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

22

February 13, 2014

Customer Presentation

23