Mass Spectrometry Service Guide

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1 Mass Spectrometry Service Guide Plan, location and Web site Samples verview / Submission MS Instruments Data analysis Fees for 2013 Take Home Messages SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

2 MS service: room 1520 Samples IN: submit Samples UT: results pumps IR Sample prep (hood) ESI IT MS GC IE MS FFICE LC ESI QTF MS LC ESI MS MALDI TF MS Sample prep SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

3 MS service: FT MS RM 1110 LSMB UPLC LTQ FT rbitrap MS Wet lab 11 T LTQ FT ICR MS ffices SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

4 Visit our web site FFICE SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

5 Samples verview (SSMI) Wide variety of components.. rganic molecules Peptides / proteins rganometallic compounds Polymers DNA Sugars, lipids,. in a wide variety of matrices Biological fluids (plasma ) Solid extracts and particules ils, and for different Users Academics (EPFL, UNIL, CHUV, CMU, IPS ) Industry SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

6 What are Your Needs? Presence of the expected compound Sample purity Accurate mass measurments Structure determination/confirmation (peptide sequencing ) Fractionation prior to MS detection (LC or GC MS) Quantification SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

7 Downloaded from the web sites: slave.epfl.ch/ Fill it properly, especially : Molecular formula Submit a sample Solubility Amount/concentration Impurities (salts), DMS, SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

8 Submit a sample Fill the goal of analysis: it'sisveryimportant, we cannot guess for each sample submitted! We'll choose the type of instrument and analyzer depending on this goal: Absence / presence of the expected compound: low resolution mass analyzers (Q and IT) Purity control: low resolution mass analyzers (Q and IT) coupled or not to LC or GC separation Accurate masse analyses: High resolution analyzers (TF, rbitrap, ICR) Structure (MS/MS): High resolution analyzers equiped with CID/HCD cells (Q TF, triple quadrupole, LTQ FT MS) and other fragmentation techniques SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

9 HPLC-Q-MS (ESI/APCI) MS platform of ISIC ESI-IT-MS MALDI-TF-MS GC-QqQ-MS (EI/CI) UPLC-ESI-QqTF-MS low res pen-access high res SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

10 MS platform of ISIC: High resolution FT MS LTQ-FT-rbitrap-MS coupled to a nanouplc system 11 T LTQ-FT-ICR-MS NEW SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

11 LCQFleet (Thermo) low res Presence/absence of the expected compound Structural analysis by tandem MS (CID) Mass range m/z 100 to 4000 open access Standard ESI + / Almost 10'000 injections in 2012! Low resolution and mass accuracy due to the mass analyzer (ion trap) ESI MS/MS (CID) for structural analysis SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

12 LCQFleet (Thermo) His Lifetime depends on you! Sample concentration should be in the μmrange (<0.1 mg/ml) Any new user should have a training provided by us Centrifuge your sample before injection No solvents such as acetone, ether, DMS and chloroform (or should be diluted in MeH) In the "Client" column of the sample list, put your 6 letters code of the magasin (scan the card) Left vials in the autosampler are kept 24h here, then thrown away Fill the notebook Please report us any problem (contamination, ). Don t leave the instrument dirty and problems for the next users! The instrument will be temporarily halted every Friday afternoon for maintenance and cleaning SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

13 LC ESI/APCI MS Waters Autopurification system low res. HPLC fractionation with ESI/APCI Q MS and UV PDA detector Presence / absence of the mass Purity control Sample fractionation (RP-HPLC: C18, C8, C4) Sample collection based on MS and UV Autosampler for automatic injection and fraction collection From analytical (<1 mg) to preparative (10 mg) scale RP HPLC Multi ionization mode: ES+, ES, APCI+, APCI open access Fraction collection based on target masses SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

14 GC EI/CI MS Gas chromatography Varian 1200L GC MS triple quadrupole low res Analysis of volatile/semi-volatile compounds Presence / absence of the mass Quantification and Structure Two ionization process: EI: causes fragmentation, EI spectra can be searched in databases M + e M e CI: causes less fragmentation, positive and negative modes. Reagent gas is ammonia NH3 + e NH e NH4 + + M NH3 + [M+H] + NH4 + + M [M+NH4] + Proton transfer from the ammonium ion protonated species Formation of ammonium ion adducts Direct Introduction or Gas Chromatography Mass range: 2 to 1500 m/z MS/MS (product ion spectrum, precursor ion spectrum, MRM ) SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

15 Axima CFR Plus Many applications: peptides, proteins, nucleotides, polymers, lipids, sugars, organometallics, organic compounds LDI / MALDI TF MS high res Presence / absence of the mass Purity control Mass accuracy ~ ppm Soft ionisation for intact bio molecules Broad mass range of analytes ( 100 to 100 kda) Highly sensitive technique ( 0.1 pmole on target for peptides) Matrices: many different matrices in open access (CHCA, DHB, DIT, THAP, NA, TCAP, PA..) depending on the application LDI (no matrix) for compounds absorbing the laser energy (337 nm) Resolution (reflectron TF analyser) Mass accuracy ppm open access SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

16 LDI / MALDI TF MS high res Sample preparation: many methods depending on the type of sample. Ask us 10 targets are available for the service. Please clean your plate when its full and bring it back to the lab for other users Complex mixture is K; salts can be removed by on target washing techniques and Zip Tips ther types of plates are available for testing: Anchorships, μfocus (x10 30 gain in sensitivity (peptides) and NALDI plates. Ask us for testing Laser and linear detector replaced in 2012 Any new user should have a training provided by us SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

17 ESI QTF MS QTF Ultima (Waters) Presence / absence of the mass, purity control, accurate mass analysis, and structure (MS/MS, CID) high res Wide mass range of analytes ( 100 to 100 kda) Standard and nanospray sources, ES+ / ES Resolution 8000 Mass accuracy < 5 ppm (Lock mass) ESI MS/MS for structural analysis Interfaced with a nano UPLC (Nanoacquity, Waters) Trapping columns: to desalt and concentrate samples Capillary RP UPLC columns ( μm I.D.) run at flow rates μl/min high pressure = high LC peak separation + high sensitivity in MS Low amount of sample (<1 pmole) SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

18 LTQ rbitrap FT MS Ultra high res High resolution (100 k) and mass accuracy (1 2 ppm) LTQ-FT-rbitrap-MS coupled to a nanouplc system Chip based ESI infusion (Triversa Nanomate ) Tandem mass spectrometry: CID, HCD and ETD fragmentation MassFrontier for MS/MS data interpretation Proteome Deconvolution, Proteome Discover and ProSight for proteomics applications For increased throughput of AM analyses For Users projects such as proteomics/peptidomics come to discuss your specific needs SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

19 LTQ FT ICR MS Ultra high res High resolution (>100 k) and mass accuracy (1 2 ppm) 11 T LTQ-FT-ICR-MS Accurate mass analyses using chip based ESI infusion Mainly used with APPI ionization for service samples that cannot be ionized by ESI, EI/CI or MALDI Structure information: MS/MS fragmentation by CID, ECD or IRMPD) SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

20 Fill the type of analysis/ionization Submit a sample ESI: more than 80% of compounds are ionized by ESI APPI/APCI: mostly for non polar compounds MALDI / LDI: macromolecules (proteins, peptides, DNA ), polymers, organometallics, small organic compounds, EI/CI: mostly for small and volatile organic compounds If you don't know, we'll choose for you.. SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

21 Ionization techniques Ionization charges molecules so that they can be measured in the mass spectrometer Electrospray (ESI): formation of charged liquid droplets from which ions are desolvated or desorbed MALDI: impact of high energy photons emitted by a laser on a sample embedded in a solid matrix EI: impact of electrons on a sample introduced in the gas phase SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

22 Ionization techniques Atmospheric Pressure Photo Ionization (APPI) NEW The analyte (M) is ionized by high energy photons from the Kr lamp causing direct or indirect (dopant D such as toluene) photoionization M+hν M +. + e if the ionization energy of M is < Kr lamp photon energy D+hν D +. + e Proton transfer from dopant or solvent Electron transfer D +. + M M +. + D Works for positive and negative ionization Low resolution (Linear Ion Trap) and High resolution (ICR) MS data D +. + M [M+H] + + D Ionization potential (IP) Krypton lamp: ev Toluene 8.82 ev Acetone 9.70 ev Acetonitrile ev Photons from the Kr lamp can only photoionize compounds of lower IP (common solvents are not ionized by APPI) SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

23 Ionization techniques: APPI P B B P B P P B C 6 H 13 Non polar compounds C 6 H 13 C 12 H 25 C 12 H 25 Polycyclic aromatics, fullerenes C 6 H 13 N N N Zn N N C 12 H 25 C 12 H 25 C 6 H 13 C 3 H 7 C 3 H 7 rganometallics Lipids Polymers, polyprenols, 12 SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

24 Submit a sample: sample preparation Sample preparation is crucial, especially for purity controls Lyophilized samples if possible If your samples are in solution: Use LC MS grade solvents Use glass vials ; no Plastic tubes with MeH and THF No DMS ; no acid for GC MS The quality of the MS analysis depends also on the way you fill the form!!! SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

25 Data Analysis: AM on the ESI TF MS Accurate mass analysis using the LockSpray interface Isotope modelling: calculated with 4 decimals (Chemdraw takes 5) Here the mass accuracy is 1.5 ppm Lock mass m/z the lock mass chosen is generally the closest signal from the analyte SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

26 Data analysis: Elemental composition ESI-TF-MS Analysis / AE (0.044) Is (1.00,1.00) C14H19N QTF 1: TF MS ES+ 8.43e12 % Isotope modelling AE 66 (1.621) AM (Cen,4, 80.00, Ar,9000.0,196.96,0.70,LS 5); Sb (1,20.00 ); Cm (66:70) : TF MS ES+ 8.42e3 % m/z SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

27 Database search (NIST11+MassFinder) Databases NIST11 and Massfinder NIST 11: > EI mass spectra Free databases: Human metabolome database: Chemspider: Fatty acids derivatives: Massbank: Metlin: SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

28 Data Analysis: AM on FT MS Full scan MS FeCl-PYR1_FT100k_30scan #1 RT: AV: 1 NL: 1.63E6 T: FTMS + p APCI corona pi Full ms [ ] R=49801 z= Relative Abundance R= z=? R= R= R=53704 R=76504 R=71004 R=65404 R=53604 R=47604 z=? z=? z=? z=? z=? z=? z=? z=? m/z Relative Abundance R=65904 z=? R=53004 z=? R=48904 z= R=50004 z= R=49801 z= R=47609 z=? R=50100 z= R=48244 z=? R=49304 z= R=47804 z= R=61004 z=1 NL: 1.63E6 FeCl- PYR1_FT100k_30scan#1 RT: AV: 1 T: FTMS + p APCI corona pi Full ms [ ] Isotopic modelling NL: 8.81E3 C 65 H 110 B 2 FeIN 7 6: C 65 H 110 B 2 Fe 1 I 1 N 7 6 p (gss, s /p:40) Chrg 1 R: R=49956 z=? R=48663 z=? R=48828 z=? R=48255 z=? R=48019 z=? R=47341 z=? m/z Elemental composition report SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

29 Data Analysis: use Chemcalc! SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

30 In depth data ANALYSIS MS/MS data interpretation using Mass Fragment (Waters) Mass Frontier (Thermo) Protein/peptide identification from biological matrix Proteome Global Server PLGS (Waters) Proteome Discover and ProSight (Thermo) Quantification MS data review (GC MS, Varian) QuanLynx (Waters) SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

31 MS Training & Learning Training courses on open access instruments for new Users LCQFleet (ESI MS), Axima CFR (MALDI MS) and ZQ4000 (LC MS) Doctoral school "Current topics in mass spectrometry" given by Pr. Yury Tsybin Books In French: Spectrométrie de masse, 3 e edition, par Edmond de Hoffmann et Vincent Stroobant In English: Mass spectrometry: principles and applications, 3rd edition, by Edmond de Hoffmann and Vincent Stroobant SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

32 Fees for 2013 MS has a cost. Prices are available on our web site pdf Type of MS analyses Details Academic EPFL Academic non EPFL Commercial Low resolution ESI IT/Q MS High resolution ESI QTF MS Ultra High resolution FT MS MALDI TF MS EI CI QQQ MS PEN ACCESS instruments Sample preparation Training on open access instruments (1 to 2 hours) Data Analysis ESI MS (off line) LC ESI MS (analytical scale)* LC ESI MS (preparative scale) 200 inquire inquire ESI QTF MS (infusion) ESI QTF MS (infusion, acc. mass analysis (< 5 ppm)) ESI QTF MS/MS (infusion, CID) nano ESI QTF MS and MS/MS (infusion) nano UPLC ESI QTF MS* nano UPLC ESI QTF MS/MS* inquire ESI LTQ rbitrap FT MS (Triversa infusion, res. 100'000) ESI LTQ rbitrap FT MS/MS (Triversa, res. 100'000, CID/HCD) ESI LTQ rbitrap FT MS/MS (Triversa, res. 100'000, ETD) nanolc ESI LTQ rbitrap MS/MS (Nanospray Flex Ion source, CID / HCD) inquire nanolc ESI LTQ rbitrap MS/MS (Nanospray Flex Ion source, ETD) inquire ESI LTQ ICR FT MS (Triversa infusion, res. 100'000) APPI LTQ ICR FT MS and MS/MS (CID/IRMPD) Standard direct analysis ** Protein identification (PMF) inquire inquire inquire CI MS (Direct Insertion Probe) GC EI/CI MS* ESI IT MS (LCQ Fleet, per sample) MALDI TF MS (per 30 min period) 60 LC ESI MS (Autoprep) (per sample, analytical scale) 80 NT AVAILABLE LC ESI MS (Autoprep) (per sample, preparative scale) 160 Sample desalting by SPE (Zip Tip, Sep pak,...) 20 inquire inquire Ultrafiltration 30 inquire inquire Protein red&alk + enzymatic (trypsin) digestion 80 inquire inquire MALDI TF MS 200 ESI IT MS 100 NT AVAILABLE Data analysis*** Advanced DA (Use of specific softs and tools) inquire inquire inquire SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

33 Take home message Please come to discuss with us for any question, request or any specific needs for your projects Everybody can make errors and cross contamination is always a risk. Please give us direct feed backs about the analysis especially if you have any kind of problem The service is opened from 8:00 am to 5:30 pm. pen access instruments available from 8:30 to 5:00 pm. Laure is at 90% (off Wednesday pm) and Daniel is at 50% (here mostly on Tuesday and Wednesday). We do our best: please come with the smile! SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

34 Samples verview of the service Total number including open access verall increase SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

35 Francisco Laure Daniel Yury's group SERVICE DE SPECTRMETRIE DE MASSE DE L'ISIC (SSMI) Pr. Yury. Tsybin Dr. Laure Menin Francisco Sepulveda Daniel Baumann

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