Agenda  Welcome from the Skyline team!  PRM Targeted Proteomics Using Full-Scan MS2  Introduction with Brendan MacLean  PRM Introduced by Bruno Domon.

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Presentation transcript:

Agenda  Welcome from the Skyline team!  PRM Targeted Proteomics Using Full-Scan MS2  Introduction with Brendan MacLean  PRM Introduced by Bruno Domon – PRM Researcher  Tutorial with Brendan MacLean  Workflow overview  Data processing tutorial  Audience Q&A – submit questions to Google Form: (also in chat window)

Parallel Reaction Monitoring Synonyms  MRM-HR™  Targeted MS/MS (MacLean, ASMS 2011) - tMSMS  Psuedo-SRM (Sherrod, JPR 2012)  PRM (Peterson, MCP 2012)  More mass spectrometry synonyms

Chromatography-based Quantification  Hypothesis testing (Verification)  SRM  MS1 chromatogram extraction  PRM  Data independent acquisition (DIA/SWATH) AcquisitionTargetedSurvey More SelectivePRMDIA Less SelectiveSRMMS1 Got HYPOTHESIS

Dynamic Range for PRM? Gillet, et. al, MCP 2012 MS1PRM?

Multiple Instrument Vendors

Webinar 1: DDA Workflow Overview

Webinar 2: DIA Workflow Overview

DIA Prior Knowledge Workflow Relative Ion Abundance Normalized RT

Label-Free PRM Workflow Overview Relative Ion Abundance Normalized RT

PRM Acquisition Ion Source CID Q1 / Trap Mass Analyzer 2 m/z isolation

Product Ion Selectivity (PRM and DDA) 2 m/z ANFQGAITNR

Product Ion Selectivity (DIA) 20 m/z ANFQGAITNR

Label-Free PRM Workflow Overview Relative Ion Abundance Normalized RT

Label-Free PRM Workflow Overview Relative Ion Abundance Normalized RT

Label-Free PRM Workflow Overview Relative Ion Abundance Normalized RT

Extraction of Fragment Ions

Precursor and Product Ion Information

Peptide Search MS/MS from PRM Sherrod, S. et al. J. Prot. Res

Proving Peak ID in Label-Free PRM

PRM with Labeled Internal Standards  Extensive support in Skyline

Labeled PRM Workflow Overview Relative Ion Abundance Normalized RT

Tutorial  Basic PRM Data Analysis

Learn More  Webinar #4: Tuesday, Feb. 10 th – Targeted Method Design  Workshops at US HUPO and ASMS  Weeklong Course in Northeastern University, Boston  May  Weeklong Course at ETH, Zurich  June  Weeklong Course at PRBB, Barcelona  November  More… TBA

Questions?  Ask any questions you have on the topic of PRM experiments with Skyline.  Take the post-webinar survey:

Tutorial Webinar #3 This ends this Skyline Tutorial Webinar. Please give us feedback on the webinar at the following survey: A recording of today’s meeting will be available shortly at the Skyline website. We look forward to seeing you at a future Skyline Tutorial Webinar.