pan-herpesvirus protein detection Michelle Kennedy, Joel Federspiel, Cora Betsinger, Matthew Tyl, and Ileana Cristea | Princeton University October 27, 2021 | Skyline User Group Meeting Declaration of interests: I.M.C., J.D.F., and M.A.K. have a provisional patent application on a "Method for quantitative...

Shimadzu 8060RX lcd contains no usable data

Hi, I've been using Skyline to process data from our Shimadzu 8060NX for a while now and everything works well. Recently we acquired a new Shimadzu 8060RX but for some reason when I import the results from this machine an error occurs: "The sample contains no usable data". When I use labsolutions from Shimadzu there is clearly data in the file. When I use SeeMS from ProteoWizard there is also...

"Day_2_am_08_30_Spencer_PriorKnowledge.pdf" attached to page "Participants"

Building on Prior Knowledge for Targeted Proteomics Sandra Spencer Postdoctoral Fellow MacCoss Laboratory Jan 2018, MSACL US Case Study: Metastatic Melanoma • Aug 2015: diagnosed with metastatic melanoma • Surgery to remove liver tumor, radiation of brain tumor • Therapeutic treatment with pembrolizumab • Dec 2015: cancer-free www.jimmycarterlibrary.gov www.accessatlanta.com ...

"catenacci method for AQUA.pdf" attached to message "signal to noise calculation and PRM"

Absolute Quantitation of Met Using Mass Spectrometry for Clinical Application: Assay Precision, Stability, and Correlation with MET Gene Amplification in FFPE Tumor Tissue Daniel V. T. Catenacci"1*, Wei-Li Liao"2, Sheeno Thyparambil2, Les Henderson1, Peng Xu1, Lei Zhao3, Brittany Rambo1, John Hart3, Shu-Yuan Xiao3, Kathleen Bengali2, Jamar Uzzell2, Marlene Darfler2, David B. Krizman2, Fabiola Cecchi4,...

"Day_1_am_10_40_Spencer_DiscoverytoTargeted.pdf" attached to page "Participants"

Moving from Discovery to Targeted Proteomics Sandi Spencer MacCoss Lab Jan 2018, Pre-Lorne Workshop So You Want to do Proteomics Proteins are…. – The major functional biomolecule of the cell – Post-translationally modified to regulate activity, localization, and degradation DNA Read-out Cell Status Indicator Actors in Disease Cytokine Receptor Growth Factor Receptor Integrin Receptor...

7 - Schubert.pdf

The Mtb Proteome Library: Development and application of assays for targeted MS analysis of the complete proteome of Mycobacterium tuberculosis by SRM and SWATH-MS Olga Schubert Group of Prof. Ruedi Aebersold ETH Zurich Skyline User Meeting 2013 Minneapolis Mycobacterium tuberculosis (Mtb) • Mycobacterium tuberculosis is the causative agent of Tuberculosis (TB) • One third of...

"PlanetOrbitrapA0003.pdf" attached to message "TARGETED APPROACH WITH LTQ-EXACTIVE"

Quantifying Peptides in Complex Mixtures with High Sensitivity and Precision Using a Targeted Approach with a Hybrid Linear Ion Trap Orbitrap Mass Spectrometer Reiko Kiyonami1, Amol Prakash2, Bradley Hart1, Jack Cunniff1, Vlad Zabrouskov1 1Thermo Fisher Scientific, San Jose, CA USA; 2Thermo Fisher Scientific BRIMS Center, Cambridge, MA, USA Application Note: 500 Key Words • LTQ Orbitrap...

Day_2_am_11_30_Borras_Clinical_Research.pdf

Targeted proteomics in Clinical Research Eva Borràs CRG-UPF Proteomics Unit Barcelona Brisbane 2019 Targeted proteomics in Clinical Research The problem of patient classification ? ? Which type of patient is him? Differentially abundant proteins not always have predictive power Protein concentration Targeted proteomics in Clinical Research The problem of patient classification MEASURE...

Day_2_pm_01_00_Jaffe_Chromatin PRM Assays.pdf

Proteomics and Biomarker Discovery When do you need a PRM assay? A case study in chromatin proteomics Jake Jaffe ASMS Short Course 2018 Outline §  Chromatin and its “issues” §  Definitions §  When do PRM assays make sense? §  Considerations for PRM method development §  Examples of “Research Grade” PRM assays PLEASE, PLEASE INTERRUPT AND ASK QUESTIONS! Histones and...

7 - Schubert.pptx

The Mtb Proteome Library: Development and application of assays for targeted MS analysis of the complete proteome of Mycobacterium tuberculosis by SRM and SWATH-MS Olga Schubert Group of Prof. Ruedi Aebersold ETH Zurich Skyline User Meeting 2013 Minneapolis 1 Mycobacterium tuberculosis (Mtb) Mycobacterium tuberculosis is the causative agent of Tuberculosis (TB) One third of the world’s population...

"1-Intro Stat (Vitek).pdf" attached to page "Design and Analysis of Quantitative Proteomics Experiments"

DESIGN AND ANALYSIS OF QUANTITATIVE PROTEOMIC EXPERIMENTS Intro to statistical methods and examples using Skyline Brendan MacLean Senior Scientist, University of Washington Lead developer of Skyline Meena Choi PhD Candidate, Purdue University Lead developer of MSstats Course organizers Olga Vitek, Associate Professor, Northeastern University 9:00-10:30 Intro to...