Topics. Protein Bioinformatics ( ) Progression of Protein Analysis by Mass Spectrometry. Protein identification by mass spectrometry

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1 Protein Bioinformatics (26.655) Lecture 15: Quantitative Proteomics Tuesday, May 5, 28 Robert N. Cole, Ph.D. Mass Spectrometry/Proteomics Facility at Johns Hopkins School of Medicine 371 Broadway Research Bldg 733 N. Broadway St. Baltimore, MD 2125 Ph: (41) /Fax: (41) Progression of Protein Analysis by Mass Spectrometry Analysis >5 years ago Now De novo sequencing Identify isolated protein Identify protein mixtures Quantify proteins Identify/Map Modifications Hard Easy Hard Hard Hard Still Hard Routine Routine Routine? Not Easy Quantify PTMs Hard Still Hard Topics Protein identification by mass spectrometry Sample preparation Relative quantification of proteins 1

Protein Identification by Mass Spectrometry (from solution, gel bands or spots, complex mixtures) Nanospray Ionization Full MS Scan Parent Mass Selection Parent Mass Fragmentation Fragment Mass Scan

2 Protein Identification by Mass Spectrometry (from solution, gel bands or spots, complex mixtures) Nanospray Ionization Full MS Scan Parent Mass Selection Parent Mass Fragmentation Fragment Mass Scan HPLC Survey Scan Collision induced MS/MS or Tandem MS Scan Intensity Intensity m/z Peptide Mass Finger Print (PMF) m/z Tandem MS PMF vs. Tandem MS PMF Uses Peptide Masses Need Protein Coverage >3% Sample Complexity Must Be Low No more than three proteins Protein modifications suggested by a change in peptide mass High resolution required Tandem MS (or MS/MS) Uses Peptide Mass and Sequence Tag Need Only One Peptide with >3 Amino Acids Masses in Sequence (at least two preferred) High Sample Complexity Tolerated Protein modifications identified and mapped to an amino acid High resolution not required Protein Identification: How much protein do you need? ng 5 kd protein 1 ng = 2 fmol -22 kd -1 kd - 5 kd Silver stained gel - 25 kd 1 fmol per protein in gel band or spot 1 fmol per protein in solution 2

3 Search Engines for Protein Identification from MS Data Summary of Programs Proteome Software ExPASy expasy.proteome.org.au Free Programs ProteinProspector XProteo Prowl Mascot prospector.ucsf.edu xproteo.com:2698 prowl.rockefeller.edu (Free up to 3 ions) Open Source Programs OMSSA pubchem.ncbi.nlm.nih.gov/omssa/ X! Tandem Commerical Programs Mascot Sequest Spectrum Mill Proteolynx fields.scripps.edu/sequest/ Next Step: Quantify Individual Proteins in Complex Mixtures (Functional Proteomics) Identify proteins expressed at different levels in diseases, mutant cell lines, during developmental stages, etc. Determine stoichiometry of proteins in protein complexes Determine protein subcellular localization Identify protein binding partners Follow protein trafficking Map metabolic pathways many, many others Quantitative Proteomics Methods Approach Labeling Method 2D Gel Based None Metabolic Chemical Gel matching Radiolabeling Difference Gel Electrophoresis (DIGE) MS Based None Spectral Counting, Peak Intensity Spiking Absolute Quantification (AQUA) Metabolic Stable Isotope Labeling of Amino Acids in Cell Culture (SILAC) Enzymatic 18 O-Labeling Chemical Isotope-Coded Affinity Tags (ICAT), Isobaric Tags for Relative and Absolute Quantitation (itraq) 3

4 Quantitative Proteomics Strategies Sample Preparation Fractionation? (sample complexity) (low abundance proteins) Protein/Peptide Label? Fluorescent tags (Cy dyes) Stable isotopes ( 13 C, 15 N, 18 O) Mass tags (Signature mass) Protein/Peptide Separation? Gel Electrophoresis Chromatography Both Quantification Protein Identification (MW, pi) (MW, charge, affinity) (comparison) (by mass spectrometry) Sample Preparation Most important step! Reproducibility essential! Variability in sample prep: Technical: good < bad hands few < many steps Biological: cells < tissue < serum yeast < mouse < human Sample Preparation Must Be Reproducible and Standardized! Biological Replicates Initial Protocol Standardized Protocol 4

Variability in sample prep: Technical: good < bad

serum yeast < mouse < human Detecting low abundance

protein) More protein 15 ug protein, 7 cm IPG strip, 1

5 Sample Preparation Most important step! Reproducibility essential! Variability in sample prep: Technical: good < bad hands few < many steps Biological: cells < tissue < serum yeast < mouse < human Detecting low abundance proteins requires Fractionation (subcellular or protein) More protein 15 ug protein, 7 cm IPG strip, 1 gel pi ug protein, 24 cm IPG strip, 3 gels 1.5 Gel Based Techniques 5

Sample 2 1 1D Gel Analysis Slice Gel slice number 22 Name of protein Polymeric immunoglobulin receptor 22 Transferrin 22 Vanin 1 21 1B-glycoprotein 21 Complement component 5 21 hgc-1 (human

6 Sample 2 1 1D Gel Analysis Slice Gel slice number 22 Name of protein Polymeric immunoglobulin receptor 22 Transferrin 22 Vanin B-glycoprotein 21 Complement component 5 21 hgc-1 (human G-CSFstimulated clone-1) 21 IgG Fc-binding protein 21 Mac-2-binding protein 18-1-antichymotrypsin 18 Albumin 17 Amylase, pancreatic, -2A 17 Amylase, salivary, -1A 17 Catalase Kristiansen et al. Molec Cell Proteomics 3: , 24. 1D Gel Analysis Strengths: Simple In expensive sample prep Membrane proteins High MW proteins (>1 kda) Limitations: Time consuming Not Quantitative Limited resolution Low MW Proteins (<7kDa) Principle of 2-D Gel Electrophoresis First dimension: according to the isoelectric point (isoelectric focusing) Second dimension: separation according to molecular weight (SDS gel electrophoresis) 6

Gel Based Techniques with Fluorescent Tags Difference Gel Electrophoresis (DIGE) Control Protein Sample Label with fluor 1 Disease Protein

7 2D Gel Analysis No Labeling pi MW Bacterial Strain #1 Bacterial Strain #2 Quantify by relative spot volume. Major problem with gel reproducibility and matching spots. Gel Based Techniques with Fluorescent Tags Difference Gel Electrophoresis (DIGE) Control Protein Sample Label with fluor 1 Disease Protein Sample Label with fluor 2 Mix labeled proteins from both samples Separate proteins on one 2-D gel Excitation wavelength 1 Image gel Excitation wavelength 2 Protein View comparison differences in a single gel! Unlu et al. Electrophoresis 18: ,

Three Fluorescent Cy Dyes Cy2, Cy3, Cy5 ε-amino group of lysine Matched for charge (carries +1 charge) Matched for MW (~45 Da) Cy2 Cy5 Cy3 Only 3-5% of proteins are labeled (minimal labeling) DIGE

8 Three Fluorescent Cy Dyes Cy2, Cy3, Cy5 ε-amino group of lysine Matched for charge (carries +1 charge) Matched for MW (~45 Da) Cy2 Cy5 Cy3 Only 3-5% of proteins are labeled (minimal labeling) DIGE Analysis Control Sample Label with Cy3 Pooled Samples labeled with Cy2 (on all gels to compare one gel to another) Disease sample Label with Cy5 Mix samples Separate proteins on one 2-D gel Excitation wavelength 1 Excitation wavelength 2 View differences Differential Protein Expression Between Two Glial Cell Lines 3. IEF 1. SDS-PAGE

9 Third Cy Dye (Cy2) Labeling as an Internal Standard All possible protein spots overlaid on every gel. Simplifies gel to gel matching. Each spot has it s own internal standard spot for normalizing across gels. Reduces experimental variations. Accounts for differences in sample load DIGE Analysis of Ecoli proteins spiked with four proteins 4 IEF 7 SDS-PAGE Phosphorylase b.5 X Albumin Conalbumin.5 X 5-1 X Trypsin Inhibitor 4 X 9

10 Relative Abundances of Four Proteins in Ecoli Lysates are within 1% of Predicted Values Spiked Proteins Expected Ratio Observed Ratio Error t-test Albumin % 2.7E-6 Conalbumin % 1.6E-14 Phosphorylase B % 1.3E-1 Trypsin inhibitor %.14 Strengths/Limitations of 2D-DIGE Gels Strengths Superb resolving power Quantitative comparisons of ~2 proteins on one gel Simplified comparison between gels Highly reproducible Detect post-translational modifications Limitations <7, and >13, Da Strongly hydrophobic Highly basic proteins Difficult to automate Multiple proteins per spot Quantify but not identify, still need MS analysis Mass Spectrometry Based Techniques 1

Col1 Col2 Multi-dimensional Chromatography Digest Load Denatured proteins Peptide mix 2D chromatography separations of peptides Peptide ID by Tandem MS (Shotgun or MuDPIT) 115 Col2 only Peptides

11 Col1 Col2 Multi-dimensional Chromatography Digest Load Denatured proteins Peptide mix 2D chromatography separations of peptides Peptide ID by Tandem MS (Shotgun or MuDPIT) 115 Col2 only Peptides Identified Col 1 and Col2 219 Link et al. Nat. Biotech 17: , 1999 Summary of Multi-Dimensional Chromatography Strengths: Reduces sample complexity Low abundance proteins Membrane proteins All MW Proteins Flexible (different column combinations) Limitations: Complex setup No faster than 2D gels Computer intensive Quantitative? Reproducibility Can automate Mass Spectrometry Based Techniques with Stable Isotopes or Mass Tags 11

Isotope Coded Affinity Tags (ICAT) O HN NH S Biotin O XX N H O O XX O N I XX XX H Linker heavy or light isotope Binds to Cysteines S H cys Reduce sample complexity.

12 Isotope Coded Affinity Tags (ICAT) O HN NH S Biotin O XX N H O O XX O N I XX XX H Linker heavy or light isotope Binds to Cysteines S H cys Reduce sample complexity. Analyze only cysteine-containing peptides. Gygi et al.nature Biotech 17: , 1999 ICAT Workflow (cysteine-containing peptides) Light Heavy mass Gygi et al.nature Biotech 17: , 1999 Hansen et al. Molec Cell Proteomics 2: , 23 Strengths/Limitations of ICAT Strengths: Overcomes many 2D gel limitations Relative quantification Reduces complexity of protein digest (only cysteine containing peptides) Low abundance proteins Compatible with gels Limitations: ~2% of proteins lack cysteines Protein identifications often based on one peptide No post-translational modification information Quantification error ~2% Multi-step process, peptide losses 12

18 O-labeling Protocol Control sample Disease sample Trypsin Trypsin + 18 O-water C-terminal Mix labeled peptides C-terminal (adds 4 Da) Analyze by mass spectrometry Yao et al. Anal. Chem 73:2836-2842, 21 Yao et al.

13 18 O-labeling Protocol Control sample Disease sample Trypsin Trypsin + 18 O-water C-terminal Mix labeled peptides C-terminal (adds 4 Da) Analyze by mass spectrometry Yao et al. Anal. Chem 73: , 21 Yao et al. J Proteome Res 2: , 23 Quantify by 18 O to 16 O peptide ratios Peptide sequence Peak intensity ratio ± error NWAAFR 2.5 ±.1 GNVYWVR 3.4 ±.7 GVIETVYLR 3. ±.3 LLTPNEFEIK 3.1 ±.5 VAITFDSSVSWPGNDR 2.9 ±.4 NLLLLPGSYTYEWNFR 2.8 ±.2 (4%) (2%) (1%) (19%) (14%) (7%) Yao et al. Anal. Chem 73: , 21 Strengths/Limitations of 18 O-Labeling No extra steps Strengths: Relative quantification using multiple peptides from same protein Post-translational modification information 18 O labeling kit (Prolytica) Limitations: No reduction in sample complexity Only 4 amu mass increase 18 O exchange with water Quantification error ~2% No good software yet 13

14 itraq Tags (Isobaric Tag for Relative and Absolute Quantitation) Isobaric Tag (Total mass = 145) Four possible tags (8 tags now available) Reporter Balance PRG Reporter Mass Balance Mass Peptide Reactive Group (binds to amines) Ross et al. Mol. Cell. Proteomics 3: , 24 Control Protein Sample itraq Workflow 1 Three Disease Protein Samples Digest Digest Digest Digest Label Peptides with Tag 114 Label Peptides with Tag 115 Label Peptides with Tag 116 Label Peptides with Tag 117 Mix Tag 114, 115, 116, and 117 Labeled Peptides Fractionate Peptide Mixture on SCX Column Analyze SCX Fractions by LC-MS/MS Strong Cation Exchange (SCX) Chromatography Removes labeling reagents and buffers Reduces sample complexity Absorbance (mau) 5 Expanded view How many fractions to collect? Depends on sample complexity speed of mass spectrometer 2 4 Time (min) 6 14

15 LCMS/MS Analysis of SCX Fraction 1 (of 24) Base Peak Chrom. of +TOF MS: Experiment 1, from 5926_VanEykJ_KL_K1.wif min Max cps Intensity, cps Time, min Mass Spectrum of itraq Labeled Peptides Eluting at 4 min +TOF MS: Experiment 1, 4.39 to min... a= e-4, t= Max counts. Intensity, counts m/z, amu Fragmentation Spectrum of 643 Ion +TOF Product ( a= Max counts. 4 Intensity, counts m/z, amu Intensity, counts Expanded Reporter Region Ratios to 114 Should be 2, 5 and 1 +TOF Product ( a= Max counts m/z, amu 15

16 itraq Workflow 2 (preferred) Two controls Two treated samples Digest Digest Digest Digest Label Peptides with Tag 114 Label Peptides with Tag 115 Label Peptides with Tag 116 Label Peptides with Tag 117 Mix Tag 114, 115, 116, and 117 Labeled Peptides Fractionate Peptide Mixture on SCX Column Analyze SCX Fractions by LC-MS/MS Protein: ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR Peptide: VLDSGAPIJ No Change Fragmentation Spectrum Expanded Reporter Region +TOF Product (594.4): Experiment 4, min from 5822_VanEyk_KL_fract... a= e-4, t= e Max. 12. counts. +TOF Product (594.4): Experiment 4, min from 5822_VanEyk_KL_fract... Max. 12. counts. a= e-4, t= e P P M M Intensity, counts Intensity, counts m/z, amu m/z, amu P = Placebo M = Morphine Protein: Cytochrome c oxidase subunit 1 Peptide: VFSWLATLHGGNIJ Up Regulated! Fragmentation Spectrum Expanded Reporter Region +TOF Product (458.5): Experiment 2, min from 5822_VanEyk_KL_fracti... a= e-4, t= e+1 Max. 58. counts. +TOF Product (458.5): Experiment 2, min from 5822_VanEyk_KL_fracti... a= e-4, t= e+1 Max. 89. counts Intensity, counts Intensity, counts P P M M m/z, amu m/z, amu P = Placebo M = Morphine 16

17 ProteinPilot software for identifying and quantifying of proteins based on itraq chemistry Protein Lists Quantification based on multiple ratios of same peptide 17

115 11 15 1 95 9 85 8 75 7 65 6 55 5 45 4 35 3 25 2 15 1 22.13 23.17 259.1 2.11 291.23 459.31 546.36 416.24 588.33 12.6 241.1 317.17 494.76 273.69 517.27 33.15 523.28 745.46 57.32 617.37 114. 115.

18 m/z, amu b m/z, amu View Spectrum Phospholipid Growth Factor (S1P) on Pulmonary Endothelial Permeability S1P Normalized Resistance Resistance = Permeability Lipid Rafts? Proteins involved? Time (min) Guo Y et al (27) Mol Cell Proteomics 6: What is next? Confirmation by an independent technique itraq Results Western blots MRP_Human GDVTAEEAAGASPAK (3+) y 1 y 3 Control S1P A. Anti-MARCKS Sample 1 Sample 2 Control S1P Control S1P Intensity, counts b 1 2+ y 3 y 2 b y y 4 y 6 b b 3 b b 5 4 b b b 2 2+ b 9 y 5 y 7 B. Anti-p-MARCKS C. Anti-MRP D. Anti-Caveolin-1 b b 9 MRP is up-regulated using both methods Guo Y et al (27) Mol Cell Proteomics 6:

New 8-plex itraq Workflow Samples: S1 S2 S3 S4 S5 S6 S7 S8 Digestion: S1 S2 S3 S4 S5 S6 S7 S8 Label Peptides S1 113 S2 114 S3 115 S4 116 S5 117 S6 118 S7 119 S8 121 Mix Labeled Peptides Fractionate

19 New 8-plex itraq Workflow Samples: S1 S2 S3 S4 S5 S6 S7 S8 Digestion: S1 S2 S3 S4 S5 S6 S7 S8 Label Peptides S1 113 S2 114 S3 115 S4 116 S5 117 S6 118 S7 119 S8 121 Mix Labeled Peptides Fractionate Peptide Mixture on SCX Column Analyze SCX Fractions by LC-MS/MS Peptide: ASYLDCIR Ratios:.5 : 1 : 3 : 5 :.5 : 1 : 3 : 5 S1 6 S2 S3 S4 S5 S6 S7 S8 Ref S4 S S7 4 Intensity S S S S S Skip m/z Micronutrient Deficiencies and Health of the Undernourished Child and Maternal Health Problems Nutritional Deficiencies Infant/ Child Infection (diarrhea, ARI) Poor growth Impaired development Childhood Death Chronic disease (?) Disability/premature death (?) Mother Obstetric morbidity Infection/sepsis Anemia Death Photo: K West From Keith West PEM Micronutrient Defic: Vitamin A, zinc, iron, iodine, folate, others Behavioral Cases: Related to breast and complementary feeding, HH diet, low SES, hygiene, poor education 19

681 65 6 55 5 45 4 35 3 25 2 15 1 5 46 44 42 4 38 36 34 32 3 28 26 24 22 2 18 16 14 12 1 8 6 4 2, 2 3 4 5 6 7 8 9 1 11 12 21.17 272.19 175.11 219.19 25.18 288.2 49.71 53.37 467.25 495.81 69.84 262.

20 , Nutrition effects on serum proteins during pregnancy in Nepal women (P. Scholl and K. West, SPH) 6 Women, 1 st / 3 rd Trimester Sample reproducibility (Folate) (Placebo) 12 samples requires two 8-plex itraq experiments. Pool of all samples used as standard in both itraq experiments. Two extra channels to evaluate technical reproducibility. Labeling was completely randomized. itraq Ratios are Reproducible for the Same Sample in Two Different Experiments Relative to a Pooled Standard itraq #2 Ratios B47 y =.981x R 2 =.8611 A1249 y =.8426x R 2 = itraq #1 Ratios Compare Peptide Ratios Across itraq Experiments (Pregnancy zone protein precursor peptide VVSVDENFRPR) Intensity Intensity itraq 1 itraq P P A A m/z m/z 2

21 itraq itraq vs. DIGE DIGE Compares up to 8 samples in one exp. Compares up to 3 samples on one gel Compare multiple experiments by including same standard sample in all experiments Compare multiple experiments by including same standard sample in all experiments Labels N-terminus + primary amines Labels N-terminus + primary amines Complex samples (can fractionate with SCX chromatography after labeling) Complex samples (can fractionate before labeling) Quantify from fragmenting peptides (MS/MS) with protein identification PTM analysis only if detect modified peptide Quantify from intact proteins (Different fluorescence emission) PTM analysis only if it changes the protein s pi or MW Best Approach? There is NO one best approach Gel based techniques - Total Protein (isoforms, PTMs) MS based techniques - Peptides (membrane proteins, large or small proteins) All approaches: Complementary Technically challenging Require fractionation to dig deeper into proteome Quantitative Proteomics Experiments Projects should meet the following requirements: Defined question, hypothesis driven Defined system Independently measurable phenotype Reproducible sample preparation Samples prepared to minimize protein degradation or contamination Buffers must be mass spectrometry or 2D Gel compatible or removed by buffer exchange 21

22 Additional Information How to prepare your samples for DIGE? Decide on what you want to compare (consult bioinformatist). Demonstrate reproducibility of sample preparation by analyzing three separate preparation on an SDS-PAGE gel. Need 15-5 µg proteins at 1-5 ug/ul. No thiols (like DTT, β-mercaptoethanol). No primary amines (including ammonium acetate or AEBSF, but TRIS buffers ok). No salts (<1 mm), HEPES or PPA buffers Detergents:.1% SDS or.5% Triton X-1 ok, but not NP-4. Denaturants: urea and guanidine HCl ok. TCA/acetone precipitation to remove interfering substances and concentrate sample. Immediately resuspend in 2ul of 7M urea, 2M thiourea, 4% CHAPS, 3mM Tris- HCl, ph 8.8. (Urea containing buffers must NEVER be heated above room temperature) How to prepare your samples for itraq? Set up a meeting to discuss your project ( ). Demonstrate reproducibility of sample preparation by analyzing three separate preparation on an SDS-PAGE gel. Need 1-1 µg proteins at 5 ug/ul. No thiols (like DTT, β-mercaptoethanol). No primary amines (including ammonium acetate, TRIS buffers, AEBSF, etc). Detergents:.1% SDS or.5% Triton X-1 ok. Denaturants: 1M urea or 1M guanidine HCl ok. TCA/acetone precipitation to remove interfering substances and concentrate sample. Immediately resuspend in 2ul of.5m TEAB (triethylammonium bicarbonate) 22

Stable Isotope Labeling by Amino Acids in

Strengths/Limitations of SILAC Strengths: No

23 Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) 12 C-Arg 13 C-Arg Mix Cells Isolate proteins and digest with trypsin Peptide ID and quantify by tandem MS Ong et al. J Proteome Res 2: , 23 Quantify by 13 C to 12 C-Arg-labeled peptide ratios Ong et al. J Proteome Res 2: , 23 Strengths/Limitations of SILAC Strengths: No extra steps Relative quantification using multiple peptides from same protein Post-translational modification information Limitations: No reduction in sample complexity Expensive Culture only Cannot use for tissue or isolated proteins Mass increase of up to 9 amu with 13 C and 15 N Arg 23

itraq versus ICAT itraq Compare up to 4 samples Labels amines Protein ID and quantification based on many peptides PTM information Peptide based Quantify from MS/MS Sample complexity not reduced LC

$18 O-Labeling itraq Compares up to 4 samples Labels N-terminus + primary amines 18 O-Labeling Compares 2 samples Labels C-terminus of peptides Complex samples (can fractionate with SCX chromatography$

24 itraq versus ICAT itraq Compare up to 4 samples Labels amines Protein ID and quantification based on many peptides PTM information Peptide based Quantify from MS/MS Sample complexity not reduced LC compatible ICAT Compare up to 2 samples Labels cysteines Protein ID and quantification based on few peptides No PTM information Protein based Quantify from MS Sample complexity reduced Gels and LC compatible itraq vs. 18 O-Labeling itraq Compares up to 4 samples Labels N-terminus + primary amines 18 O-Labeling Compares 2 samples Labels C-terminus of peptides Complex samples (can fractionate with SCX chromatography after labeling) Sample complexity limited (due to 18 O exchange with water over time) Quantify from fragmenting peptides (MS/MS) Adds one step to protein identification Analysis Software available Quantify from intact peptides (MS) No steps added to protein identification No Analysis Software available Absolute Quantification (AQUA) Scheme Select a peptide from the protein. Synthesize of this peptide using stable isotopes (e.g., 13 C, 15 N, etc.) at a single amino acid. Spike protein sample with synthetic peptide. Compare abundance of synthetic peptide with the native peptide. Gerber et al. PNAS 1: , 23 24

In silico Analyses for Selecting Peptides Norovirus Coat Protein

per virus Standard Curve for AQUA Peptides TLPIEVPLEDVR* R* addes 12

coli spiked with VLP and AQUA All Peptides 15 μg E.

25 In silico Analyses for Selecting Peptides Norovirus Coat Protein (VLP) TGGGTGDSFVVAGR* TLPIEVPLEDVR* IMLAGNAF*TAGK Δ = 1 Da 18 copies per virus Standard Curve for AQUA Peptides TLPIEVPLEDVR* R* addes 12 DA IMLAGNAF*TAGK TGGGTGDSFVVAGR* E. coli spiked with VLP and AQUA All Peptides 15 μg E. coli VLP 1 fmol VLPs fmol AQUA peptides AQUA Calculated recovery: 79 ± 14.6 % VLP AQUA 25

number of peptides from protein Compares multiple LCMS/MS experiments Peak Intensity 1-Overlay Base

26 Mass Spectrometry Based Techniques No Labeling Spectral Counting Each sample separate LCMS/MS experiment Each protein in an LCMS/MS experiment, Count number of times a peptide is detected Count number of peptides from protein Compares multiple LCMS/MS experiments Peak Intensity 1-Overlay Base Peak Chromatograms 3-Construct 3D Peak Intensity Map m/z 2-Align Chromatograms Time 4-Annotation of Spots 26

27 Strengths/Limitations of Non-Labeling Methods Strengths: No limit on number of samples No added steps in protein identification Limitations: No limit on number of samples Instrument intensive Reproducibility over many experiments LC system Ionization Detection 27

Quantitative mass spec based proteomics

Quantitative mass spec based proteomics Tuula Nyman Institute of Biotechnology tuula.nyman@helsinki.fi THE PROTEOME The complete protein complement expressed by a genome or by a cell or a tissue type (M.