New instruments and

services

Resolving power up to 140,000 FWHM and Highmass accuracy <1ppm

Fast scanning at 12hz and spectral multiplexingsuited to UHPLC applications

Rapid polarity switching in both MS and MS/MSmodes

In-source CID, and HCD.

Extended mass range to 6,000m/z

Great dynamic range (>4 orders of magnitude),along with femtogram-level sensitivity

High spectral quality and a wide dynamic rangemake it possible to identify and quantify even lowabundant proteins.

Quan/qual capability make it easier to transitionfrom proteomic discovery experiments to targetedprotein quantification

Thermo Q Exactive Plus

Thermo Q Exactive Plus

http://planetorbitrap.com

Quad

S-lens

C-trap

HCD

cell

Orbitrap

Bottom-up proteomics

1D and 2D discovery proteomics analysis

Intact peptide and protein analysis

Analysis of PTMs

Targeted proteomics studies

Quantitation-SILAC, label-free approaches

Crosslinking studies

Untargeted metabolomics

Applications

New, fast autotune improves sensitivity up to 5x for small molecule applications

Autotune technology also helps preserve fragile compounds for improved detection

New Agilent high voltage pulser and power supplies increase mass resolution performance and enhanced mass accuracy to 0.8 ppm

New ion optics elements provides greater robustness

New ion beam shaping optics provide more consistent results and longer usage time between cleanings

CID fragmentation

Applications: untargeted metabolomics

Agilent 6545 Q-TOF LC-MS

Agilent 6545 Q-TOF LC-MS

Bruker 15T FT ICR-MS

Ultimate mass resolving power in excess of RP =

10,000,000

Apollo II Ion Funnel Electrospray Source enabling high

ion transmission efficiency over a broad mass range

Optimized ion optics for sensitivity and mass range

coverage

Proprietary ParaCell ICR cell with patented SIDEKICK™

ion accumulation system for high detection efficiency.

Wide range of fragmentation techniques including CID

and ECD

Dual ionization source: MALDI source with Smartbeam II

laser and ESI source

Bruker 15T FT ICR-MS

High End Proteomics Studies (Top-down and Bottom-up workflows)

PTM Investigation

Accurate de novo sequencing

Molecular Imaging of Tissue—Distribution of Drugs, Metabolites, and Biomarkers

Petroleum Product Analysis

Complex Environmental Sample Analysis

Metabolomics Research

Bruker 15T FT ICR-MS applications

Thermo Quantiva

Thermo Scientific™ active ion

management (AIM™) technology —

electrodynamic ion funnel, ion beam guide

with neutral blocker, Thermo Scientific™

HyperQuad™ quadrupole mass filter, and

active collision cell — enables attogram-

level sensitivity

Ultrafast selected-reaction monitoring

(SRM) of 500 SRM/s, with up to 30,000

definable SRMs, enables quantification of

more compounds in less time

Intuitive drag-and-drop method editor

software with application templates

simplifies method development and

operation

Applications: Targeted metabolomics

Thermo TSQ Quantiva

Bruker timsTOF Pro

Ion mobility time-of-flight mass spectrometer

Inclusion of IM permits differentiation between modified

peptides of same mass-different PTM sites in the same

peptide

Increased sensitivity due to ion trapping with virtually

100% duty cycles: Allows in-depth analysis from very

small sample sizes, with 50-250 ng injections routine

High dynamic range: Allows low abundance proteins to

be identified in presence of many higher abundance

proteins

High MS/MS fragmentation rate: Enables sequencing of

many peptides, and hence greater number of protein

identificationswithin shorter analysis time

Bruker timsTOF Pro

The gas flow "behind" the ions and the electric potential allow for accumulation and staging of ions

separated by their collisional cross sections and charges.

Selected precursors are ejected from the device by scanning (lowering) the retarding potential in the

second stage

Precursor m/z 825.9613

RT 56.08 min

Precursor m/z 825.9604

RT 55.95 min

Without ion mobility separation these overlapping

precursors would give chimeric MSMS spectra

Bruker timsTOF Pro: Co-eluting peptides

Slide courtesy of Gary Kruppa, Bruker Daltonics

Precursor m/z 825.9613

Precursor m/z

825.9604

Without ion mobility separation these

overlapping precursors would give chimeric

MSMS spectra

• Those two peptides are co-eluted

• They are 0,0009Da apart

• Distinguishing them, based on resolution only, would have required

a resolving power > 900 000 !

• … and that alone would not have allowed to isolate them

separately

PASEF DOES IT…

@ > 100 Hz MS/MS

While preserving sensitivity !

Bruker timsTOF Pro: Co-eluting peptides

Slide courtesy of Gary Kruppa, Bruker Daltonics

Bruker timsTOF Pro: Iosbaric peptidesTIMS separation of co-eluted isobaric HEK Phosphopeptides

• Similar seqences

• Several Phosphoryation sites

on the sequence

• Probable isoforms

Slide courtesy of Gary Kruppa, Bruker Daltonics

New services

Proteomics Quantitation-label free, TMT, SILAC

2D LC/MSMS for Protein Identification and PTM Study on both Orbitrap Fusion and QE

MADLI Tissue Imaging

Top-down Proteomics

Slide courtesy of Nilini S. Ranbaduge

High pH fractionation with Low pH separation

Dionex 3000 2D System

$60/fraction on the orbitrap XL

$75/fraction on the orbitrap Fusion or

Q Exactive

Fractionation (F)

pH 10.0

Gradient separation19

RT: 0.00 - 90.00

0 10 20 30 40 50 60 70 80 90

Time (min)

0

10

20

30

40

50

60

70

80

90

100

Rela

tive

Abun

danc

e

45.29

45.96

43.94

38.87

54.28

61.83

30.0765.4629.06

25.19

22.86 68.9071.054.27 21.37 87.65

NL: 2.71E8

Base Peak F: FTMS + p NSI Full ms [400.00-1600.00] MS NR_20141223_HCC15_pooled_test

RT: 0.00 - 89.99

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85

Time (min)

0

5

10

15

20

25

30

35

40

45

50

55

60

65

70

75

80

85

90

95

100

Rel

ativ

e A

bund

ance

NL: 2.89E8

Base Peak F: FTMS + p NSI Full ms [400.00-1600.00] MS NR_20150321_A549T_LKB-FT_test

RT: 0.00 - 79.99

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75

Time (min)

0

5

10

15

20

25

30

35

40

45

50

55

60

65

70

75

80

85

90

95

100

Re

lativ

e A

bu

nd

an

ce

NL: 2.31E8

Base Peak F: FTMS + p NSI Full ms [400.00-1600.00] MS NR_20150201_A549_LKB-P_15F_80min_F2

RT: 0.00 - 80.00

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75

Time (min)

0

5

10

15

20

25

30

35

40

45

50

55

60

65

70

75

80

85

90

95

100

Rela

tive

Abun

danc

e

NL: 2.74E7

Base Peak F: FTMS + p NSI Full ms [400.00-1600.00] MS NR_20150201_A549_LKB-P_15F_80min_F15

F1

F2

F15

Slide courtesy of Nilini S. Ranbaduge

High pH fractionation with Low pH separation

Top Down vs Bottom up

Pflugers Archiv-European

Journal of

Physiology, 2014, 466, 1199-

1209.

m/z750730710690670650630610590570550

c17+84

c26+70

c26+112

c12+42

c22+112

c12+42

c13+42

c25+112

c23+112

c40+70

c40+112

C24+70

c24+112

c7+42

c15+42

c37+70

c55+112

c37+140

c37+112

c38+112

c26+70

c26+112

c52+70

c52+112

c54+70

c54+112

c18+84

z35+14

z35+56

z12

c59+70

c59+112

z20

C60+112

m/z750730710690670650630610590570550

c17+84

c26+70

c26+112

c12+42

c22+112

c12+42

c13+42

c25+112

c23+112

c40+70

c40+112

C24+70

c24+112

c7+42

c15+42

c37+70

c55+112

c37+140

c37+112

c38+112

c26+70

c26+112

c52+70

c52+112

c54+70

c54+112

c18+84

z35+14

z35+56

z12

c59+70

c59+112

z20

C60+112

1000900800700600 780770760750

m/z

+1Ac + 2Me

+1 Ac+ 4Ac

+ 5Ac

+ 2Ac + 2Me

Parents ions (750 - 770, 15+) 758.0864 15+

754.7814 15+

+ 4Ac

- 15+

15+

1000900800700600 780770760750

m/z

+1Ac + 2Me

+1 Ac+ 4Ac

+ 5Ac

+ 2Ac + 2Me

Parents ions (750 - 770, 15+) 758.0864 15+

754.7814 15+

+ 4Ac

- 15+

15+

ECD MS/MS

m/z1000990980970960950940930920910900

z32

z48

z64

z49+14

z9

z65

z49z66

z25+16

z50

z34

z67

z76

z42

z42+14

z59

z51

z68

z43

z78z61 z79

z62

z27z75

m/z1000990980970960950940930920910900

z32

z48

z64

z49+14

z9

z65

z49z66

z25+16

z50

z34

z67

z76

z42

z42+14

z59

z51

z68

z43

z78z61 z79

z62

z27z75

Histone H4

Slide courtesy of Liwen Zhang

Protein Identification by Top Down MS/MS

N-AGRGK5GGK8GLGK12GGAK16RHRK20VLRDNIQGIT H4

Ac Ac Ac Ac Ac

Me Me

Ac Ac Ac

Known Modification

Modification Detected

Protein Identification by Top Down MS/MS

$500 on Fusion or ICR

Slide courtesy of Liwen Zhang

Large molecules >10,000 Da

$750/sample TOF-TOF

Small molecules <10,000 Da

$750/Sample on 15T ICR

Imaging Mass Spectrometry

• High Mass Accuracy (FT ICR)

assists in chemical formula

determination

• Changing Matrix can help with

interference

• Derivatization for unstable

molecules

Anal. Chem., 2011, 83 (24), 9694–9701

RT: 40.31 - 210.44

50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210

Time (min)

0

10

20

30

40

50

60

70

80

0

10

20

30

40

50

60

70

80

Re

lative

Ab

un

da

nce

0

10

20

30

40

50

60

70

80172.3651.09 74.43

147.2873.4659.81

83.0067.5146.94

84.43125.6190.98

98.24

102.59 154.41135.68

107.81113.21 129.55 156.09140.88 161.85121.24 203.90186.96 193.16175.36

96.30

74.03

72.89 97.42 164.8778.17 82.2072.6559.3690.1855.88 185.19123.9166.13 128.35

101.89153.68113.47 188.09 199.8052.73

50.86 130.21 163.13141.80 195.09178.09 208.48120.3046.39

146.51171.8573.23

171.2978.49

97.0378.6667.29

56.1859.48 82.84 85.96 128.6398.06 185.93113.7690.37

168.18124.41 189.02 200.9953.11 153.97105.4151.41124.14 135.09 155.6747.08

210.16184.39 200.06120.75

NL:9.28E7

Base Peak MS 145-300-1

NL:8.28E7

Base Peak MS 145-3000-2

NL:1.15E8

Base Peak MS 145-3000-3

Slide courtesy of Liwen Zhang

Laser Capture Microdissection Proteomics

Laser capture

microdissection

available through the

laser capture

molecular core

https://lcm.osu.edu/

Additional facility MS instrumentation

Thermo Fusion

Thermo Orbitrap XL

Thermo LTQ

Bruker ultrafleXtreme MALDI-TOF TOF

Bruker amaZon ion trap with ETD

Bruker maXis UHR QTOF

Thermo DSQ II GC-MS

http://www.ccic.ohio-state.edu/MSP