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Accelerating Innovation Dual-Pressure Linear Ion Trap Thermo Scientific Velos Pro Ion Trap LC-MS n Designed for quantitation UHPLC data rates Diversity in dissociation Fast and sensitive MS n

Velos Pro Ion Trap LC-MSn - Dual-Pressure Linear Ion Trap ... · 925.42+2 MS3 795.84+2 MS4 1274.92 MS5 b1 3 b1 3 b1 3 b1 2 b1 2 b1 2 b1 3 b1 2 a1 a1 a1 a1 6 ... CID MS2 Parent N N

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Accelerating InnovationDual-Pressure Linear Ion Trap

Thermo Scientific Velos ProIon Trap LC-MSn

Designed for quantitation • UHPLC data rates • Diversity in dissociation • Fast and sensitive MSn

The Thermo Scientific Velos Pro is the pinnacle of ion trap mass spectrometry

that delivers enhanced performance for complex sample analyses. A novel wide

dynamic range discrete dynode detection system offers the ultimate in identification

and quantitation of low-abundance compounds and provides absolute confidence

in every result. For the first time ever with an ion trap, the Velos Pro™ offers Trap-

HCD (Higher-Energy Collisional Dissociation) combined with CID (Collision-Induced

Dissociation), PQD (Pulsed-Q Dissociation) and ETD (Electron Transfer Dissociation)

to solve the most difficult analytical problems. With the improved robustness of

generation II/G2 ion optics, the Velos Pro delivers reliability on the fastest, most-

sensitive, highest capability ion trap available today. The Velos Pro can also be

enhanced with the ultra-high resolution and mass accuracy of Thermo Scientific

Orbitrap Velos Pro or Orbitrap Elite™ technology.

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Accelerating Innovation

Triple quadrupole-like fragmentation with no precursor dependent low mass cutoff is now available on the Velos Pro.Precursor ions collide with N2 in a high pressure octopole where collision energy can be tuned to maximize specific fragments at any mass-to-charge relative to parent. Collision energy is normalized for mass-to-charge and for charge state to deliver optimum fragmentation for all precursors across the entire mass range. Trap-HCD of small molecules furnishes higher energy transitions; trap-HCD of peptides offers strong y- and b-ion series as well as highly specific immonium ions. With CID, PQD, and ETD, Trap-HCD adds capability and flexibility to MSn on the Velos Pro.

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The Velos Pro takes ion trap technology to new heights: with CID, PQD, ETD, and now Trap-HCD available at any level of MSn, the Velos Pro is the most versatile MS instrument on the market.

CID of Caffeine

40 60 80 100 120 140 160 180 200 220m/z

Trap-HCD of Caffeine

40 60 80 100 120 140 160 180 200 220m/z

Freedom of Dissociation

|4

The Velos Pro presents the latest advancements in ion optics design: the S-Lens delivers dramatically higher ion currents, and G2 Ion Optics provide a novel mechanism of blocking neutrals outside the path of the ion beam. These features in combination provide maximum uptime and total confidence for the most challenging applications.

The revolutionary Velos Pro is an optimized dual-pressure ion trap with a high pressure and a low pressure cell. The high pressure cell offers maximum ion trapping, fragmentation, and isolation efficiency. The low pressure cells enable better resolution and higher scan rates than any other ion trap mass spectrometer. This dual-pressure trap technology in Velos Pro offers a scan speed for every application: from fast survey scans in the new Rapid Scan mode to maximum resolution in Ultra ZoomScan mode.

2.000

1.500

1.000

0.500

0.0000 200 400 600 800 1000 14001200

Injection Number

Are

a R

atio

RSD: 2.07%Injections: >1300

Rapid: 66.6 kDa/s3,500 M/∆M

Enhanced: 10 kDa/s7,600 M/∆M

Ultra Zoom: 27.7 Da/s36,440 M/∆M

1818 1820 1822 1824 1826 1828

1818 1820 1822 1824 1826 1828

1818 1820 1822 1824 1826 1828

Amazing Sensitivity – Maximum Robustness

Speed and Selectivity

50 pg on column of Alprazolam and internal standard in singly crashed plasma

|5

The Velos Pro blurs the lines between traditional ion trap and triple quadrupole performance. The first trap of the dual-pressure cell is designed to act like a single quadrupole during the ion loading process, removing chemical background and minimizing space charge. Once trapped, precursor ions are fragmented and detected by a custom-designed

high-performance discrete dynode system optimized to capture the ultra-high flux of ions ejected from the Velos Pro. The quadrupole-like isolation combined with high data rate detection produces results only possible on the Velos Pro… designed with quantitation in mind.

Iso

lati

on

Eff

icie

ncy

0

20

40

60

80

100 m/z 524

-8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8

m/z at Isolation q

Quantitate Like Never Before

AlprazolamY = 6852.68*X R^2 = 0.9918 W: 1/X

0 2000 4000 6000 8000 10000

pg on Column

0

10000000

20000000

30000000

40000000

50000000

60000000

70000000

Pea

k A

rea

for

2 E

xtra

cted

Ions

0.0 0.2 0.4 0.6Time (min)

0

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Rela

tive

Abun

danc

e

RT : 0.25SN : 4

Isolation efficiency of the Velos Pro during the ion loading process

Quantitation of Aprazolam from 10fg-10ng on column

10fg of Alprazolam on column

For All Levels of Every Target

6|

Maximum Identifications

Routine analysis of complex proteomics samples is often confounded by the inability to adequately detect low-abundance proteins, by the large number of PTMs (Post-Translational Modifications) possible, and because of the dynamic nature of the proteome. Ion trap-based mass spectrometry has demonstrated a superior ability to rapidly identify and characterize low-abundance proteins and determine their relative expression levels. It has become an essential tool in proteomics labs.

The Velos Pro enables a new level of proteomics sample interrogation, made possible by improve-ments in acquisition rates, MSn sensitivity, selec-tive accumulation of low-abundance ions and the addition of a novel fragmentation methodology: Higher-Energy Collisional Dissociation (HCD). HCD allows access to low mass fragments such as im-monium ions which increases the confidence in and total number of peptide identifications.

Maximum Coverage

Achieving complete coverage for the purpose of sequencing a protein, including its site-specific post-translational modifications, requires maximizing the number of peptides detected in a single experiment. The application of multiple activation methods, i.e. Collision-Induced Dissociation (CID), Electron Transfer Dissociation (ETD), and now the new Higher-Energy Collisional Dissociation (HCD) achieves this goal. An all ion trap-based HCD/ETD decision tree is now possible on the Velos Pro providing maximum coverage and characterization of target proteins.

Full Scan MS followed by HCD for doubly charged precursor (bottom, left) and ETD for triplycharged precursor (bottom, right).

100 150 200 250 300 350 400 450 500 550 600 650 700 750 800m/z

0

20

40

60

80

100432.92

648.88413.32

239.20 269.04163.04 659.84359.28 513.32105.04 191.04 301.20 441.32 692.84597.04

200 400 600 800 1000 1200m/z

0

20

40

60

80

100

Rela

tive

Abun

danc

e

Rela

tive

Abun

danc

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Rela

tive

Abun

danc

e

649.08

784.58269.33

569.50 1028.75392.92 1000.75110.25

200 400 600 800 1000 1200m/z

0

20

40

60

80

100 649.58

433.17

1298.92

592.00289.33 1009.75910.67 1238.83

253.33

HCD of DR VYIHPFHL 2+ ETD of DR VYIHPFHL 3+

432 433 434 435m/z

432.92

433.24

433.60

433.92

434.24

3+

648 649 650 651m/z

648.88

649.36

649.88

650.36

648.40650.88

2+

Venn diagram from Thermo Scientific Proteome Discoverer 1.3 software showing C. elegans peptide identifications by HCD and CID.

Maximum Information from Proteomics samples...

MSn spectra and block structure for 9 unit glycan determined by LC-MSn on the Velos Pro.

Average of the coefficients of variation for each protein in a 12 protein mixture and number of IDs by trap-HCD fragmentation.

For All Levels of Every Target

|7

Sample HCD MS2 spectrum for TMT 6-plex labeled protein digest.

Maximum Structural Characterization

Mass spectrometry has emerged as one of the most powerful tools for the structural elucidation of glycans due to its sensitivity and its ability to analyze complex mixtures. Ion trap mass spectrometry offers multistage fragmentation (MSn) which is a critical tool for glycan structure elucidation as it allows for determination of structural heterogeneity and differentiation of isomers. It is commonly necessary to acquire six or seven levels of fragmentation (MS6 or MS7) to differentiate potential glycan structural isomers.

Relative Quantitation by TMT Labeling

Tandem Mass Tag (TMT) and other isobaric tagging technologies are based on the release of low-mass reporter ions during fragmentation, allowing simultaneous identification and quantitation of peptide ions. Both MS3 and Pulsed-Q Dissociation (PQD) methods are well established linear ion trap applications of these technologies. The Velos Pro linear ion trap mass spectrometer features a new option. Higher-Energy Collision Induced Dissociation which utilizes a high-pressure RF-only octopole. HCD is a triple quadrupole-like fragmentation method which produces high intensity reporter ions resulting in enhanced accuracy and precise quantitation.

Absolute Quantitation Using AQUA™ Peptides

Absolute quantitation strategies such as AQUA center around MS2 detection of targeted peptides and their analogues labeled with stable isotope amino acids. The Velos Pro dual-pressure linear ion trap with ultra-fast scanning and multiple fragmentation techniques delivers high precision and accurate quantitation even over multiple orders of magnitude and in complex matrices.

b 4+

642.67

b 3+

529.51

Y 4+

733.62b 1

+

343.55

Y 6+

917.68

Y 7+

1032.69

b 2+, y 6²+

458.57

200 400 600 800 1000 1200m/z

0

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120

140

Inte

nsity

[cou

nts]

(10^

3)

ITMS, HCD, z=+2, Mono m/z=688.02769 Da, MH+=1375.04810 Da, Match Tol.=1.2 Da

Peptide Spectral Matches 4363

Peptides Quantified 3269

Percent Quantifiable 75%

Average Protein Level CVs 2.5%

Results of Trap-HCD TMT Experiments

1054.92+2

MS2

925.42+2

MS3

795.84+2

MS4

1274.92+1

MS5

b1 3

b1 3

b1 3

b1 2

b1 2

b1 2

b1 3 b1 2

a1

a1

a1

a1

6

6

3

3b1 4

b1 4

b1 4

b1 4

MS2

MS4

MS5

MS6

MS3

a1

6

b1 43

a1b1 3 b1 2

a1

6

a1

b1 4

b1 4 b1 43

a1

b1 4 b1 43

b1 4 b1 4

1070.84+1

MS6

0.00E+00

2.00E+07

4.00E+07

6.00E+07

8.00E+07

1.00E+08

1.20E+08

1.40E+08

1.60E+08

1.80E+08

2.00E+08

0 2 4 6 8 10

pmol GPGEDFR

0.00E+00

1.00E+06

2.00E+06

3.00E+06

4.00E+06

5.00E+06

6.00E+06

0 0.05 0.1 0.15 0.2 0.25

pmol GPGEDFR

r2 = 0.9995

Peak area vs amount of GPGEDFR injected for 4 orders of magnitude change in concentration. GPGEDFR was spiked into unfractionated human cerebral spinal fluid.

Maximum Information from Proteomics samples...

The power of MSn can be observed with the fragmentation and interpretation of Trifluoperazine and its metabolites which include multiple oxidative metabolites. MS3 data from HCD fragmentation provides useful diagnostic fragments not readily observed in a CID MS3 scan.

Parent

CID MS2 Hydroxylated Metabolite

CID MS3 of m/z 296

CID MS2 Parent

N

N

N

S

F

F

F

+N

F

F

S

F

+N

FOH

F

S

F

of Complex Drug Metabolism Samples

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Inte

nsity

50

70.1

98.2

84.2

141.2

113.2

296.3

264.2

278.2324.3

424.3

100 150 200 250m/z

300 350 400

Inte

nsity

100

227.2

263.2

264.2

262.1276.2 296.2

150 200 250m/z 300

Inte

nsity

50 100

70.1

98.2

141.2

113.2

280.2

230.2

248.3

262.2 308.3 408.4

409.384.2

150 200 250m/z

300 350 400

Maximum Productivity The characterization of drug metabolites plays a pivotal role in pharmaceutical discovery and development. Parent drug and metabolites need to be identified in a variety of biological matrices over a wide range of concentrations for both in vivo and in vitro studies. Thermo Scientific MetWorks and Mass Frontier software, when used with the Velos Pro create a robust, sensitive, and integrated workflow for identification, characterization, and quantitation of drugs and their metabolites in biological matrices.

Inte

nsity

50

235.3

263.5276.3

296.3

264.2

100 150 200 250m/z

300

F

F

F

+NH.

Trap-HCD MS3 of m/z 296; shows more diagnostic fragments

Comprehensive Identification and Quantitation

F

N

N

N

S

OH

F

F

Hydroxylated Metabolite

CID MS2 Dextromethorphan Trap-HCD MS2 Dextromethorphan

With different fragmentation techniques available, researchers can tailor their choice to meet the demands of the analysis. For the quantitation of Dextromethorphan, CID generates an MS2 spectrum with a single strong ion, ideal for quantitative sensitivity, while signal intensity following HCD fragmentation is spread over multiple MS2 ions.

4.0E+07

3.5E+07

3.0E+07

2.5E+07

2.0E+07

1.5E+07

1.0E+07

5.0E+06

0.0E+00

Peak

Are

a

Concentration (ng/mL plasma)

y = 34201x + 289667R2 = 0.99974

0 100 200 300 400 500 600 700 800 900 1000

of Complex Drug Metabolism Samples

|9

Inte

nsity

10050

81.1293

121.0078

147.0023171.0491

213.0572

198.0466

241.2167

272.1483

150 200 250m/z

Inte

nsity

100

147.0

213.1

215.1

150 200 250m/z

Maximum Performance

The increased sensitivity of the Velos Pro allows simultaneous qualitative and quantitative metabolite analyses to be carried out easily for both in vivo and in vitro studies. The faster scan rates of the Velos Pro allow the acquisition of more MSn spectra in shorter chromatographic runs. With a full range of fragmentation techniques available for use at all MSn stages, researchers can construct higher-quality ion trees for qualitative metabolite analysis and characterization. The use of Data Dependant acquisition coupled with Dynamic Exclusion provides a methodology for the analysis of both predicted and unexpected metabolites.

Comprehensive Identification and Quantitation

Africa-Other +27 11 570 1840Australia +61 3 9757 4300Austria +43 1 333 50 34 0Belgium +32 53 73 42 41Canada +1 800 530 8447China +86 10 8419 3588Denmark +45 70 23 62 60

Europe-Other +43 1 333 50 34 0Finland/Norway/Sweden

+46 8 556 468 00France +33 1 60 92 48 00Germany +49 6103 408 1014India +91 22 6742 9434Italy +39 02 950 591

Japan +81 45 453 9100Latin America +1 561 688 8700Middle East +43 1 333 50 34 0Netherlands +31 76 579 55 55New Zealand +64 9 980 6700Russia/CIS +43 1 333 50 34 0South Africa +27 11 570 1840

Spain +34 914 845 965Switzerland +41 21 694 71 11UK +44 1442 233555USA +1 800 532 4752

www.thermofisher.com/velospro©2016 Thermo Fisher Scientific Inc. All rights reserved. TMT is a registered trademark of Proteome Sciences plc. Mass Frontier is a trademark of by HighChem Ltd. ProSightPC is a trademark of the University of Illinois at Urbana-Champaign. AQUA™ Peptide is a trademark of Sigma. All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries. Specifications, terms and pricing are subject to change. Not all products are available in all countries. Please consult your local sales representative for details.

BR63415_E 09/16S

Xcalibur™ data system Stable operating platform Thermo Scientific Xcalibur software is the versatile, easy-to-use data system that controls all Thermo Scientific MS systems. The home page of the Xcalibur software offers easy navigation through the process of instrument setup, sequence setup, and data acquisition. The XReport package simplifies custom reporting with drag-and-drop functionality.

Proteome Discoverer software Mass informatics platform for protein scientists Thermo Scientific Proteome Discoverer software is a workflow-based proteomics data processing software for in-depth data mining of complex LC-MSn data sets. With the ability to exploit data from different dissociation techniques (CID, HCD, IRMPD, ETD and ECD), Proteome Discoverer software provides extra certainty for peptide and protein identifications. Optional inclusion of multiple search algorithms increases analytical flexibility, and results can now be merged into a single report for easier interpretation.

ProteinCenter™ softwareFrom data sets to meaningful biologyThermo Scientific ProteinCenter is a web-based data interpretation tool that enables scientists to compare and interpret data sets in minutes instead of months. The software enables filtering, clustering and statistical bioinformatics analysis utilizing a regularly updated, consolidated protein sequence database containing >10 million non-redundant proteins.

Pinpoint softwareAccelerating targeted protein quantitation in biological researchThermo Scientific Pinpoint software facilitates the transition from early-stage biomarker discovery to larger-scale, quantitative verification of putative biomarkers and general quantitative proteomics.

MetWorks™ software Simplify the interpretation of complex metabolism data Thermo Scientific MetWorks software simultaneously searches multiple modifications of one or more parent drugs and interprets simple to complex isotope patterns, or unexpected or low-abundance metabolites.

Mass Frontier™ software Confident path from spectra to structure Thermo Scientific Mass Frontier software allows confident structural elucidation through chemically intelligent spectral annotation, state-of-the-art fragmentation prediction, and unparalleled spectral and fragmentation mechanism knowledge management.

SIEVE™ software Analysis of differential expression based on comparison of LC-MS datasets Thermo Scientific SIEVE software provides label-free, semi-quantitative differential expression analysis of proteins, peptides, or metabolites from the comparison of multiple LC-MS data sets. It is a statistically rigorous tool for analyzing data from metabolism or biomarker discovery experiments.

Turning Data Into InformationThermo Scientific Application-Specific Software