PLATFORM SOLUTION

TRANSOMICS

BEST-IN-CLASS OMICS SOFTWARE

MEETS HIGH DEFINITION ESI LC/MS HARDWARE.

Last but not least they demanded a

common omics workflow to turn large,

biologically significant, multi-run

LC/MS datasets into meaningful,

publication-ready, reports.

Big challenge. Big solution.

T he Waters TransOmics™ Solution

integrates the most powerful

technologies from our unique

portfolio: Exclusive Sample Preparation

Chemistries, UltraPerformance

Liquid Chromatography (UPLC®),

UltraPerformance Convergence

Chromatography™ (UPC2®) and

High Definition MS (HDMS™),

with Progenesis® QI software

from Nonlinear Dynamics,™

a Waters company.

T he Waters TransOmics Solution

for Proteomics and/or for

Metabolomics & Lipidomics,

redefines the benchmarks for

resolving complex biological

samples and streamlining the

omics workflow – from sample

preparation to publication.

Our Centers of Innovation program

has been designed to foster

collaborations with leading life

scientists worldwide. T he keen insights

we gain from working with our

academic partners focuses our

R&D resources on developing solutions

that deliver meaningful impact to

their and your research initiatives.

Our collaborators challenged us to

develop an integrated multi-omics

research solution that:

■■ Focuses on the preferences of

proteomic researchers, molecular

biologists, and biochemists

■■ Redefines the boundaries of

sensitivity without compromising

dynamic range

■■ Maximizes feature identification

while minimizing false discovery

■■ Delivers a comprehensive range

of onboard statistical tools and

provides the ability to import

and process other vendor’s

LC/MS data (i.e., Agilent,

Bruker, ABSciex, Thermo)

The world’s leading OMICS researchers drive purposeful innovation at Waters.

“ While the last 10 years of MS-based proteomics were driven by

improvements in MS-hardware performance, it is my feeling that

the next 10 years will be driven by informatics... I am pleased

to see two strong partners in the field [Waters and Nonlinear

Dynamics] are teaming up to address this area.”

BERNHARD KUSTER, Ph.D.Chair of Proteomics and Bioanalytics, Technische Universitaet Muenchen, Germany

Waters TransOmics Solution.

TRANSOMICS SOLUTIONwith Progenesis QI Software

Waters TransOmics Solution for Proteomics and/or

Metabolomics & Lipidomics combines our uniquely powerful

High Definition Mass Spectrometry® technology (ion mobility

enhanced time-of-flight mass spectrometry (Tof MS)) with

Nonlinear Dynamics’ acclaimed bioinformatics. Each TransOmics

Solution can be configured as a dedicated system or a multi-omics

platform based on your choice of a single MS core instrument.

Choosing the Waters SYNAPT® G2-Si High Definition MS (HDMS)

System enables you to perform LC/MS and MALDI on a single

platform with the following critical features:

■■ Versatile cost-effective electron transfer dissociation (ETD)■■ Data dependant acquisition (DDA) and data independent

acquisition (DIA) ■■ Targeted analysis software for triple quadrupole-like quantification■■ Comprehensive label free data acquisition and quantification■■ MALDI acquired images enhanced by mobility separations

Or choose the Xevo® G2-S QTof, which offers a compact benchtop

platform with attomole sensitivity.

FOR P ROT EOMICS

SAMPLE PREPARATION

■■ Waters RapiGest™ enzymatic digest promoter

■■ Waters MassPREP™ quantitative standards

CHROMATOGRAPHY ■■ Waters ACQUITY UPLC® M-Class

■■ One-dimensional reversed phase (RP)■■ Two-dimensional RP/RP for low pH/

high pH separations

BIOINFORMATICS■■ Progenesis QI for Proteomics

■■ Sample comparisons across multiple groups,

analytical and biological replicates■■ Peptide/protein ID from DDA and/or DIA■■ Hi3 quantification■■ Flexible statistical tools including ANOVA, PCA,

hierarchical clustering, power analysis■■ Flexible report generator for information sharing■■ Quality Metrics, a rapid visual check of sample

measurements and analytical quality

SYSTEM VERIFICATION

■■ Waters Proteomics System Verification Kit

FOR METABOLOMICS & LIP IDOMICS

SAMPLE PREPARATION

■■ Waters Ostro™ and Oasis® chemistries for lipid

extraction/fractionation in an automatable

96-well format

CHROMATOGRAPHY

■■ Waters ACQUITY UPLC I-Class

■■ Waters ACQUITY UPLC I-Class (2D)■■ HILIC (inter-class) x RP (intra-class)

■■ Waters ACQUITY® UPC2 (1D)■■ Direct injection of organic extracts ■■ Rapid HILIC intra-class selectivity

BIOINFORMATICS■■ Progenesis QI

■■ Sample comparisons across multiple groups,

analytical and biological replicates■■ Database search for metabolite and lipid ID using

retention time, CCS, and fragmentation information■■ Flexible statistical tools including ANOVA, PCA,

hierarchical clustering, power analysis■■ Flexible report generator for information sharing■■ Quality Metrics, a rapid visual check of sample

measurements and analytical quality

■■ EZinfo Multivariate Analysis by Umetrics ■■ OPLS, PLS, PLS-DA, and S-Plot

SYSTEM VERIFICATION

■■ Waters Metabolomics System Verification Kit

Think in three dimensions of resolution.

The 3D combination of UPLC,

IMS, and MS allows the total peak

capacity (c.f. resolution) of the

analytical system to be increased

by an order of magnitude

compared to the conventional

2D LC and MS methodologies.

TW-IMS is a dispersive (i.e.,

parallel/multiplexed) technique

that separates ions according

to their Collision Cross-Section

(CCS) or size.

CCS is a precise and reproducible

physicochemical property of

an ionized molecule, delivering

four key advantages: Structure,

specificity, separation,

and sensitivity.

Thousands of structurally similar

analytes, distributed over a

daunting dynamic range pose a

massive analytical challenge.

Waters’ analytical strategy

combines three orthogonal

techniques to separate,

characterize, and quantify

the components of very

complex biological samples.

We integrate UltraPerformance

Chromatography (UPLC and

UPC2), Traveling Wave Ion

Mobility Separation (TW-IMS) and

high resolution Time-of-flight

(Tof) mass spectrometry to

deliver high definition analysis.

INTERROGATE THE M

OST COMPLEX

BIOLOGICAL SAMPLES IN THREE DIM

ENSIONS.

CCS is directly related to the size,

shape/conformation, or charge of

an analyte providing an insight to

molecular STRUCTURE.

SEPARATION by CCS allows

isobaric precursor ions to

be resolved preventing

co-fragmentation.

CCS SPECIFICITY enables

structural isomers (i.e., lipids)

to be assigned.

CCS separation delivers ions to

the Tof MS in ascending order

of size allowing optimization

of Tof duty cycle and

optimized SENSITIVITY.

UltraPerformance Chromatography, Traveling Wave Ion Mobility Separation, and High Resolution Time-of-Flight MS

Three coeluting isobaric peptide precursor ions (left) are completely resolved by TW-IMS (right).

Protein ID: SYNAPT G2-Si HD-DDA and the leading competitor DDA. 100, 500, and 1000 ng, 120 min RP, n=2, 1% FDR. SYNAPT G2-Si (blue), leading competitor (green), common identifications (grey).

High Definition Mass Spectrometry.

fold change0 0.4 0. 8 1.2 1. 6 2

0

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1800

fold change0 0.4 0. 8 1.2 1. 6 2

0

1000

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frequ

ency

Accuracy and precision for a 1:1 fold change: SYNAPT G2-Si HDMSE (blue) and leading competitor DDA (green).

Sensitivity: peptides spiked into an E.coli matrix. HD-MRM (PRM) LOD ≤5 amol.

High Definition Imaging MALDI: ion maps for two endogenous species differing by 0.3 mDa. Equivalent to 1,800,000 FWHM.

ng100 500 1000

0

500

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ng100 500 1000

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HeLayeastE.coli

# p

rote

ins

2

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log

resp

onse

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IGDYAGIK

EALDFFAR

LVNELTEFAK

TRANSOMICS SOLUTIONwith Progenesis QI Software

Comprehensive data from a common workflow.

INNO

VATI

ON

IMPA

CT

P ROT EOMICS Accurate label-free quantification of proteins over a wide dynamic range

■■ Ultimate peak capacity

■■ Unique combination

of IMS and Tof MS for

unrivalled peak capacity

■■ Maximum in-spectrum

dynamic range

■■ Simple, scalable

informatics for

qualitative and

quantitative profiling

■■ Robust statistical

treatment of data

with simple reporting

and exporting

■■ CID and ETD

fragmentation

provides maximum

versatility

“ With Waters, you have an incredibly powerful

analytical tool capable of measuring hundreds

or thousands of molecules at the same time,

in one sample, and in one analytical run.”

JEREMY NICHOLSON, Ph.D.Professor and Chair, Biological Chemistry,Head of Department, Surgery and Cancer,Imperial College, United Kingdom

“ The results from the latest version of TransOmics have

been incorporated into the now long awaited paper

submission, and my collaborators were very pleased

with the results. Accurate mass and retention time

matching across LC/MS runs as provided by TransOmics

is essential for large-scale protein profiling – it is not

worth doing such an experiment without it.”

LEWIS BROWN, Ph.D.Director, Comparative Proteomics Center,Biological Sciences, Columbia University, United States

Standardized and normalized relative peptide abundance.

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Proteomics principal component analysis.

HDMSE (IM-DIA-MS) peptide identification.

PEPT

IDE

& PR

OTEI

N ID

■■ High peak capacity and

mass accuracy provided

by UPLC/HDMSE

■■ Powerful LC/MS technology

to routinely screen large

numbers of samples

■■ Simple data processing

and easy identification

of statistically significant

quantitative changes

■■ Export of mass information for

identification by comparison

to custom databases

METABOLOMICS Accurate sample differentiation through quantitative LC/MS

■■ Advanced liquid phase

separations provides class

definition of lipids

■■ Unique gas phase

separation of isobaric

lipid species by IMS

LIP IDOMICS Detailed quantitative and qualitative lipid characterization

■■ Confirmation of lipid identity

by CID fragmentation

■■ Quantitative profiling

of lipids by LC/MS

■■ Spatial localization of lipids

with MALDI imaging

MET I

D LIPID ID

“ We are ready to publish very soon, and with

TransOmics, it is much easier to publish results with a

single software package that does everything, rather

than explaining the different software packages we

normally use for our statistics.”

GEERT GOEMINNEDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Belgium

Interactive review of metabolite or lipid data for maximum confidence in results reported.

Metabolite/lipid identification using retention time, CCS, and fragmentation information.

TRANSOMICS SOLUTIONwith Progenesis QI Software

SALES OFFICES:

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Australia 61 2 9933 1777

Belgium and Luxembourg 32 2 726 1000

Brazil 55 11 4134 3788

Canada 1 800 252 4752

China 86 21 6156 2666

Czech Republic 420 2 617 11384

Denmark 45 46 59 8080

Finland 358 9 5659 6288

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Spain 34 93 600 9300

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Switzerland 41 56 676 7000

Taiwan 886 2 2501 9928

UK 44 208 238 6100

US 1 800 252 4752

Waters, The Science of What’s Possible, ACQUITY UPLC, UPLC, SYNAPT, High Definition Mass Spectrometry, Oasis, Progenesis, Xevo, and UPC2 are registered trademarks of Waters Corporation. TransOmics, Ostro, UltraPerformance Convergence Chromatography, Nonlinear Dynamics, MassPREP, RapiGest, and HDMS are trademarks of Waters Corporation. All other trademarks are the property of their respective owners.

©2014 Waters Corporation. Printed in the U.S.A. January 2014 720004282EN LM-IGS

www.waters.com/transomics

Waters Corporation 34 Maple Street Milford, MA 01757 U.S.A. T: 508 478 2000 F: 508 872 1990 www.waters.com