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Full-MS/ddMS2 data import

Hello, I have encountered an issue that I'm unable to solve. So far I have used SkyLine (21.1.0.278) to process Full-MS small molecule data and I have found it to be the most user friendly and well designed tool so far. _Thank you very much, developers because SkyLine has truly helped to ease our lab's daily tasks _ :-) However, I wanted to process some Full-MS/ddMS2 data acquired on Orbitrap using...

IC-HRMS data for metabolomics

Hello, I recently heard about Skyline after ASMS 23 (everyone was using it!) and I have a few questions! I'm fairly new to the mass spec community and currently use compound discoverer/tracefinder for processing small molecule data for the metabolomics core I work in. These softwares are a bit more new-user friendly (AKA faster for me to be trained on/put to work on my own) but now that I know a little...

Day_2_pm_02_45_Vitek_Intro to MSstats.pdf

INTRODUCTION TO MSSTATS Meena Choi, Olga Vitek College of Computer and Information Science WHY STATISTICS? • Variation and uncertainty are unavoidable • Technical variation: sampling handling, storage, processing • Instrumental variation: matrix effects, ion suppression • Signal processing: peak boundaries, identity, intensity • Biological variation: variation in protein abundance • Overall...

SWATH without internal standards?

Hello. We were hoping that the recent webinar would answer this question, but we couldn't get any sound during the webinar. We went into SWATH a little bit blind and didn't realise the need for iRT or some other kind of internal standard. So we did our experiment and have tried to analyse it with Skyline. We see some huge fold changes but only one is considered statistically significant. The samples...

04-Sadowski.pdf

C R IC O S N o .0 0 2 1 3 J Pawel Sadowski, PhD Laboratory Manager, CARF Proteomics Laboratory Skyline User Meeting June 02, 2019 Adaptation of Skyline to Analyze Untargeted Metabolomics Data Collected on GCMS Instrument C R IC O S N o .0 0 2 1 3 J CARF Proteomics Laboratory • Central Analytical Research Facility (CARF) is a multi-user multi-laboratory facility with instrumentation...

Peptide settings with multiple enzymes - assay library and SWATH analyses

Hi Skyline team, I would like to ask you how to set multiple enzyme option in Peptide settings (Digestion). We typically use enzyme combination of LysC and Trypsin in our sample preparation workflow. Is it possible to set this combination in Skyline -> cleave C-terminal to K (always) and cleave C-terminal to R unless followed by P? We use Mascot as a search engine (LysC+Trypsin digestion, 1 allowed...

2019-ASMS-Pratt.pdf

Figure 5: Multi-replicate MS2 data analysis of IM assisted DIA data in Skyline with and without IM filtering using quadratic curve fitting. The same data set was imported twice with filtering either enabled or disabled (data annotated as ‘’noIM’). Shown inset within the chromatographic pane is IM resolved MTX, illustrating that quantitation without IMS filtering could lead to overestimation...

S2-1_Crawford_ASMS Skyline Users Meeting_Crawford2025_FINAL.pdf

Emily Crawford Skyline User Meeting June 1, 2025 Assessing Antidepressant Pharmaceuticals in the Environment through the Development of a Multidimensional Liquid Chromatography-Ion Mobility Spectrometry-Mass Spectrometry Library Antidepressant (AD) Use in the United States https://www.nimh.nih.gov/health/statistics/major-depression -National Institute of Mental Health 21 million adult...

Chromatogram information unavailable

Hi! I am working with a Q exactive in PRM mode. I created a transition list with my internal standard and thiol precursors. All compounds work well except my internal standard. I get a message saying Chromatogram information unavailable. I am sure about my retention time and fragmentation (I got them with a full ms d2). I don't understand that with the same parameters, I get a signal on Chromeleon...

Peak Area Integration

Hi Brendan, I was working in Skyline yesterday and I notice something a bit strange. In the PowerPoint file I’m sending to you, you can see the issue I’m having. I created a Peak Area Report so that I can export things out of Skyline to work with. For this particular peptide, I have an isotopically labeled peptide standard that I spiked in with the native peptide. I’ll give you this slight...

Event Information

Welcome Skyline Users, The Skyline Team is pleased to announce the Tenth Annual Skyline User Group Meeting before ASMS. Once more, we will be online with two webinars during the week before ASMS, due to the lingering situation with COVID-19. That said, there is just too much exciting work going on, by you the research community using Skyline, not to share once again this year -- and hopefully for...

Thanks!

Thanks for helping make this year's online Skyline User Group Meeting very much a success! With coronavirus still a concern, we reluctantly opted to take our annual face-to-face event online again over two days -- Oct 27 and 28, 2021 - hopefully for the very last time! Without missing a beat, Skyline users rallied once again to hear 11 speakers on a diverse spectrum of mass spectrometry topics plus...

Day_1_pm_01_00_Vitek_Failed Studies.pdf

INTRODUCTION TO EXPERIMENTAL DESIGN AND STATISTICAL ANALYSIS Olga Vitek College of Science College of Computer and Information Science WHY STATISTICS? • Variation and uncertainty are unavoidable • Technical variation: sampling handling, storage, processing • Instrumental variation: elution time, ion suppression • Signal processing: peak boundaries, identity, intensity • Biological variation:...

"Day_2_pm_02_30_Schilling_MS1_Filtering.pdf" attached to page "Design and Analysis of Quantitative Proteomics Experiments"

Section9 : Real-World MS1 Filtering with Skyline - targeting posttranslational modifications US HUPO workshop, March 18-19 2017 NH3 + HNCOCH3 acetyl transferases deacetylases Birgit Schilling Buck Institute for Research on Aging OH OPO3H- kinases phosphatase Methods Development Stem Cells (AMD) Prokaryotic Metabolic Regulation Tissue Homeostasis (‘Secretomics’) Biology of AgingAlzheimer’s...

Webinar 17 (Sabido).pptx

PRM Method Development and Data Analysis with Skyline Tutorial Webinar #17 With Brendan MacLean (Principal Developer, Skyline) Eduard Sabidó, Ph.D. (Head of the UPF/CRG Proteomics Unit) Cristina Chiva, Ph.D. (PRM researcher, CRG Proteomics Unit) Agenda Welcome from the Skyline team! PRM Method Development and Data Analysis with Skyline Introduction with Brendan MacLean Theoretical concepts...

"Day_3_pm_04_00_Aebersold_keynote.pdf" attached to page "Participants"

Design and biological relevance of targeted proteomic experiments January 30th, 2018 Ruedi Aebersold ETH Zurich Proteomic studies frequently fail at the computational level • 20 highly purified proteins at equimolar levels • 27 participating groups • Eventually every group met some success Bell et al Nature Methods , 2009 Outline • Some general considerations about proteomics...

Day_1_am_09.00_Collins_BiologicalSignificance.pdf

Biological significance of targeted proteomics experiments Ben Collins Queen’s University Belfast | School of Biological Sciences Quantitative Targeted Proteomics Workshop, ACGT Capetown – 18-21 Nov 2019 Many thanks to: • African Centre for Gene Technologies (ACGT) • Participants! Instructors – Brendan MacLean (UW) – Birgit Schilling (Buck Institute) – Lindsay Pino (U Penn) – Ben Collins...

Skyline External Tools-2_1.pdf

1 Skyline External Tools Documentation External Tools are customizable functions that can be accessed through the Tools drop down menu of the main Skyline window. The external tools framework allows researchers to share programs they have written to process the raw mass spectrometer data from a Skyline document in a user friendly manner. One example of an external tool would be an R script...

"Day_2_am_09_45_Spencer_Quantification.pdf" attached to page "Participants"

Protein Quantification Sandi Spencer MacCoss Lab Jan 2018, Pre-Lorne Workshop Complete Assay Validation Requires…. • Accuracy • Stability • Selectivity • Precision • Linearity • LLOQ Measurements are all Relative 940 kg 40 kg Quantitative Analysis 101 Calibration Curves Amount (moles) M ea su re d In te ns ity (A re a) LOD LLOQ ULOQ Linear Dynamic Range LOD: Limit...

"Day_3_am_11_00_Spencer_CaseStudies2.pdf" attached to page "Participants"

Applying Targeted Mass Spectrometry to Clinical Proteomics Sandra Spencer Postdoctoral Fellow MacCoss Laboratory Jan 2018, MSACL US 190 Years of Clinical Proteomics • Kidney Disease1 – Albumin precipitation by heat/acid – Now: Colorimetric pH test • Cancer – Light chain immunoglobulin, multiple myeloma2 – Now: Urine protein electrophoresis • Alzheimer’s Disease (amyloidosis) – Amyloid...