Bruker Daltonics. Introduction

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1 Bruker Daltonics Application ote # M-96 alling - and -terminal Protein Sequences with High onfidence and Speed: MALDI-DS applied to the ABRF-SRG 2009 Research Study his study describes the analysis of the 2 samples provided by ABRF-SRG 2009 using op-down Sequencing on a MALDI-OF/OF [1]. We report the use of MALDI-op- Down Sequencing (MALDI-DS) with an ultraflex III to sequence the 2 protein samples that were provided by SRG. It turned out that MALDI-DS on the ultraflex was the most frequently applied top-down sequencing method. It provided reliable -terminal and -terminal protein sequences for both samples of the study. Introduction dman sequencing has been indispensable for -terminal protein sequencing in a number of applications for decades..g., confirmation of -termini of recombinant proteins, domain mapping, monitoring of proteolytic in vivo and in vitro processing, protein structure validation of therapeutic proteins with 100 % sequence coverage and the identification or de novo sequencing of proteins from organisms with unsequenced genomes. As some of these problems are solved today rather by DA sequencing and by more and more advanced MS methods, throughout the past few years dman sequencers have been gradually phased out of operation. he removal of dman sequencing from the market was accelerated recently, when the last manufacturer selling to the US market discontinued its dman sequencers in summer his caused the dman Sequencing Research Group of the ABRF to seek alternative technologies for protein sequencing [2]. MS approaches based on proteolytic digests (Bottom-Up approach) have never been shown to provide simple, quick and reliable answers for recombinant protein analysis work and applications such as domain mapping. Direct erminal Sequence Readouts For a number of years op-down sequencing was used as a novel approach to derive protein sequence information by MS/MS techniques directly in mass spectrometers without initial protein digestion [3, 4]. All of the currently employed MS techniques SI-D, SI-D/PR and MALDI-ISD [1] share an electron/radical transfer induced fragmentation step that takes place on a sub-nsec time scale MALDI-ISD occurs right in the ion source during the MALDI process (Fig. 1). his does not permit the dissipation of excitation energy along the peptide backbone, which is typical for the classical ID processes utilized in peptide MS/MS analyses. Rather, the fragmentation occurs right at the site of radical/electron transfer. herefore, MALDI- ISD spectra typically provide equi-intense sequence ladders of ions, particularly of c-ions [5] that permit the straight readout of near -terminal sequence information.

2 he ultraflex and the MALDI-DS related fragmentation methods Sample arget ID Precursor Ion Selector (PIS) LID Source 2 (LIF) ISD ollision ell Ion Source Fig. 1: he ISD fragmentation occurs in the ion source of the ultraflex (the laser beam pointing to it). Subsequent ³-sequencing analysis permits the extension of internal sequence calls towards the termini. It implies selection of -terminal c- or -terminal y-ions as precursor ions in the PIS and their laser induced decomposition (LID) MS/MS analysis by the OF/OF. LID is a slow process that takes place in the field-free region between ion source and LIF cell. MALDI-ISD spectra typically contain -terminal a- and c-, -terminal y- and [z+2]-ions that allow the direct sequence determination of proteins from both termini (Fig. 2). As the available mass range to read out sequence tags is typically around 1-8 kda of single charged fragments, the terminal sequences 1 to ~10 are not directly observed in reisd spectra (Fig. 3). his information, however, can be retrieved by additional ³-Sequencing, in which ISDfragment ions that always include either the - or the -terminus, are selected in the precursor ion selector (Fig. 1) and are further fragmented by metastable laser induced decomposition (LID) prior to the 2nd ion source. MALDI-DS was applied to the research study 2009 for which the ABRF-SRG (dman Sequencing Research Group of the Association of Biomolecular Research Facilities) provided 2 samples and expected -terminal sequence assignments from both proteins. xperimental Samples (50 pmol) were prepared using the sdhb matrix (#209813, Bruker) and analyzed on a MALDI-OF/OF (ultraflex III, Bruker) by in-source decay (ISD) essentially as previously described [5, 6]. Instrument settings were essentially as described in the Bioools op-down Sequencing utorial that is accessible through Help in the software. In short, the Flexontrol 3.0 method proteomics_hpc.par for peptide analysis in reflector mode was chosen and modified for ISD analysis by increasing mass range to Da and detection gain to at least 30x. Additionally, low mass deflection was set to 900 Da and laser power was increased to 10% above threshold. Several hundreds to thousands of shots were accumulated and processed as described above. xternal calibration was performed using ISD c-fragment ions of intact BSA. Reflector mode ISD spectra (reisd) which were peak picked in FlexAnalysis 3.0, submitted to Bioools 3.2 (both from Bruker) and directly analyzed by database searching using a Mascot 2.2 (Matrix Science, UK) in-house server. A new instrument type MALDI-ISD was created on Mascot Server with the following specification: 1+ ions only, a, c, z+2 and y-ions, as this reflects the typical ion types in ISD spectra that we used for MALDI-DS (Fig. 4). All protein sequencing work that was required in this study was performed through straight MS/MS ion searches, where arbitrary strong ISD fragment ions were specified as virtual parent ions in the Mascot search dialog. Search parameters are shown in Fig. 4. In general, SwissProt was used for Mascot searches. Only the -terminus of sample 1 was identified by searching the BI database as it also contains recombinant protein constructs. Interactive or automatic de novo sequencing was added to the simple standard procedure only when analyzing the fusion site; here the missing sequence between the -term His 6 -tag and ADH_1 was annotated manually using the Annotation feature in FlexAnalysis 3.0. c-ions have a structure that is identical to -terminally amidated peptides. herefore, in all Mascot searches that involve c-ions either as virtual precursors or after selecting a c-ion for ³-Sequencing, this nature was considered in the search dialog as Amidated (-term) (Fig. 4).

3 MALDI-DS spectra are acquired in seconds R M S Q U R M M R M R M R R M R M R M R M S Q U M R Fig. 2: Principle of MALDI-DS: ISD appears to occur through hydrogen radical transfer mediated events at the site of reaction (indicated by the laser). On the sub nsec timescale no energy relocation occurs to labile bonds. herefore, ISD ion formation does not vary much based on the protein sequence, which is well suited to protein sequencing. Intense c-ions directly access -terminal sequencing (here, ISD fragmentation after provides a c-ion containing ) and y-ions permit -terminal protein sequencing A H SAM IM. Reading terminal sequences with ISD and 3 -Sequencing Protein Sequence ISD fragmentation 1-8 kda 1 8 kda y-ions 8 1 kda 3 -Sequencing (LID/ID) -terminal peptides -terminal peptides Fig. 3: echniques applied in MALDI-DS studies: ypical ISD fragment ions are near terminal as they are observed in the 1-8 kda range. herefore, readout starts around residue 10 from either terminus. ³-Sequencing : o extend a sequence tag towards the terminus, c- or y-ions are selected for downstream MS/ MS analysis by LID or ID in the PIS (Fig. 1). ISD basically produces erminal peptides that are then further sequenced in the OF/OF part of the instrument (³).

4 Results Our results on the ultraflex [7] were tabulated in the official SRG documentation [8, 9] as SRG-002 (ab 1). Both samples (~ 40 kda) provided sequence calls from the -terminus and the -terminus from the same dataset permitting their identification as ADH1_YAS and G3P_RABI. All samples were prepared with the 3 matrices sdhb, SA and DA as each provides certain advantages in the analysis process (ab. 2). In terms of call length, however, sdhb turned out to be the best suited matrix and was used throughout this study. For beginners in the MALDI-DS field, 1,5-diaminonaphthalene is a very good starting point providing a robust MALDI-DS sample preparation platform (A ; Acros Organics, Geel, Belgium) [6]. Sample 1 A database search using the MALDI-DS spectrum and selecting m/z 5383 as virtual parent ion amongst others provided for straight ID of ADH1_YAS. Import of the sequence into Bioools however only provided for a matching -terminus (Fig. 5a). Subsequent elucidation of the -terminus required an BI search with an intense c-ion at lower molecular weight revealing the fusion protein nature of the protein in Sample 1. he match identified an IPG inducible -terminal His 6 -tag ß-Gal expression vector with a perfectly matching sequence tag (c 8 -c 30, Fig. 5b). Selection of ISD fragment c 12 permitted the acquisition of a ³-Sequencing spectrum and extending the sequence call toward the -terminus with a 2 /b 2 as closest spectral assignment to the -terminus (Fig. 6a). Software assisted de novo sequencing eventually closed the gap c 30 -c 34 (DPL) between the vector sequence and the -terminus of the cloned ADH yielding ~70 sequence calls from - and -termini (Figs. 6b, 8a). Sample 2 Selection of m/z 6086 as virtual precursor permitted the direct identification of G3P and import of the desmet sequence into Bioools provided an instant match of -term 73 and -term 47 residues (Fig. 7). ³-Sequences also called the -terminus (data not shown). A putative sequence database error A286D was detected in the assigned spectrum. he search for it was triggered by the rabbit sequence being uniquely distinguished from many other mammal sequences at that position (Fig. 8b). he official SRG study result poster [8] was compiled into ab. 1. ven more participants in the study (excluding the letter coded organizers: A, B,..) used a op-down strategy rather than dman sequencing, 13 of whom used a Bruker MALDI instrument! he average read length with MALDI- DS was higher than dman sequencing, plus significant -terminal sequence calls were provided by most MALDI- DS participants. Almost all participants utilizing MALDI- DS identified both protein sequences, while the ADH1 fusion protein was not reported by any participant using MALDI-DS analysis by Mascot library searching Fig. 4: ypical Mascot MS/MS ions search conditions as specified in the Bioools 3.2 search dialog: no enzymes, variable modifications Amidated (-term) provides for y- or c-ion nature of the selected ISD-fragment as virtual parent ion. he MALDI-ISD instrument definition in Mascot Server 2.2 is shown on the right.

5 Zur Anzeige wird der Quickime Dekompressor Zur Anzeige wird der Quickime Dekompressor benötigt. benötigt. dman sequencing. Most striking (and as to be expected) the Bottom-Up approaches were quite unreliable in providing terminal sequences [8,9] but typically provided correct protein identifications. In contrast to dman sequencing, MALDI-DS does not provide safe assignments of the isobaric Leu vs. Ile (L/I) and of the near isobaric Lys vs. Gln (K/Q) these assignments were inferred by matching to the sequences in the databases. his is typically not critical for protein Q work but may become an issue in organisms with unsequenced genomes. However, search engines such as MS-BLAS (MBL, Harvard) permit homology searching leaving the K/Q and L/I ambiguities open. In addition, c-ions are formed by cleavage of the bond -terminal to the peptide amide bond. -terminally to proline, the formation of c-ions would require a cross-ring cleavage of proline. As this does not happen, XP tags need to be resolved at every occurrence of P. As prolines are a major cause of sequence readout termination, XP diaminoacid sequences are routinely checked by the software to fill gaps in the sequence. his provides specific and reliable results if reisd sequential mass errors are < 5 ppm. In the SRG study such ambiguities were not counted as correct calls rather as inferred calls, which provided lower correct call numbers in the official poster [8] compared to our assignments [7]. Important for successful MALDI-DS is the availability of a single pure protein in ~10 pmol quantities. In the case of heterogeneous protein mixtures such as when analyzing ragged ends, a prior protein chromatographic step is required and has been successfully applied to the analysis of -terminal heterogeneity in the ABRF-PRG 2008 study as described in the Bruker Application ote M-90 [10]. Sample 1: matching the termini to a His-tag vector and ADH1-YAS m/z Fig. 5a: MALDI-DS Spectrum of Sample 1 in sdhb; MS/MS search with y 48 (m/z 5383) identifies -terminus of ADH1_YAS. Fig. 5b: MS/MS search using c 30 matches -terminus of Sample 1 to His-tagged IPG inducible expression vector

6 onclusion op-down protein sequencing on a MALDI-OF/OF instrument applied to the ABRF-SRG 2009 research study proved its utility for the -terminal and -terminal identification and characterization of proteins [7]. It matches dman sequencing capabilities and even adds significant analytical benefits: -term and -term calls were in the range up to 70 residues from either terminus! MALDI-DS works as well for -term modified proteins [5] A single MALDI-DS spectrum provided for the reported sequence calls Analysis time for protein Q (reference sequence available): few minutes ime for study samples: 0.5 working days hemical costs < 1 $ per sample (ml of matrix solution, solvents) ³-Sequencing allows validation of termini in case of unexpected terminal modifications Standard MS/MS searches were used for most of the study, just as typical proteomics approaches to protein identification In this study, MALDI-DS clearly demonstrated its capacities and certainly will become the ext Generation Protein Sequencing method due to performance, speed, reliability and costs. Fulls terminal characterization of Sample 1 ADH1_yeast Fig. 6a: xtending the sequence call to the -terminus: ³-Sequencing spectrum of c 12 (m/z ) confirms the Histag structure; b 2 is in accordance with -terminal sequence GG extending the near--terminal sequence tag towards the -terminus. Abs. Int. * 1000 a H H H H H b H H H H H G M A y H H H H HHHH y10b7 H b a 2 HH y10b a y b 4 HHH y10b b a y a y b a b b y a y b a y b b b a m/z Fig. 6b: Full - and -terminal sequence assignment: MALDI-DS-Spectrum of Sample 1 fully assigned to the established sequence; calling 70 -terminal and 71 -terminal residues. Sample 2: Instant match of MALDI-DS spectrum to G3P_RABI termini Fig. 7: Use of 6086 as parent ion in a Mascot MS/MS search (for parameters see Fig. 4) provided for direct ID of rabbit glyceraldehyde-3-phosphate dehydrogenase. Sequence alls: -term 68 and -term 47 residues.

7 Protein sequences of samples 1 and 2 and their coverage by MALDI-DS In red: matching sequences based on MALDI-DS reisd and ³-confirmation work. Fig. 8a: Sample 1: Yeast alcohol dehydrogenase 1 fusion protein, native sequence begins at M35. Fig. 8b: Sample 2: G3P-Rabbit A286D, a putative sequence database error was detected during this study at position 286!! (circled). Parameters used by participating laboratories and results from both samples ab. 1: ontent compiled from SRG Poster [8], color code added: failed: red, < 10 -terminal calls: orange, < 20 calls: blue, < 50 calls: yellow, > 50 calls: green. he table indicates that reisd based MALDI-DS measurements are established for protein sequencing today in many labs. Although currently only limited experience may exist in many labs using that technology so far compared to dman sequencing, the results are extremely encouraging.

8 Bruker Daltonics is continually improving its products and reserves the right to change specifications without notice. Bruker Daltonics , M-96 # MALDI-ISD matrix selection guide for the OF/OF Matrix sdhb SA DA Sensitive/robust Automation terminal calls terminal calls ³-Sequencing asy to interprete ab. 2: sdhb is a mixture of 2,5-dihydroxybenzoic acid and 5-methoxysalicylic acid; SA: sinapinic acid; DA: 1,5-diaminonaphthalene. References [1] Hardouin J. Protein Sequence Information by Matrix-Assisted Laser Desorption/Ionization In-Source Decay Mass Spectrometry Mass. Spectrom. Rev. 26: [2] Studies/coverlett_esrg2009[1].pdf [3] Brown RS, Lennon JJ. Sequence-specific fragmentation of matrix assisted laser-desorbed protein/peptide ions Anal hem 67: [4] Zubarev RA, Kelleher L, McLafferty FW. lectron apture Dissociation of Multiply harged Protein ations. A onergodic Process J. Am. hem. Soc. 120: [5] Suckau D, Resemann A. ³-Sequencing: argeted haracterization of the - and -ermini of Undigested Proteins by Mass Spectrometry Anal. hem. 75: [6] Demeure K, Quinton L, Gabelica V, De Pauw Rational Selection of the Optimum MALDI Matrix for op-down Proteomics by In-Source Decay 2007 Anal. hemistry 79: [7] study_u_dsu.pdf [8] Posters/SRG2009_poster(2009_02_03).pdf [9] Posters/SRG2009PresentationFIAL.pdf [10] DS-2.pdf Authors Anja Resemann, Detlev Suckau; Bruker Daltonics, Bremen, Germany. Acknowledgements he samples used in this work were kindly provided by the ABRF-SRG for participation in the 2009 research study. Keywords dman Sequencing ABRF study protein sequencing recombinant proteins op-down sequencing 3 -Sequencing DA Instrumentation & Software ultraflex III OF/OF Bioools For research use only. ot for use in diagnostic procedures. Disclaimer: he ABRF PSRG group prepared and provided the sample to all members and vendors, but did not participate in the vendor s study and does not endorse any specific manufacturer, instrument or strategy. Bruker Daltonik GmbH Bremen Germany Phone +49 (421) Fax +49 (421) sales@bdal.de Bruker Daltonics Inc. Billerica, MA USA Phone +1 (978) Fax +1 (978) ms-sales@bdal.com