Accurate Mass Mapping and Sequencing of Corpus Cardiacum Neuropeptides by means of Nanoscale LC-MALDI-Tof MS/MS

This application note shows an LC-MALDI MS/MS based study of a biological mixture of natural peptides freshly collected from living tissue.

The combination of off-line nanoscale LC separation – including direct spotting on a stainless steel target plate – with MALDI MS/MS offers an alternative separation and identification strategy compared to the more “traditional” on-line electrospray data directed analysis for complex protein/peptide mixtures.

With the advent of novel orthogonal acceleration Time-of-Flight (Tof) mass spectrometers exhibiting ever increasing sensitivity, mass accuracy and resolution, it is becoming more and more evident that naturally occurring neuropeptides which can be readily analyzed from biological tissue sources are far more complex than could previously be imagined.

This is illustrated in this note, where we show an LC-MALDI MS/MS based study of a biological mixture of natural peptides freshly collected from living tissue. Whereas in principle any living tissue releases peptides into its environment, here we focus on an easily accessible and particularly rich source of biological peptides, i.e. the insect master neurosecretory gland (equivalent to the mammalian pituitary). The corpus cardiacum of a large cockroach species (Blaberus giganteus) was used as model tissue.

The method employs the separation of freshly prepared extracts with a MALDI spotting device utilizing reversed phase chromatography, microfraction collection and direct spotting on a standard MALDI target plate including co-deposition of a matrix solution. Subsequently to an MS acquisition, data files were processed with MALDI-merge (Waters Corp.) software that generates precursor ion information based on ion intensities detected across all fractions deposited on the MALDI target. The most intense precursor ions were selected and exported as an include list for automatic MS/MS fragmentation experiments.

Verhaert and co-workers previously demonstrated that neuropeptides can be analyzed by MALDI instruments, requiring very little, if any, sample manipulations of the neurosecretory tissue prior to the actual spectrum acquisition.¹ Using this approach, neuropeptide spectra are typically generated directly from the tissue placed on a MALDI target, or after a brief one-minute extraction.

Identification of peptides is based on exact precursor mass as well as exact fragmentation data considering specific modifications that frequently occur in (insect) neuropeptides. This study was performed with two freshly prepared tissue extracts and three independent LC-MALDI MS/MS experiments. The results of one of the latter experiments are explained in more detail in this application note.

Sample Preparation

Giant cockroaches, Blaberus giganteus, were obtained from a standard culture maintained at Antwerp Zoo. Corpora cardiaca were rapidly micro-dissected and briefly (1 min) extracted in 10 μL of a 50% MeOH, 0.1% TFA solution. 5 μL of tissue extract was 10 fold diluted with an 0.1% TFA solution and loaded on a Symmetry 5 mm x 300 μm C₁₈, 5 μm Pre-column at flow rate of 20 μL/min. 60 fractions of 1 min were directed onto a MALDI standard target plate with a CTC PAL microfraction collector (Figure 1).

A 2 mg/mL α-cyano-4-hydroxycinnamic acid solution (plus 5mM ammonium dihydrogenphosphate) was added post-column via a y-connector and co-deposited during sample collection (0.8 μL/min flow rate) utilizing a syringe pump.

LC Fractionation and MS Conditions

Nanoscale LC fractionation experiments were conducted using a 1 hr reversed-phase gradient at 300 nL/min (5 to 40% acetonitrile over 60 minutes) conducted with a nanoACQUITY System (Waters Corp.) utilizing an Atlantis 3 μm C₁₈ NanoEase 75 μm x 15 cm Column (Waters Corp).

The MALDI Q-Tof Premier Mass Spectrometer (Waters Corp.) was externally calibrated with a polyethyleneglycol mixture (m/z 50 to m/z 3000). During acquisition the data were lock mass corrected using the monoisotopic mass of [Glu1]-Fibrinopeptide B on the near-point lock mass spot on the MALDI target plate. Data were acquired automatically in MS and MS/MS mode. MALDI Merge Software² allows merging of all MS information and peptide sorting according to their mass and intensity. This information was used for defining an include list of all precursors in order to perform unattended, automated MS/MS fragmentation experiment with pre-defined collision energies. Deisotoping of the fragmentation spectra was conducted with MaxEnt3 prior to de novo sequence annotation with PepSeq Software.

Figure 3 shows an MS spectrum of the sample mixture before separation, i.e. direct tissue analysis utilizing 160 mg/mL DHB as a matrix. Although the information content of the spectrum is dense, gathering sequence information from selected precursors – applying a data directed analysis experiment – would be challenged due to ion suppression effects and rapid sample consumption.

Therefore, an off-line LC-MALDI MS/MS experiment using a precursor inclusion list consisting only of potentially interesting neuropeptides detected in a preceding MS run is a suitable approach, as demonstrated here. Figure 2 illustrates the MALDI merge software tool that allows handling MS data acquired in a first instance. Several different sorting strategies are possible, but the most common strategy was employed in this study – analyzing the most intense precursors first.

Sequence Motives

The results of the two sequence annotation experiments – shown in Figures 4 and 5 – confirm the presence of a common sequence motive (-(PF)XPRI/L-NH₂) previously observed by Verhaert et al.¹ These common sequence motives often give rise to signature/fingerprint MS/MS profiles, which reflect various neuropeptide classes sharing ‘base’ amino acid sequences, but also distinct in a large number of possible post-translational modifications (PTMs) and a complex combination thereof. Several of these modifications comprise easily identifiable known mass differences. A considerable number, however, are defined by mass differences which have not been characterized before.

The biological and physiological implications of these findings are intriguing. We believe that the presence of many variants of neuropeptides synthesized in vivo comprise PTMs representing numerous subtle regulation steps modulating the peptide's biological (in)activity.

Thus, the strategy of decoupling a separation step from MS acquisition allows a more in depth selection for targeted precursors, avoiding redundant MS/MS acquisition in subsequent runs.

Over 80 useful MALDI-MS/MS spectra were automatically collected with the presented approach, which is a significant improvement compared to direct tissue analysis neuropeptide approaches. This is a result of reduced ion suppression as the components are separated in time and space from each other. The main challenge, however, still remains the (automated) annotation of the MS/MS spectra. Development of software that allows for the sequencing of non-tryptic peptides – taking into account the analysis of internal fragments, such as the intense fragments with an aminoterminal proline as observed here, as well as possible rearrangements – would greatly facilitate de novo sequencing of ‘native’ neuropeptides.

• Nanoscale LC allows for the easy, robust and unattended fractionation and off-line collection of peptides prior to MALDI-MS/MS analysis.
• MALDI-MS/MS is a rapid and sensitive sequencing technique leading to unambiguous peptide identification.
• The processing of LC-MALDI data using automated software tools, allows a non-redundant list of peptides to be generated for each well position.
• MS/MS fragmentation information from more than 80 precursors were automatically obtained and selected from the intensity sorted merge list.

1. P. Verhaert, S. Uttenweiler-Joseph, M. de Vries, A. Loboda, W. Ens, K.G. Standing Matrix-Assisted Laser Desorption/Ionization Quadrupole Time-of-Flight Mass Spectrometry: An Elegant Tool for Peptidomics. Proteomics 2001, 1, 118–131
2. G.S Cavey, E. Claude, P. Davidson, J. Langridge, T. McKenna, D. Monsma, M. Snel, R. Tyldesley-Worster. Quantitative Analysis of Complex Peptide Mixtures Derived from Mouse Serum using Liquid Chromatography Coupled with MALDI MS and MS/MS. Poster P63, ABRF Meeting 2006.

Future Work

Future work will focus on optimization of separation and spotting with the MALDI spotter in order to increase system versatility. In addition, comparison with electrospray data will reveal whether the identified sequences are unique to the applied nanoscale LC-MALDI MS/MS approach.

Acknowledgements

We gratefully thank Jan Wens and Philippe Jouk of the Antwerp Zoo for their generous donation of giant cockroaches. Cover photography of Blaberus giganteus courtesy of Ellen Mattaar. Marten Snel and Richard Tyldesley-Worster are kindly acknowledged for their assistance and contributions.