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Application Note: 30224 Biological Applications of AP MALDI with Thermo Scientific Exactive MS

Kerstin Strupat, Olaf Scheibner, Tabiwang Arrey, Maciej Bromirski, Thermo Fisher Scientific, Bremen, Germany

Overview Key Words The use of an AP MALDI source coupled to the • Exactive Thermo Scientific Exactive enables for a fast and sensitive analysis of: • AP MALDI • A proteolytic digest of a • High Resolution/ • of small Accurate Mass • N- and C-terminal sequences of intact Performance via MALDI In Source Decay • In Source Decay • Straight forward exchange with ion sources such as HESI or APCI on a daily basis • Orbitrap™ Technology Introduction Figure 1: AP MALDI PDF+ coupled on Exactive MS. Atmospheric Pressure Matrix-Assisted Desorption/ This application note focuses on experimental results (AP MALDI) is a similar ion source technique from coupling the AP MALDI PDF+ ion source with the to that of vacuum MALDI, utilizing UV or IR laser for ion Exactive™ mass spectrometer, a high resolution accurate formation. However, with AP MALDI, are created mass (HRAM) mass spectrometer. A brief description of at atmospheric pressure instead of under vacuum. This the AP MALDI PDF+ ion source is also provided. ionization method has been shown to be an even “softer” AP MALDI ions are resolved up to 100,000 (at m/z 200) ionization technique than vacuum MALDI due to fast at a rate of 1 per second with mass accuracy of thermalization/cooling of the ions’ internal at atmo- 2 ppm or better. spheric conditions. This feature is particularly important in the analysis of labile bio-molecules. AP MALDI is often Methods utilized in many different applications including conven- tional analysis of bacteria, lipids, proteomics, small mol- Sample Preparation ecule and but also in recent times in applications Analytes are dissolved in HPLC grade and mixed such as analysis of antioxidants and paint (pigments). with alpha-cyano-4-hydroxy cinnamic (CHCA) or An additional benefit of using an AP source is the 1,5 diamino naphthalene (1,5-DAN) matrix according to easy source interchange without venting the system and published procedures. 0.5 μl of matrix-analyte mixtures consequent long pumping time. AP MALDI allows the are spotted on a stainless steel plate and air dried. MS use of matrices and matrices that are not vacuum and MS/MS are acquired at resolution setting of RP compatible, without inhibiting vacuum conditions of the 100,000 at m/z 200. Plate, , tube lens, skimmer mass spectrometer. , capillary temperature, and the distance “plate – In the herein described geometry, ion source and mass capillary” are varied and optimized for best conditions to analysis are decoupled; i.e. MALDI ion production and liberate ions. Intact proteins are prepared using 1,5-DAN mass analysis in the Orbitrap-based instrumentation is matrix for the detection of sequence specific In Source decoupled. As a consequence, sample morphology – such Decay (ISD) fragment ions with HRAM performance. as thickness of matrix crystals – does neither sacrifice mass resolution nor accurate mass measurement. In the past, the main disadvantage of AP MALDI All experiments were performed on a Thermo Scientific technique compared to the conventional vacuum MALDI Exactive benchtop mass spectrometer powered by Orbi- has been its limited sensitivity. With the introduction of trap™ technology using an AP MALDI PDF+ source. A AP MALDI Pulsed Dynamic Focusing (PDF) by MassTech, Nd:YAG laser beam at 355 nm was coupled into a 400 µm Inc. (Columbia, MD, USA) in 2004, ions are transferred core diameter fiber forming a spot size of 500 x 650 μm2. into the mass spectrometer with high efficiency and at- The mass spectrometer was operated in either negative or tomole quantities of peptides have been reported in the positive ion mode with Orbitrap full scan setting using re- peer-reviewed literature.[1] PDF removes the solving power of 50,000 or 100,000 at m/z 200 (FWHM). that exists between sample plate and the ion inlet, thought to be responsible for the loss of ions during ion transfer to the ion inlet. Results Despite MALDI ion production under atmospheric pres- Figure 2 displays the FTMS full scan information sure, sensitivity of the herein described instrumentation obtained from 1 fmol deposits of Angiotensin II on plate. can nicely compete with previously published, non AP Each spectrum results from single FTMS full scan MS. MALDI work. MH+ ion of Angiotensin is measured with accurate mass; signal-to-noise ratios of single FTMS scans are reported to be well above 50/1.

Angiotensin II amino acid sequence: DRVYIHPF FTMS + p NSI Full ms [500.00-4000.00] sum formula: C50H72N13O12 1046.54089 1046.54114 Monoisot. Mass MH+: 1046.541791 R=50100 R=50100 Angio_1fmol_steel_001 100 ZOOM ZOOM MH+, -0.6 ppm 80 MH+, -0.9 ppm > x50 60 1046.54089

1047.54443 40 1048.54700 Relative Abundance 20 1030 1040 1050 1060 1070 1045 1050 1055

0 500 1000 1500 2000 2500 3000 3500 4000 500 1000 1500 2000 2500 3000 3500 4000 m/z m/z Figure 2: Two examples of an FTMS full scan acquired form a 1 femtomol deposit of Angiotensin II on plate, two different individual sample preparations. CHCA matrix. Single FTMS full scan, m/z 500 - 4000. S/N ratio > 50 / 1 in single scans can be obtained. Sample is not depleted, some hundreds of scans can be done from such 1 femtomole deposits.

A 10 fmol proteolytic digest of Human Serum Albu- The zoomed spectrum in Figure 3 shows the assigned min was deposited with CHCA matrix. A single FTMS full peptide with the sequence VFDEFKPLVEEPQNLIK scan onto such a sample is shown in Figure 3. Peak lists of measured with 33,000 resolution (at m/z 2,045). Isotope monoisotopic masses of proteolytic fragments are submit- pattern of this peptide agrees nicely with its theoretical ted to Mascot for protein ID in a Peptide Mass Fingerprint distribution. (PMF) approach.

FTMS + p NSI Full ms [200.00-4000.00] VFDEFKPLVEEPQNLIK Monoisot. Mass +MH+: 2045.095369 100 1639.93775 ZOOM 1911.91490 80 2046.09730 2045.09473 MH+,-0.3 ppm 2047.10035 60 2046.09730 2048.10243 1467.84458 1700.76052 40 2044 2046 2048 MH+,+1.0 ppm

Relative Abundance 960.56347 20 1294.63298 2108.01563 2492.26953 1226.60717 2262.00666 2554.18835 2929.32791 0 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 3000 m/z

Figure 3: FTMS full scan of a 10 fmol proteolytic digest of Human Serum Albumin. Data displayed derives from a single scan (1 second). Mass accuracy is < 1 ppm (internal calibration). Using 1.5-diamino naphthalene­ (1,5-DAN) as matrix, This is exemplified by Lysozyme in Figure 6. Frag- sequence-specific fragments such as b-, c-, y- and z-type ment ions are detected without any precursor selection or ions can be generated simultaneously from intact proteins; induced dissociation; fragment ions observed are intrinsi- fragments derive from N- and C-terminal ends of the cally created upon the MALDI process with this particular protein. matrix. For further reading see Reference [3].

(A) C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26

K V F G R C E L A A A M K R H G L D N Y R G Y S L G N W V C A A K F E S N F N T Q A T N R N T D G S T D Y G I L Q I N S R W W C N D G R T P G S R N L C N I P C S A L L S S D I T A S V N C A K K I V S D G N G N A W V A W R N R C K G T D V Q A W I R G C R L

Z14 Z13 Z11 Z10 Z9 Z7

c ZOOM c17 ZOOM ZOOM 10 c12 c13 0.51 ppm 1092.59826 0.28 ppm 100 0.38 ppm 1887.03754 1294.67550 1422.77028 c9 0.12 ppm 2174.46438 c 1021.56103 11 c 0.12 ppm 18 2001.06036 c 75 1163.63567 19 c20 c6 1.18 ppm c14 0.08 ppm c8 c c 0.65 ppm 15 2279.17023 22 c26 708.40039 950.52368 0.13 ppm 1.17 ppm y10 1578.87091 2.87 ppm b18 c7 1201.66711 z 1715.93062 c 2492.29259 c23 50 11 w 16 1984.03235 2912.48802 z9 15 0.811 ppm 1.68 ppm z8 0.81 ppm 1772.95088 2655.35437 1656.86252 c z z 2434.26696 24 10 12 z14 b17 z7 1597.56981 1869.00698 25 888.48776 z13

0 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 2200 2400 2600 2800 3000 3200 m/z m/z m/z

(B) FTMS + p NSI Full ms [650.00-4000.00]

1887.04578 100

1092.60303 1294.68115 2002.07263

1578.87781 1021.56549 2174.47388 50 708.40039 2279.18018 Relative Abundance 2492.30347 2912.50073 2655.36597 3048.52515

0 1000 1500 2000 2500 3000 m/z

Figure 6: (A) amino acid sequence of Lysozyme and the alocated fragment ions. (B) FTMS full scan, intact Lysozyme analyzed with 1,5-DAN matrix. In Source Decay creates sequence specific N- and C-terminal fragment ions of proteins deposited as intact entities. Insets - displayed in red m/z( 700 - m/z 1500), blue (m/z 1500 - m/z 2100) and green (m/z 2100 - m/z 3200) colored spectra - provide further insight into sequence specific fragment ions observed. Refer to the bottom spectrum to see the entire FTMS full scan information. It is an average of 30 single FTMS full scan spectra. c ZOOM c17 ZOOM ZOOM 10 c12 c13 0.51 ppm 1092.59826 0.28 ppm 100 0.38 ppm 1887.03754 1294.67550 1422.77028 c9 0.12 ppm 2174.46438 c 1021.56103 11 c 0.12 ppm 18 2001.06036 c 75 1163.63567 19 c20 c6 1.18 ppm c14 0.08 ppm c8 c c 0.65 ppm 15 2279.17023 22 c26 708.40039 950.52368 0.13 ppm 1.17 ppm y10 1578.87091 2.87 ppm b18 c7 1201.66711 z 1715.93062 c 2492.29259 c23 50 11 w 16 1984.03235 2912.48802 z9 15 0.811 ppm 1.68 ppm z8 0.81 ppm 1772.95088 2655.35437 1656.86252 c z z 2434.26696 24 10 12 z14 b17 z7 1597.56981 1869.00698 25 888.48776 z13

0 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 2200 2400 2600 2800 3000 3200 m/z m/z m/z

Conclusions References

AP MALDI combined with the HRAM performance of the 1 Trimpin et al.; Anal Chem. (2010) 82 4998, (e.g.), and other papers by Exactive MS enables: Trimpin et al. on “Laserspray Ionization” 2 • The analysis of small molecules at low ng concentrations Strupat et al.; J. Am. Soc. Mass Spectrom. (2009) 20 1451 3 without sacrificing the baseline or a loss of accurate mass. Thermo Scientific Application Note: 30218 • Identification of peptides from proteolytic digests of proteins at low concentrations upon a PMF approach + using accurate MmonoisotopicH masses. • The analysis of N- and C-terminal sequences of proteins – deposited as intact species – upon MALDI In Source De- cay specifically enabled using 1,5-DAN matrix. Sequence specific fragment ions can be assigned unambiguously. • Further benefit of an AP MALDI ion source is the straight- forward exchange with ion sources such as H-ESI, APCI, APPI, DART and other ionization techniques. • Ease of use and no down time due to source exchange. waspresentonthesampleplate. Figure 4:InsetintoanFTMSfullscan( displayed inthefigure. mass resolutionandaccuracyforeachcompoundare Buspirone andLoperamideinCHCAmatrix.Achieved MALDI matrix.Figure4displaysamixtureofAtropine, can beanalyzedatlowconcentrationandinpresenceofa Exactive massspectrometer,amixtureofsmallmolecules the ionsource allowssourceconnection toThermo Scientificiontrap and Orbitrapbasedinstrumentations. Figure 5:APMALDI

Relative Abundance 100 50 Due tothesensitivityandhighresolutionof 0 C 290.17536 0.99 ppm R=90961 Atropine 17 FTMS +pNSIFullms[125.00-1000.00] H 23 NO 3 300 PDF + ionsource,source opened toseetheMALDIsampleplate positioned onanxystagelocatedthe righthandside.Leftsideof 320 m/z 125– 340 m/z 1000)ofthreesmallmolecules,Atropine,BuspironeandLoperamide;CHCAmatrix.Atotal1ngeach 360 379.09297 CHCAdimer

R=82080 380 C 386.25542 Buspirone R=82381 26 H m/z 31 N 0.95 ppm 5 the Buspironepeak. suppress oraffecttheaccuracyofmassdetermination matrix signal(CHCAdimerat O 2 Note that,eventhoughthereisaprominentCHCA 400 420 440 m/z 379.09297), itdoesnot 460 C Loperamide 29 477.23107 R=73727 1.55ppm H 33 Cl 480 1 N 2 O 2 Laboratory Backed by Worldwide Service and Support In addition to these offi ces, Thermo Fisher Scientifi c maintains Tap our expertise throughout the life of your instrument. Thermo Scientific Services a network of represen- extends its support throughout our worldwide network of highly trained and certified tative organizations throughout the world. engineers who are experts in laboratory technologies and applications. Put our team of experts to work for you in a range of disciplines – from system installation, training and technical support, to complete asset management and regulatory compliance consulting. Improve your productivity and lower the cost of instrument ownership

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