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Two friendly suggestions

1: Sometimes I run a peptide-concentration-curve series of replicates, and I get down to the limit of detection. Say I am targeting a peptide using 6 transitions, and that I have a replicate with a peptide abundance near the limit of detection, and say three of the transitions are useful, and the other three are too noisy and not used for quantitation. In the chromatogram of this precursor for...

Natan Basisty

  Natan Basisty, Ph.D., is a tenure-track investigator and PI of Translational Geroproteomics Unit at the National Institute on Aging (NIH). He received his Ph.D. in Pathology and B.S. in Biochemistry from the University of Washington, where he investigated the role of protein turnover in mammalian aging and longevity using combinations of metabolic labeling, LC-MS/MS, and software tools. In...

Import MRM Data

Hi, Brendan: Thank you very much for developing this user friendly useful software for MRM experiments. After learning the skyline tutorial, I am trying to import some of my data from TSQ ultra into skyline 0.7.0 in windows.My files contains MRM analysis for 7 peptides with 2 transitions for each peptide. I also include one full mass scan besides the MRM scans. The raw files seem to be imported....

06 - Kirkwood.pdf

The Flux Capacitor: Using Skyline for efficient processing of LC-MS/MS metabolic flux data Jay Kirkwood, PhD Work presented here performed at CSU Proteomics and Metabolomics Facility Dr. Jessica Prenni, Director Fort Collins, CO Currently at UW School of Pharmacy Seattle, WA Overview • Metabolic flux analysis introduction • Advantages over non-flux based approaches • Stable isotopic labels...

S1-2_Lee_ASMS_Skyline_User_Meeting_2025_blee_presentation.pdf

The world leader in serving science For Research Only | britt.lee@thermofisher.com1 Brittany Lee Lipidomics at scale: Skyline- powered targeted workflows on the Stellar Mass Spectrometer R&D Application Scientist, Thermo Fisher Scientific 73rd Conference on Mass Spectrometry and Allied Topics June 2, 2025 Conflict of interest disclosure: B.L., P.R., S.B., R.D., and C.J. are employees of Thermo...

Discrepancy in MS1 filter between Bruker MaXis raw data and Skyline

Hi, I am new to the Skyline software but already a big fan. I am running Skyline version 1.4.0.4421 (with Brukers Compass Xport tool- which all works brilliantly), on a Windows XP operating system.I appear to be having a couple of teething problems with the generated data set though.(The data were recorded on a Bruker MaXis Q-TOF Mass Spectrometer). 1. Skyline sometimes assigns the wrong charge...

Failind to build Skyline from source (proteowizard 2186)

Hi, I'm attempting to compile Skyline from source, but can't get past these strange "<build>no in common properties" errors. I've followed the build steps on the <a href="http://proteowizard.sourceforge.net/docs.html">proteowizard homepage</a> and am running on a 64-bit Windows 7 Professional installation. Any help would be greatly appreciated! The build printout it attached below. ...

Day_2_pm_02_15_Pino_StatDesignAnalysis.pdf

Study Design and Statistical Considerations 2019 Cape Town Targeted Quantitative Proteomics Course Lindsay Pino Lindsay.Pino@Pennmedicine.upenn.edu | www.lindsaykpino.com | @lkpino Replication 2xkcd.com/242 Objectives • Relate experimental design methods to LC-MS experiments • Assess the impact of variation on statistical analyses and interpretations • Build a conceptual foundation...

5 - Pennington.pdf

+ Steve Pennington UCD Conway Institute, UCD, Dublin Development of a serum protein assay for organ confined prostate cancer 15thth June 2014 + Discovery Sample accrual Protein Discovery Protein Identification and Characterisation Other analytes (anything measurable) Confirmation Assay development Antibody based Western blotting ELISA Mass Spectrometry based Multiple...

Thanks!

The seventh annual Skyline User Group Meeting was held in June 3rd at the spectacular San Diego Central Library. Within the architecturally award-winning facility, our space featured a folding glass wall where attendees could enjoy lunch "al fresco" on the outside patio beforehand and then we moved into a lovely auditorium to hear about new "omic's" research approaches and methods using Skyline and...

Event Information

Welcome The Skyline Team is pleased to announce the Seventh Annual Skyline User Group Meeting, which will be held in San Diego, CA on Sunday afternoon before ASMS.  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 spec techniques.   --Brendan When: Sunday, June 3,...

"LPino_StatisticalDesign.pdf" attached to page "Participants"

Lindsay Pino, MacCoss and Noble Labs Department of Genome Sciences, University of Washington 25 April 2016 lpino@uw.edu 1 Too long, don’t read: 2 •Replication is experiment-dependent •Block what you can •Randomize what you can’t block • Include all sources of variation in models Statistical design of experiments: From data collection, to analysis, to interpretation 3 Figure 1, Table...

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

INTRODUCTION TO MSSTATS Olga Vitek College of Science College of Computer and Information Science Example: A label-free experiment Question: which proteins change in abundance? 2 Normoxia Hypoxia 6 hrs 24 hrs 6 hrs 24 hrs MCF7 Culture 1 Culture 2 Culture 1 Culture 2 Culture 1 Culture 2 Culture 1 Culture 2 Culture 1 Culture 2 Culture 1 Culture 2 Culture 1 Culture 2 Culture 1 Culture 2...

05-ChenY.pdf

Global Characterization of Oxidative Stresses of IgG1 mAb YAO CHEN SCIENTIST, PROCESS DEVELOPMENT 03 JUNE 2018, SAN DIEGO, CA © 2018 Catalent. All rights reserved. Why Global Characterization? 1 X-ray crystal structure source (PDB): 1HZH Majority of conventional protein stability characterization monitors Met and Asn © 2018 Catalent. All rights reserved. Why Global Characterization?...

DIA analysis; unable to remove precursors

Hi , I have recently done a DIA analysis of whole proteome CLL cells after drug treatments. I could not resolve the issue of precursor removal in my analysis. I have unchecked the include DIA precursor window in transition settings --> filter and added "Start by precursor" in the document grid as recommended by one of the expert here. I am still getting this error (mentioned below) I am analysis...

"Day_1_am_09_00_Vitek_Intro_Design.pdf" attached to page "Design and Analysis of Quantitative Proteomics Experiments"

MSSTATS Meena Choi, Olga Vitek College of Science College of Computer and Information Science OUTLINE • Methods: background • Linear mixed effects models • Evaluation • Spike-in and experimental datasets 2 MSSTATS • Statistical relative quantification of proteins and peptides • Which protein changes in abundance? • Complex experimental designs • Multiple conditions, factorial experiments,...