download/files/Proteomics brochure 7-08-04.pdf

Solutions for Protein
Mass Spectrometry
Innovation you can’t afford to miss
Analyze • Detect • Measure • Control TM

• Ultra-Sensitive Protein Analysis
Finnigan LTQ linear ion trap mass spectrometer
• Sheer Analytical Power
Finnigan LTQ FT hybrid mass spectrometer
• Rapid, Confident Protein ID
Finnigan LTQ with vMALDI source and Ettan DIGE
• Ultimate Analytical Flexibility
MDLC LTQ workstation
• Integrated Proteomics Workstation
Finnigan ProteomeX LTQ workstation
• Powerful Bio-Software Solutions
2
Including BioWorks software with
SEQUEST ® algorithm and DeNovoX
sequencing software
Thermo is Revolution
With the complete sequencing of the human genome, accomplished in 2000, a significant
milestone in human scientific pursuit was reached. No sooner was this accomplished, however,
than the race to characterize the protein products of all of those newly-discovered genes began.
The concept of the human proteome and the science of proteomics were born.
The characterization of proteins has proven to be a formidable analytical challenge. Proteins in
biological samples are present in vast numbers, at widely varying concentrations, and in myriad
modified forms. Combine this overt complexity with universal organizational demands for
increased throughput and operational efficiency and the challenge can seem insurmountable.
Fortunately, Thermo Electron can help. With an impressive array of innovative new products,
technologies, and integrated solutions, Thermo is redefining the practical limits of what is
possible in proteomics research.

izing Proteomics
Innovation you can’t afford to miss!
3

Ultrasensitive Protein Analysis
Finnigan LTQ Linear Ion Trap Mass Spectrometer
4
The revolutionary Finnigan LTQ
linear ion trap mass spectrometer
has pushed protein detection limits
to unimaginably low levels. The
large-capacity linear ion trap stores
dramatically more ions and uses
dual detectors for 100% detection
efficiency.
Thermo’s patented linear ion trap
provides superior effective trapping
capacity with its segmented design.
Complete with radial ejection and
dual detectors, the Finnigan linear
ion trap is the most efficient trap
available, providing power and
sensitivity for all proteomic
applications.
Extremely rapid scan speeds result
in many more MS/MS and MS n
sequencing attempts per unit
time, resulting in far greater
protein coverage than has ever
been possible before.
Finnigan LTQ
linear ion trap

Sheer Analytical Power
Finnigan LTQ FT Hybrid Mass Spectrometer
47 kDa protein
(+ 31 charge
state)
Relative Abundance
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
antiVFab # 99-127 RT: 9.70-14.13 AV: 29 NL: 9.84E4
T:FTMS + pNSIsid = 10.00 Full ms2 1241.00@0.00 [700.00-1800.00]
Relative Abundance
1241.5134
100
95
1241.4363
90
1241.5903
85
80
1241.3849
75
70
65
1241.6418
60
55
50
1241.3335
1241.6932
45
40
35
1241.2823
1241.7445
30
25
1241.2309
1241.7957
20
15 1240.9230
1241.1798
1241.0515
1241.9234 1242.1024
1242.1541
1242.3078
10
5
0
1242.4613
1240.8 1241.0 1241.2 1241.4 1241.6
m/z
1241.8 1242.0 1242.2 1242.4 1242.6
1241.5517
1210.4679
Remove uncertainty from peptide
and PTM assignments. The
extraordinary new Finnigan LTQ FT
incorporates an FT-ICR detector for
ultra-high resolution (>100,000) and
extremely accurate mass measurements
(

Rapid, Confident Protein Identification
Finnigan LTQ with vMALDI Source and Ettan DIGE
Data Dependent MS/MS
of a protein mixture with
several MS/MS spectra
shown
6
Quickly determine which proteins
are present during rapid screening
of proteomics samples by combining
the speed of MALDI ionization
with the sensitivity and MS/MS
performance of the Finnigan LTQ.
Finnigan vMALDI Ion Source
Achieve confident, high-throughput
protein ID with the new intermediate-pressure
Finnigan vMALDI ion
source for the Finnigan LTQ mass
spectrometer. Quickly generate
SEQUEST-searchable MS/MS
spectra for unambiguous protein
identification based on peptide
sequence, not just peptide molecular
weight. And with unique MS n
capability, even post-translational
modification (PTM) spectra (e.g.
phosphorylation, glycosylation)
are easily obtained.
2D Gels and DIGE Chemistry
Chemistry and hardware must
work together to ensure a seamless
system for proteomic research.
Ettan DIGE (2-D Fluorescence
Difference Gel Electrophoresis)
from GE Healthcare (formerly
Amersham Biosciences) is the
state-of-the-art 2D protein expression
visualization system. The Ettan
DIGE system is perfectly suited to
the new vMALDI LTQ mass spectrometer
workstation for maximum
protein throughput.
Cytochrome-C Lactalbumin BSA
Finnigan vMALDI
source with LTQ
linear ion trap

CCD image of protein digest
with α-cyano matrix
Analysis of a four-peptide mixture,
200 amol each, with α-cyano matrix
The Perfect System for High-
Throughput Protein Analysis
The Finnigan vMALDI ion source is
completely optimized to harness the
incredible sensitivity of the Finnigan
LTQ for high-throughput MALDI-
MS/MS analysis. The Finnigan
vMALDI ion source utilizes:
• Crystal Positioning System (CPS) to automatically target
the optimum sampling pattern
• Automated Spectral Filtering (ASF) for real-time monitoring
of spectral quality
• Automatic Gain Control (AGC )
to determine the optimum
number of laser shots for the
best possible sensitivity
Angiotensin I fragment 1-7
Bradykinin
Angiotensin I
Neurotensin
The system is designed to allow
walk-away automation during data
acquisition and has the intelligence
to change experimental conditions
to provide the best possible outcome:
First, the CPS performs a
digital analysis of the sample spot
image to rapidly identify crystals
with good signal-to-noise potential.
CPS also remembers the ablated
path, so that only fresh crystals are
interrogated. Then, the Finnigan
vMALDI ion source begins sampling,
using ASF for real-time monitoring
of spectral quality. When high
quality spectra are detected, the
Finnigan vMALDI ion source uses
AGC to determine the optimum
Automated sampling pattern
mapped with CPS
MS/MS of 50 fmol myoglobin digest,
precursor is the T2 fragment at m/z 1606.9
number of laser shots to achieve
the highest possible sensitivity
without sacrificing spectral quality.
Data Dependent MS/MS is immediately
performed on all precursor
ions, giving MS/MS spectra to identify
all peptides that are present.
Poor signal: Move to different crystal
CPS
ASF
AGC
Good Signal
Excellent Quality Spectra
Examine Spectra
Optimize Laser
CPS, ASF, and AGC allow automated acquisition
of high quality MS and MS/MS spectra
MS 3 of 50 fmol myoglobin digest,
precursor is at m/z 1192.7
Move to next sample: Repeat process
7

Ultimate Analytical Flexibility
MDLC LTQ Workstation
Analytical precision
demonstrated by
duplicate analyses
with the MDLC LTQ
8
Relative Abundance
The combination of the Ettan MDLC
chromatography system from GE
Healthcare and the Finnigan LTQ
from Thermo creates a powerful
new integrated LC/MS system
with extraordinary flexibility and
innovative applications.
RT: 0.00 - 60.01
100
90
80
70
60
50
40
30
20
10
0
RT: 0.00 - 60.02
100
90
80
70
60
50
40
30
Relative Abundance
20
10
0
0.10
518.7
5.06
519.0
7.24
535.8
8.60
535.8
11.36
535.8
13.08
518.8
The pumps perform high pressure
mixing and the system uses realtime
flow monitoring to assure
absolute gradient reproducibility.
The entire system flowpath is bioinert,
allowing high-yield analysis
of post-translationally modified
17.67
563.4
17.86
465.6
19.80
501.9
19.77
501.9
20.67
636.8
22.68
536.8
22.73
536.8
25.32
748.3
27.67
616.3
29.29
460.6
31.14
908.5
peptides. The system can perform
rapid LC/MS separations using a
single column or high resolution
multidimensional separations,
allowing customization of separations
for optimal detection of
peptides by the Finnigan LTQ.
34.75
557.6
36.62
518.7
40.34
518.8
42.27
518.7
44.78
518.7
48.53
518.8
MDLC LTQ provides
ultimate versatility
29.28
460.6
0.23
519.0
5.13
535.8
5.41
518.7
7.62
519.0
9.92
518.7
12.90
518.8
16.24
597.4
17.70
465.6
21.53
650.4
25.31
748.3
26.72
771.4
31.04
908.5 34.45
557.7
37.05
789.5
40.38
518.7
0 5 10 15 20 25 30
Time (min)
35 40 45 50 55 60
41.65
518.7
45.26
518.8 45.61
518.8
52.64
783.8
53.00
783.8
53.56
727.3
56.58
518.7
0 5 10 15 20 25 30 35 40 45 50 55 60
Time (min)
49.75
518.8
53.01
462.2
55.93
519.1
57.91
519.1

Integrated Proteomics Workstation
Finnigan ProteomeX LTQ Workstation
Use turnkey, customized proteomics
application methods to perform
advanced protein analysis.
The Finnigan ProteomeX LTQ workstation
integrates optimized, colorcoded
combinations of columns,
Finnigan ProteomeX LTQ workstation with new Micro AS
autosampler for integrated proteomics analysis
plumbing kits, and methods into
easy-to-use configurations for very
specific analytical objectives:
High-Throughput Protein ID
Maximum Sequence Coverage
Phosphorylation Site Mapping
MudPIT
9

High-Throughput Protein ID
Perform a rapid desalting, concentration, and LC/MS analysis for high-throughput protein ID.
Enzymatic digest
of excised
protein spots
Relative Abundance
100
90
80
70
60
50
40
30
20
10
20
90
0
60
22.0 23.0 24.0 25.0 26.0 27.0 28.0 29.0 30.0
10
50
80Time
(min)
100
90
80
70
60
50
40
30
20
Relative Abundance
100
90
80
70
60
50
40
30
Relative Abundance
100
90
80
70
100
0
40
70
26.30
22.0 23.0 24.0 25.0 26.0 27.0 28.0 29.0 30.0
100
30
20
60
50
Time (min)
90 Spot # Base Peak
422.0
26.25
422.0
26.34
421.9
80
10
26.23
421.9
40
26.37
422.1
0
70
26.21
25.0
26.0 27.0 28.0 29.0
23.0 24.0
30
422.0
20
60
Time (min)
26.39
422.0
26.41
50
26.19
422.1 422.0
10
26.43
40
422.0
0
23.0 24.0 25.0 26.0 27.0 28.0 29.0 30.0
26.48
30
Time (min)
26.16
422.1 422.1
Rapid desalt and
full mass scan
Relative Abundance
Relative Abundance
20
26.53
421.9
25.56 25.61
523.6 523.6 26.14
27.44
422.0 26.64 27.37 27.3727.44
422.0 738.4 738.3 27.48
422.0
10
27.35 738.327.86 738.327.86
25.52 25.77
26.75 26.7527.35
738.3
767.7
523.5 523.6 422.0 422.0738.3
28.0428.26
28.93
767.8
29.06
840.0 419.3419.2
0
22.0 23.0 24.0 25.0 26.0 27.0 28.0 29.0 30.0
Time (min)
29.27
419.2
85.73
85.83
100
80
60
40
20
0
782.1
882.2
981.3
680.3
567.3
1094.3
1336.4
92.69
10
60.93
0
63.94 67.61 72.07 73.60 76.24
82.06
81.62
80.54
89.36 91.84 92.87
101.23
106.35
104.30
107.37
115.51
118.98
121.94
123.74
126.11
60 70 80 90 100 110 120
96.27
97.27
101.75
87.27 95.48
112.10
111.02
Time (min)
Rapid identification of
proteins from 2D gel
using MS/MS data and
SEQUEST searching
algorithms
500 1000 1500 2000
Maximum Sequence Coverage
and perform a Data Dependent Top Ten MS/MS experiment with the Finnigan LTQ.
10
Base Peak
Automated Data
Dependent MS/MS
with Dynamic
Exclusion for
high sensitivity
A mixture of proteins was digested
with enzyme and analyzed with a
120-minute reversed phase gradient.
The Finnigan LTQ, using a Top Ten
Data Dependent Dynamic Exclusion
experiment, conclusively identified
multiple peptides resulting in significant
coverage for all proteins in
the mixture.
Relative Abundance When maximum protein coverage is important, use longer gradients to achieve better peptide resolution
ProteomeX
Methods
Accession
Number Protein
1 P43652 Afamin precursor (Alpha-albumin) (Alpha-Alb).
2 P05091 ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL PRECU
3 P35221 Alpha-1 catenin (Cadherin-associated protein) (Alpha E-catenin).
4 P05067 ALZHEIMER'S DISEASE AMYLOID A4 PROTEIN PRECUR
5 P51693 AMYLOID-LIKE PROTEIN 1 PRECURSOR (APLP)
6 P20073 ANNEXIN A7 (ANNEXIN VII) (SYNEXIN)
7 Q9BZC7 ATP-BINDING CASSETTE, SUB-FAMILY A, MEMBE
8 P02730 Band 3 anion transport protein (Anion exchange protein 1)
9 P01884 BETA-2-MICROGLOBULIN PRECURSOR
10 P55290 CADHERIN-13 PRECURSOR (TRUNCATED-CADHERIN)
11 O14967 Calmegin precursor
12 P17655 Calpain 2, large [catalytic] subunit precursor (EC 3.4.22.17)
13 Q15699 Cartilage homeoprotein 1
14 Q13033 Cell-cycle autoantigen SG2NA (S/G2 antigen)
15 P54219 Chromaffin granule amine transporter (VAT1).
16 P10645 CHROMOGRANIN A PRECURSOR (CGA) (PITUITARY
17 O95239 CHROMOSOME-ASSOCIATED KINESIN KIF4A (CHRO
18 Q9NYC9 CILIARY DYNEIN HEAVY CHAIN (AXONEMAL DYNE
19 Q12860 Contactin precursor (Glycoprotein gP135).
20 P01034 CYSTATIN C PRECURSOR (NEUROENDOCRINE BASIC
21 P00156 CYTOCHROME B
22 Q16850 CYTOCHROME P450 51 (CYPL1) (P450L1) (STERO
23 P17611 Desmin
24 Q9UBP4 DICKKOPF RELATED PROTEIN-3 PRECURSOR (DKK
25 Q12805 EGF-CONTAINING FIBULIN-LIKE EXTRACELLULAR
26 Q15668 EPIDIDYMAL SECRETORY PROTEIN E1 PRECURSOR
27 P23142 FIBULIN-1 PRECURSOR
28 Q9UEY8 GAMMA ADDUCIN (ADDUCIN-LIKE PROTEIN 70)
29 Q9Y6H8 GAP JUNCTION ALPHA-3 PROTEIN (CONNEXIN 46)
30 Q16478 Glutamate receptor, ionotropic kainate 5 precursor
31 P55318 Hepatocyte nuclear factor 3-gamma (HNF-3G)
32 P18065 INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN
33 P24592 Insulin-like grow th factor binding protein
34 Q9UKP45 Kelch-like protein 1
35 P10586 LAR protein precursor (Leukocyte antigen related)
36 P03952 lasma kallikrein precursor (EC 3.4.21.34)
37 P08547 LINE-1 reverse transcriptase homolog
38 P07864 L-lactate dehydrogenase C chain (LDH-C) (LD
39 O94759 LONG TRANSIENT RECEPTOR POTENTIAL CHANNEL
40 O00754 Lysosomal alpha-mannosidase precursor (Man
41 P04156 MAJOR PRION PROTEIN PRECURSOR (PRP) (PRP27-
42 P40925 Malate dehydrogenase, cytoplasmic (EC 1.1.1.37).
43 O60476 Mannosyl-oligosaccharide 1,2-alpha-mannos
44 P16035 Metalloproteinase inhibitor 2 precursor
45 P20774 Mimecan precursor (Osteoglycin) (Osteoinductive factor)
46 O95255 Multidrug resistance-associated protein 6
47 Q92859 Neogenin precursor.
48 P13591 NEURAL CELL ADHESION MOLECULE, 140 KDA ISO
49 Q9N0X5 Neural proliferation differentiation and control protein-1 precursor
50 P19022 Neural-cadherin precursor (N-cadherin) (Cadherin-2).
51 P07197 Neurofilament triplet M protein (160 kDa neurofilament protein)
52 O43613 Orexin receptor type 1 (Ox1r) (Hypocretin
53 P20774 OSTEOINDUCTIVE FACTOR PRECURSOR (OIF) (OSTEO
54 P10451 OSTEOPONTIN PRECURSOR (BONE SIALOPROTEIN 1)
55 P55058 PHOSPHOLIPID TRANSFER PROTEIN PRECURSOR (L
56 P43034 PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE
57 P07602 Proactivator polypeptide precursor
58 O60883 Probable rRNA processing protein EBP2
59 Q15113 Procollagen C-proteinase enhancer protein precursor (PCPE)
60 P01210 PROENKEPHALIN A PRECURSOR [CONTAINS: MET-EN
Amount Sequence
Protein Injected Peptides Coverage
BSA 100 amol 2 3.95%
Catalase 1 fmol 13 26.48%
Lactoglobulin 1 fmol 2 17.28%
Carbonic Anhydrase 100 fmol 3 15.44%
Lactoperoxidase 100 fmol 24 44.24%
Carboxypeptidase 1 pmol 21 73.06%

Phosphorylation Site Mapping
Identify sites of protein phosphorylation using chromatography columns that provide a high yield of
phosphopeptides plus Data Dependent Neutral Loss MS 3
scanning with the Finnigan LTQ to selectively
perform MS 3
on phosphopeptides.
Relative Abundance
100
50
100
90
80
70
60
50
40
30
20
10
20 .1 5
22 .6 4
27 .6 3
33 .1 3
28 .2 0
33 .5 9
35 .7 6
37 .3 6
39 .5 2
41 .4 0
MS
MS 2
MS 3
41 .7 1
19 .7 3
0
4. 55 9. 44
15 .4 6 42 .7 6 49 .0 4 57 .3 4
0 10 20 30 40 50 60
100
0
476.27 706.08
688.29
1031.78
1058.62
982.624
747.31 1013.78
503.37 632.39 876.39
1105.42
390.18
844.91
1375.65
1490.75
1361.58
1619 .71
1619.72
80
964.67
60
747.34
1688.81
632.38
40 328.26
503.42
20
603.30
345.07
827.52
1088.34
859.53
1105.56 1361 .71 1601.85
1332 .52
1233.69
1491.61
1070.57
1199.39
1574.61
1817.71
1800 .74
Time (min) m/z
0
0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100
Time (min)
100
50
0
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
Time (min)
100
50
0
0 10 20 30 40 50
100
50
0
40 m M
150 160
0 10 20 30 40 50 60 70 80
Time (min)
90 100 110 120 130 140
100
50
0
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
Time (min)
100
50
80 m M
0
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
Time (min)
100
50
0
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
Time (min)
100
50
0
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
Time (min)
100
50
0
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
Time (min)
100
50
0
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
Time (min)
100
50
0
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
Time (min)
100
50
(Shows
neutral loss)
0 m M
10 m M
20 m M
60 m M
100 m M
120 m M
150 m M
200 m M
400 m M
800 m M
0
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
Time (min)
Relative Abundance
40 0 60 0 80 0 1000 1200 1400 1600 1800 2000
Analysis of a beta casein digest, showing base peak LC/MS analysis, MS spectrum, MS/MS spectrum showing neutral loss
indicative of a phosphopeptide, MS 3 spectrum showing excellent fragmentation, and definitive identification by SEQUEST.
FQS*EEQQQTEDELQDK
Multidimensional Protein ID (MudPIT)
Analyze complicated protein digest mixtures with automated, on-line multidimensional LC/MS analysis. Peptides
are retained on a strong cation exchange column, desalted and concentrated on peptide traps, then resolved on a
high-performance C18 column and extensively mined for peptides by the Finnigan LTQ. Results from all salt steps
are compiled in a final Multiple File Consensus Report by BioWorks.
Neurofilament triple-m protein (125 ng/L in normal CSF)
present at < 1 fmol in this analysis
Partial list of
proteins found
ProteomeX
Methods
Accession Unique Coverage
Number Protein Peptides Percentage
P02763 ALPHA-1-ACID GLYCOPROTEIN 2 PRECURSOR 5 18
P19652 ALPHA-1-ACID GLYCOPROTEIN 2 PRECURSOR 8 28
P04217 ALPHA-1B-GLYCOPROTEIN 12 25
P01009 Alpha-1-antitrypsin precursor 10 26
P02765 ALPHA-2-HS-GLYCOPROTEIN PRECURSOR 10 31
P01023 ALPHA-2-MACROGLOBULIN PRECURSOR 35 48
P01011 ALPHA-1-ANTICHYMOTRYPSIN PRECURSOR 25 84
P43652 AFAMIN PRECURSOR (ALPHA-ALBUMIN) 3 25
P02768 SERUM ALBUMIN PRECURSOR 67 58
P01876 IG ALPHA-1 CHAIN C REGION 2 25
P01019 ANGIOTENSINOGEN PRECURSOR 11 25
P01008 ANTITHROMBIN-III PRECURSOR (ATIII) 3 24
P02647 APOLIPOPROTEIN A-I PRECURSOR (APO-AI) 6 16
P02652 APOLIPOPROTEIN A-II PRECURSOR (APO-AII) 5 20
P06727 APOLIPOPROTEIN A-IV PRECURSOR (APO-AIV) 4 15
P06727 APOLIPOPROTEIN A-IV PRECURSOR (APO-AIV) 7 25
P05090 APOLIPOPROTEIN D PRECURSOR 8 49
P02649 APOLIPOPROTEIN E PRECURSOR (APO-E) 11 32
P02749 Beta-2-glycoprotein I precursor (Apolipopro 5 12
P32247 BOMBESIN RECEPTOR SUBTYPE-3 (BRS-3) 5 24
P09871 COMPLEMENT C1S COMPONENT PRECURSOR 2 35
P49454 CENP-F KINETOCHORE PROTEIN 3 45
P00450 CERULOPLASMIN PRECURSOR (FERROXIDASE) 4 25
P00751 COMPLEMENT FACTOR B PRECURSOR 23 37
P08603 COMPLEMENT FACTOR H PRECURSOR 15 42
P10909 Clusterin precursor (Complement-associated 15 25
P09871 Complement C1s component precursor 2 24
P01024 COMPLEMENT C3 PRECURSOR 38 37
P01028 COMPLEMENT C4 PRECURSOR 32 23
Q12860 CONTACTIN PRECURSOR (GLYCOPROTEIN GP135) 6 16
P11532 DYSTROPHIN 5 25
P02671 FIBRINOGEN ALPHA/ALPHA-E CHAIN PRECURSOR 13 34
P02751 FIBRONECTIN PRECURSOR (FN) (COLD-INSOLUBLE 3 24
P01857 IG GAMMA-1 CHAIN C REGION 21 60
P01859 IG GAMMA-2 CHAIN C REGION 14 30
P01860 IG GAMMA-3 CHAIN C REGION (HEAVY CHAIN DISEA 13 34
P01861 CHAIN C REGION 3 15
P01777 HAIN V-III REGION TEI 3 14
P01834 HAIN C REGION 3 50
P80362 HAIN V-I REGION WAT 7 21
P18136 HAIN V-III REGION HIC PRECURSOR 6 16
P06396 GELSOLIN PRECURSOR, PLASMA 16 27
P02023 HEMOGLOBIN BETA CHAIN 32 23
P02790 HEMOPEXIN PRECURSOR (BETA-1B-GLYCOPROTEIN) 12 25
P00738 HAPTOGLOBIN-2 PRECURSOR 15 25
P00739 HAPTOGLOBIN-RELATED PROTEIN PRECURSOR 2 24
P01042 Kininogen Alpha-2-thiol proteinase inhibitor 38 37
P01597 KAPPA CHAIN V-I REGION DEE 32 23
P01842 IG LAMBDA CHAIN C REGIONS 3 50
Q92876 KALLIKREIN 6 PRECURSOR (PROTEASE M) (NEURO 2 23
P29622 Kallistatin precursor (Kallikrein inhibitor) 2 25
Q9UM88 Beta 2-microglobulin protein 9 70
P36955 MENT EPITHELIUM-DERIVED FACTOR PRECURSOR 6 23
P05155 PLASMA PROTEASE C1 INHIBITOR PRECURSOR (C1 I 13 34
P00747 PLASMINOGEN PRECURSOR 33 44
P02787 SEROTRANSFERRIN PRECURSOR 34 44
P05452 TETRANECTIN PRECURSOR (TN) (PLASMINOGEN-KRI 6 16
P07477 TRYPSINOGEN I PRECURSOR 15 33
P02766 Transthyretin precursor (Prealbumin) (TBPA) 6 16
P02774 VITAMIN D-BINDING PROTEIN PRECURSOR (DBP) 7 18
P04004 TRONECTIN PRECURSOR (SERUM SPREADING FACTOR) 2 35
11

Powerful Bio-Software Solutions
Achieve Dramatic Productivity Gains
100
80
60
40
20
0
100
80
60
40
20
0
100
80
60
40
20
0
100
80
13 .1 9
Efficiently turn data into information,
and then into knowledge, with
Thermo’s solutions:
BioWorks–Protein identification
software, based on SEQUEST
SEQUEST Cluster–Parallel
processing for accelerated database
searching
DeNovoX–Automated de novo
sequencing software
SALSA–Spectral pattern
recognition software
Starting with MudPIT data, BioWorks identifies and highlights the b- and y-ions
matched within the peptide chain of the first identified protein candidate.
12
RT: 0.00 - 147.01
Relative Abundance
25 .6 3
43 .98
43 .1 0
BioWorks Protein
Identification Software
Use the most-cited protein identification
algorithm in the scientific
literature–SEQUEST–to correctly
match MS, MS/MS, and MS n
spectra with protein databases.
Renowned for its sensitivity and its
ability to identify PTMs, the power
of BioWorks is amplified by:
3. 85
45 .49 48 .38
53 .4 2 62 .96 79 .4 8 97 .29 11 1.60 12 1.87
13 0.22
27 .6 7
23 .3 0
43 .0 8
19 .68 39 .16 29 .3 4
18 .10
14 .07 51 .0 5
53 .6 7
61 .2 6 75 .8 2 94 .59 1 04. 07
11 6.91
12 8. 6 6 13 2. 90
13 5. 25
28 .2 3
24 .11
33 .86
23 .2 1 36 .15
16 .50
44 .1 4 57 .31
14 .6 5
10 .12
62 .0 0
75 .8 4
97 .1 4 10 2. 90 12 2. 3 7 13 0. 0 0
38. 40 46 .50
29 .91
57 .2 1
60
25 .0 2
40
20
0
15 .27 19 .7 9
1.30
58. 33
75 .9 5 98 .8 4 101 .2 1
12 4.47 13 2. 44
0 20 40 60 80 100 12 0 14 0
Time (min)
Post-Translational
Modification Searches
Automatically set up and execute
searches for static and dynamic
modifications such as phosphorylation
and oxidation
Protein Quantitation
using XPRESS Automatically generate relative
quantitation levels in peptides
tagged with any label such as
ICAT reagent labeled peptides
Multiple File Consensus
Consolidate and sort results from
a number of SEQUEST searches
–essential for MudPIT analyses
Customized Results
Filtering and Sorting
Incorporate XCorr vs. Charge State
filter to automatically eliminate
low-scoring peptides and proteins,
and reduce the amount of time
spent verifying results
Database Management
Automatically download protein
database updates from public web
sites, index them to increase their
specificity, and create customized
databases with proprietary proteins
SALSA
Mine MS/MS spectra for unexpected
post-translational modifications
or mutations with this spectral
matching tool

SEQUEST Cluster
SEQUEST searching speed can
be scaled to the needs of each
individual lab. As overall throughput
and data processing needs
increase, computational capacity
can be easily added. The SEQUEST
Cluster creates a parallel processing
software architecture to distribute
searches across many
individual processors, greatly
reducing search times.
Absolute and relative probabilities of partial and
completed sequences are sorted and displayed
in this colorful results table.
Singly and doubly-charged b- and y-ions are highlighted in the spectral
display, while amino acid positions are annotated individually.
DeNovoX—the “One-Click”
Solution to Automated
de novo Sequencing
Use this software to sequence
a novel protein or confirm the
identity of a protein candidate
from a BioWorks database search.
DeNovoX uses a rigorous, probability-based
algorithm to derive
sequences for peptides from the
information contained in their
MS/MS spectra.
Interactive and intuitive graphics
guide a user through a list of possible
peptide tags, their b- and y-ion
series, and fragment assignments.
Sequence gaps are automatically
revealed to help assign PTMs.
This Cluster has the ability to search 20,000 spectra against
the human database in just a few minutes to dramatically
streamline the protein identification process.
13

Complete Proteomics Workflow
Effective Analysis of Proteins
14
Sample Preparation
Effective analysis of proteins
requires a strategy for reduction
of sample complexity using gels,
chromatography, or affinity-based
separations. A strategic Proteomics
Alliance with GE Healthcare gives
Thermo customers direct access
to GE Healthcare technologies and
support. You can call upon us to
help solve your most challenging
separations needs utilizing Ettan
gels, CyDye reagents, DeCyder
software, and AKTA and Ettan chromatography
systems and supports.
Sample
preparation
Protein Identification
using MALDI
The Finnigan vMALDI source for
the Finnigan LTQ creates a powerful
new system for high-throughput
protein ID using MALDI-MS/MS
capability to provide protein ID
based on peptide structure, not
just peptide MW. This allows rapid
identification of proteins by effective
analysis of protein digest mixtures.
2D gel
electrophoresis
Multidimensional
liquid chromatography

Protein Identification
using Electrospray
The Finnigan LTQ is the ideal MS
system for protein analysis. The
sensitivity and rapid scanning of
the LTQ are combined to provide the
best possible protein coverage and
PTM identification for both simple
and complex samples.
The Finnigan ProteomeX LTQ system
provides an integrated, turnkey
solution for most proteomics applications,
including high throughput
protein ID, phosphorylation site
mapping, and MudPIT.
Protein identification using
mass spectrometry
Where additional capability is
required, the MDLC LTQ system
delivers ultimate versatility and
analytical performance.
FT-MS
The Finnigan LTQ FT Hybrid provides
extraordinary mass accuracy and
resolution for difficult challenges
such as PTM characterization and
complex sample analysis.
Bioinformatics
TurboSEQUEST, incorporated into
BioWorks, is the most cited protein
identification algorithm in the scien-
tific literature, yielding highly
sensitive and confident answers.
Both false positive and false negative
rates for incorrect protein identification
have fallen dramatically,
reducing the burden of manual,
post-analysis data review.
Where increased computational
speed is required, the SEQUEST
Cluster can apply the power of a
supercomputer to the analysis of
your data, scalable to the needs
of your lab.
Bioinformatics
• Identification
• Quantification
• Characterization
15

Laboratory Solutions Backed by
Worldwide Service and Support
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worldwide by a network of factory trained and highly qualified scientists
and engineers. Our experts help you choose the right instruments for your
lab, then keep the instruments performing to specification.
Contact us today for more information on how our specialized sales and
service engineers can help you meet your laboratory needs.
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