Introducing MassHunter Profinder - Agilent€¦ · Introducing MassHunter Profinder A Key New Component of Agilent’s LC/MS Profiling Workflow February 13, 2014 Customer Presentation
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Introducing MassHunter Profinder
A Key New Component of
Agilent’s LC/MS Profiling
Workflow
February 13, 2014
Customer Presentation
1
Agenda
• Profiling Workflows
• Agilent’s Profiling Workflow and Software Tools
• MassHunter Profinder
• How to Obtain MassHunter Profinder
February 13, 2014
Customer Presentation
2
What is Profiling?
• Customers using a profiling
workflow are trying to
discover the differences in
their data sets
• They usually use untargeted
techniques to first determine
as many compounds in their
samples as possible
• They then use software tools
to find statistically
significant differences
February 13, 2014
Customer Presentation
3
What Types of Customers Do Profiling?
• Biomarker discovery, i.e. find some compound that
distinguishes between healthy and diseased states
• Metabolomics
• Proteomics
(In biological systems, a two-fold change is considered large!)
• Food profiling
• Impurity analysis (e.g. lot-to-lot variation)
• Water analysis (e.g. emerging water contaminants)
February 13, 2014
Customer Presentation
4
Agilent’s Profiling Workflow
February 13, 2014
Customer Presentation
5
GC
MS
L
CM
S
Separate &
Detect
GC/MSD
GC-QQQ
GC/QTOF
LC-TOF/QTOF
LC-QQQ
Feature
Finding
MassHunter Qual AMDIS or Find by
Chromatogram
Deconvolution
MassHunter
Profinder MFE, Find by Ion,
Find by Formula
Alignment &
Statistics
Mass Profiler
Mass Profiler
Professional
(MPP)
Identify
ID Browser
Pathways
Pathway
Architect
G3297AA Mass Profiler
• Designed for LC/MS data
• Import, store, and visualize
- Agilent LC/MS TOF, Q-TOF
• Two Group comparison (i.e. A vs B, healthy vs. diseased)
• Performs simple comparisons and visualizations (e.g. Mass vs. RT)
• ID Browser for compound identification
February 13, 2014
Customer Presentation
6
G3835AA Mass Profiler Professional
• Designed for Mass Spectrometry data
• Import, store, and visualize
- Agilent LC/MS TOF, Q-TOF, and QQQ
- Agilent GC/MS Quad, QQQ, and Q-TOF
- Agilent ICP-MS
- Generic file import (NMR data)
• Performs many types of statistical analysis
- ANOVA, clustering, PCA, class prediction
tools
• ID Browser for compound identification
• Pathway Architect for biological
contextualization
February 13, 2014
Customer Presentation
7
MassHunter Profinder High-throughput compound finding
MassHunter Profinder is a
productivity tool for processing
multiple samples in profiling
analyses
Fast Compound Finding
• Untargeted using MFE
• Targeted using Find by Formula
Visualize, review, and edit results
by compound across many
samples
Higher quality results based on
cross-sample processing
February 13, 2014
Customer Presentation
8
Aligned
EICs of
six
replicate
injections
MassHunter Profinder - Main View Only Four Linked Windows
February 13, 2014
Customer Presentation
9
Compound Group Table
Compound Details Table
EIC’s Spectra
1. Batch Molecular Feature Extraction
• Recursive MFE reduces false positives
2. Batch Recursive Feature Extraction
• Greater “missing feature” recovery
• Allows manual editing of compounds
3. Batch Targeted Feature Extraction
• Also allows manual editing
• Data source
Profinder’s Three Feature Extraction Algorithms
February 13, 2014
Customer Presentation
10
MFE rMFE
Find by Ion
Find by Formula
MFE rMFE
Molecular Feature Extraction
• Batch Molecular Feature Extraction begins with MFE on
each data file
• Features are extracted as in MassHunter Qualitative
Analysis, one file at a time
• Batch MFE then aligns across all sample files
February 13, 2014
Customer Presentation
11
raw grouped filtered features aligned
MFE
Why Batch MFE?
• MFE can sometimes assign different adduct species for each data file
• As an example, in one file the 537 species was identified as M+H, but in the other there was sufficient evidence to declare it M+Na
• Batch MFE will correct the assignment to M+Na, given the consensus assignment across all sample files
• This technique reduces false positives by pulling ONLY signal out of noise
February 13, 2014
Customer Presentation
12
537.3950 as M+H
537.3950 as M+Na
rMFE
1. Batch Molecular Feature Extraction
• Recursive MFE reduces false positives
2. Batch Recursive Feature Extraction
• Find by Ion reduces false negatives
• Allows manual editing of compounds
3. Batch Targeted Feature Extraction
• Also allows manual editing
• Data source can be .CEF files, a .CSV file
Profinder’s Three Feature Extraction Algorithms
February 13, 2014
Customer Presentation
13
MFE rMFE
Find by Ion
Find by Formula
MFE rMFE
1. Batch Molecular Feature Extraction
• Recursive MFE reduces false positives
2. Batch Recursive Feature Extraction
• Find by Ion reduces false negatives
• Allows manual editing of compounds
3. Batch Targeted Feature Extraction
• Also allows manual editing
• Formula source can be .CEF files, a .CSV file or a PCD/L
Profinder’s Three Feature Extraction Algorithms
February 13, 2014
Customer Presentation
14
MFE rMFE
Find by Ion
Find by Formula
MFE rMFE
Proteomics Analysis of Yeast Samples in Profinder Excellent Reproducibility on Technical Replicates
Active Dry (AD) Rapid Rise (RR)
February 13, 2014
Customer Presentation
15
Profiling of Raspberry Varieties Batch Processing using MassHunter Profinder
• 54 samples of four varieties of
raspberry grown in the UK
February 13, 2014
Customer Presentation
16
Heat map
Principal Component Analysis (PCA)
using 1148 compounds
MassHunter Profinder What’s Not Supported for B.06.00
• Pos/neg switching data
• All Ions MS/MS data
• GC/MS data
• Does not perform compound identification on its own
• “Not a replacement for Qual”
• Must be used with MPP 12.6.1 or greater
February 13, 2014
Customer Presentation
17
How Customers Can Obtain MassHunter Profinder
• MassHunter Profinder is free for MPP customers
• It will be placed on the MPP Supplemental DVD and the
software kit rolled
• It will also be available on Agilent SubscribeNet in the near
future to update existing customers
February 13, 2014
Customer Presentation
18
Benefits of MassHunter Profinder
• Fast processing of many samples
• Select data files
• Select feature extraction algorithm
• Go!
• Confidence in results
• Feature extraction eliminates false positive and false negatives
• Manual review and integration, even on sample groups
• Easy to use
• Just four review windows that are linked
• Wizards to run processing
February 13, 2014
Customer Presentation
19
Training Materials:
• ASMS 2013 Poster MP379 A Novel Two-Pass Feature
Extraction Workflow for the Statistical Profiling of Mass
Spectrometric Data
• Recorded Webex: http://www.chem.agilent.com/en-
US/TrainingEvents/eSeminars/en-US/Pages/masshunter-
profinder-webinar.aspx
• PDF copy of above Presentation: Profinder Webinar.pdf
• MassHunter Profinder Quick Start Guide:G3835-90014
February 13, 2014
Customer Presentation
20
Please Provide FEEDBACK… It’s Critical for Improving the program and prioritizing new features in the program.. What would you like… send us your wish list!!!!
February 13, 2014
Customer Presentation
21
Known Issues….
• Computer Configuration Memory - Batch Recursion utilizes LOTS of memory to draw EIC’s ..
- Performance improves as a function of memory.. More the better
- 32 GB is ok.. 60GB on Cloud is good.. 128 GB cluster amazing
• Data File Size effects # Features Found - All back to limits in Memory
• Manual Integration (Agil)
• Performance Speed: cloud and clusters
• Exported CEF Files: - Only can be used in MPP program
February 13, 2014
Customer Presentation
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February 13, 2014
Customer Presentation
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