MALDI In-Source Decay, from Sequencing to Imaging
Edwin De Pauw2012, Topics in Current Chemistry
Sign up for access to the world's latest research
checkGet notified about relevant papers
checkSave papers to use in your research
checkJoin the discussion with peers
checkTrack your impact
Abstract
The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein.
Related papers
A parallel approach to post source decay MALDI-TOF analysis
Journal of the American Society for Mass Spectrometry, 2006
We present a novel enhancement to matrix-assisted laser desorption ionization (MALDI) post-source decay (PSD) analysis whereby fragment ions from multiple precursor ions are acquired into the same spectrum without employing a timed ion gate to preselect each parent ion. Fragment ions are matched to their corresponding precursor ions by comparing spectra acquired at slightly different reflectron electric fields. By measuring the difference in time-of-flight (TOF) between the two spectra for each fragment, it is possible to calculate the mass of the fragment ion and its parent. This new "parallel PSD" technique reduces analysis time and consumes less sample than conventional PSD, which requires an ion gate for serial preselection of precursor ions. (J Am Soc Mass Spectrom 2006, 17, 60 -66)
MALDI In-Source Decay of Protein
Mass Spectrometry
e in-source decay (ISD) phenomenon, the fragmentation at an N-C α bond of a peptide backbone that occurs within several tens of nanoseconds in the ion-source in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), is discussed from the standpoints of the discovery and early publications dealing with MALDI-ISD, the formation of c-ions in energy-sudden desorption/ionization methods, the formation of radical species in a MALDI, model construction for ISD, and matrix materials that are suitable for use in MALDI-ISD. e formation of c-ions derived from peptides and proteins in MALDI-ISD can be rationalized by a mechanism involving intermolecular hydrogen transfer, denoted as the "Takayama's model" by De Pauw's group (Anal. Chem. 79: 8678-8685, 2007). It should be emphasized that the model for MALDI-ISD was constructed on the basis of X-ray crystallography and scanning probe microscopy (SPM) analyses of matrix crystals, as well as the use of isotopically-labelled peptides.
An analytical pipeline for MALDI in-source decay mass spectrometry imaging
Analytical chemistry, 2011
University of Li ege, B-4000 Li ege (Sart-Tilman), Belgium b S Supporting Information
Rational selection of the optimum MALDI matrix for top-down proteomics by in-source decay
Analytical chemistry, 2007
In-source decay (ISD) in MALDI leads to c-and z-fragment ion series enhanced by hydrogen radical donors and is a useful method for sequencing purified peptides and proteins. Until now, most efforts to improve methods using ISD concerned instrumental optimization. The most widely used ISD matrix is 2,5-dihydroxybenzoic acid (DHB). We present here a rational way to select MALDI matrixes likely to enhance ISD for top-down proteomic approaches. Starting from Takayama's model (Takayama, M. J. Am. Soc. Mass Spectrom. 2001, 12, 1044-9), according to which formation of ISD fragments (c and z) would be due to a transfer of hydrogen radical from the matrix to the analyte, we evaluated the hydrogen-donating capacities of matrixes, and thus their ISD abilities, with spirooxazines (hydrogen scavengers). The determined hydrogen-donating abilities of the matrixes are ranked as follows: picolinic acid (PA) > 1,5-diaminonaphtalene (1,5-DAN) > DHB > sinapinic acid > r-cyano-4-hydroxycinnamic acid. The ISD enhancement obtained by using 1,5-DAN compared to DHB was confirmed with peptides and proteins. On that basis, a matrix-enhanced ISD approach was successfully applied to sequence peptides and proteins up to ∼8 kDa. Although PA alone is not suitable for peptide and protein ionization, ISD signals could be further enhanced when PA was used as an additive to 1,5-DAN. The optimized matrix preparation was successfully applied to identify larger proteins by large ISD tag researches in protein databases (BLASTp). Coupled with an adequate separation method, ISD is a promising tool to include in a top-down proteomic strategy.
New advances in the understanding of the in-source decay fragmentation of peptides in MALDI-TOF-MS
Journal of the American Society for Mass Spectrometry, 2010
In-source decay (ISD) is a rapid fragmentation occurring in the matrix-assisted laser desorption/ionization (MALDI) source before the ion extraction. Despite the increasing interest for peptides de novo sequencing by ISD, the influence of the matrix and of the peptide itself is not yet fully understood. Here we compare matrices with high ISD efficiencies to gain deeper insight in the ISD fragmentation process(es). The major ISD fragments are the c- and z-ions, but other types of fragments are also observed, and their origin is studied here. Two main pathways lead to fragmentation in the source: a radical-induced pathway that leads to c-, z-, w-, and d- ions, and a thermally activated pathway that leads to y-, b-, and a-ions. A detailed analysis of the ISD spectra of selected peptides revealed that (1) the extents of the two in-source pathways are differently favored depending on the matrix used, that (2) the presence of a positive/negative charge on the radical-induced fragments is necessary for their observation in positive/negative mode, respectively, and that (3), for a same peptide, the patterns of the different types of fragments differ according to the matrix used.
A Programmable Fragmentation Analysis of Proteins by In-Source Decay in MALDI-TOF Mass Spectrometry
Analytical Chemistry, 2002
Evaluation of Sibling and Twin Fragment Ions Improves the Structural Characterization of Proteins by Top-Down MALDI In-Source Decay Mass Spectrometry
Analytical Chemistry, 2020
Comprehensive determination of primary sequence and identification of post-translational modifications (PTMs) are key elements in protein structural analysis. Various mass spectrometry (MS) based fragmentation techniques are powerful approaches for mapping both the amino acid sequence and PTMs; one of these techniques is matrix-assisted laser desorption/ ionization (MALDI), combined with in-source decay (ISD) fragmentation and Fourier-transform ion cyclotron resonance (FT-ICR) MS. MALDI-ISD MS protein analysis involves only minimal sample preparation and does not require spectral deconvolution. The resulting MALDI-ISD MS data is complementary to electrospray ionization-based MS/MS sequencing readouts, providing knowledge on the types of fragment ions is available. In this study, we evaluate the isotopic distributions of z′ ions in protein top-down MALDI-ISD FT-ICR mass spectra and show why these distributions can deviate from theoretical profiles as a result of co-occurring and isomeric z and y-NH 3 ions. Two synthetic peptides, containing either normal or deuterated alanine residues, were used to confirm the presence and unravel the identity of isomeric z and y-NH 3 fragment ions ("twins"). Furthermore, two reducing MALDI matrices, namely 1,5diaminonaphthalene and N-phenyl-p-phenylenediamine were applied that yield ISD mass spectra with different fragment ion distributions. This study demonstrates that the relative abundance of isomeric z and y-NH 3 ions requires consideration for accurate and confident assignments of z′ ions in MALDI-ISD FT-ICR mass spectra.
In-Source Decay during Matrix-Assisted Laser Desorption/Ionization Combined with the Collisional Process in an FTICR Mass Spectrometer
Analytical Chemistry, 2013
The type of ions detected after in-source decay (ISD) in a MALDI source differs according to the ion source pressure and on the mass analyzer used. We present the mechanism leading to the final ISD ions for a Fourier transform-ion cyclotron resonance mass spectrometer (FTICR MS). The MALDI ion source was operated at intermediate pressure to cool the resulting ions and increase their lifetime during the long residence times in the FTICR ion optics. This condition produces not only c′, z′, and w fragments, but also a, y′, and d fragments. In particular, d ions help to identify isobaric amino acid residues present near the Nterminal amino acid. Desorbed ions collide with background gas during desorption, leading to proton mobilization from Arg residues to a less favored protonation site. As a result, in the case of ISD with MALDI FTICR, the influence of the Arg residue in ISD fragmentation is less straightforward than for TOF MS and the sequence coverage is thus improved. MALDI-ISD combined with FTICR MS appears to be a useful method for sequencing of peptides and proteins including discrimination of isobaric amino acid residues and site determination of phosphorylation. Additionally we also used new software for in silico elimination of MALDI matrix peaks from MALDI-ISD FTICR mass spectra. The combination of high resolving power of an FTICR analyzer and matrix subtraction software helps to interpret the low m/z region of MALDI-ISD spectra. Finally, several of these developed methods are applied in unison toward a MALDI ISD FTICR imaging experiment on mouse brain to achieve better results.
The initial-ion velocity as a marker for different desorption-ionization mechanisms in MALDI
International Journal of Mass Spectrometry, 2003
While the high, mass-independent and matrix-determined initial velocity of matrix-assisted laser desorption ionization (MALDI) ions has been proposed to be a meaningful characteristic feature of the MALDI process and indicative for the generation of a jet of clusters, considerably lower values as obtained for some low-mass non-protein analytes and certain preparation protocols pointed to a possible second and different process
Geena 2, improved automated analysis of MALDI/TOF mass spectra
BMC Bioinformatics, 2016
Background: Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps. For the analysis of MALDI/TOF spectra, a number of pre-processing steps are required, including joining of isotopic abundances for a given molecular species, normalization of signals against an internal standard, background noise removal, averaging multiple spectra from the same sample, and aligning spectra from different samples. In this paper, we present Geena 2, a public software tool for the automated execution of these pre-processing steps for MALDI/TOF spectra. Results: Geena 2 has been developed in a Linux-Apache-MySQL-PHP web development environment, with scripts in PHP and Perl. Input and output are managed as simple formats that can be consumed by any database system and spreadsheet software. Input data may also be stored in a MySQL database. Processing methods are based on original heuristic algorithms which are introduced in the paper. Three simple and intuitive web interfaces are available: the Standard Search Interface, which allows a complete control over all parameters, the Bright Search Interface, which leaves to the user the possibility to tune parameters for alignment of spectra, and the Quick Search Interface, which limits the number of parameters to a minimum by using default values for the majority of parameters. Geena 2 has been utilized, in conjunction with a statistical analysis tool, in three published experimental works: a proteomic study on the effects of long-term cryopreservation on the low molecular weight fraction of serum proteome, and two retrospective serum proteomic studies, one on the risk of developing breat cancer in patients affected by gross cystic disease of the breast (GCDB) and the other for the identification of a predictor of breast cancer mortality following breast cancer surgery, whose results were validated by ELISA, a completely alternative method. Conclusions: Geena 2 is a public tool for the automated pre-processing of MS data originated by MALDI/TOF instruments, with a simple and intuitive web interface. It is now under active development for the inclusion of further filtering options and for the adoption of standard formats for MS spectra.
Related papers
MALDI mass spectrometric imaging - aspects of sample preparation
2018
Der Schwerpunkt der vorgelegten Dissertation liegt in der optimierten Probenpräparation von Rohgewebeproben für die bildgebende matrix-unterstützte Laser Desorptions/Ionisations Massenspektrometrie (MALDI MSI). Um qualitativ hochwertige MSI-Analysen zu gewährleisten, muss die Gewebeintegrität erhalten bleiben. Mit anderen Worten, die Analyten müssen in den Gewebeproben exakt lokalisiert bleiben, während die Empfindlichkeit der Messung durch optimierte Einbettung von Molekülen in die MALDIMatrixkristalle erhöht wird. Eine der Haupteinschränkungen und -herausforderungen in MALDI MSI ist die räumliche Auflösung. Matrixkristalle, die kleiner als der emittierte Laserstrahl sind, stellen einen Schlüsselparameter für eine Mikrometerauflösung in MALDI MSI dar. In der vorgelegten Dissertation wird eine selbstgebaute Sublimationsapparatur vorgestellt, die eine optimierte Matrixapplikation mit kleinen Kristallgrößen für verschiedene gängige Matrices ermöglicht. Sublimationsbedingungen für hoch...
Fragmentation of Peptides in MALDI In-Source Decay Mediated by Hydrogen Radicals
Analytical Chemistry, 2005
Coordination of alkali metal ions to model branched hexasaccharides dictates fragment yield in MALDI in-source decay with hydrogen abstraction using 5-nitrosalicylic acid as the matrix
Journal of mass spectrometry : JMS, 2014
Matrix-assisted laser desorption/ionization (MALDI) in-source decay (ISD) is a powerful method for top-down sequencing of intact proteins. [1] MALDI-ISD is initiated by hydrogen atom transfer from matrix to analyte in a matrix crystal. [2] The resulting "hydrogen-abundant" peptide radical preferentially produces the c'/z• fragment pair by radical-induced cleavage. [3] Subsequently, radical z• fragments undergo a variety of radical reactions. [3, 4] The a and y' ions are alternatively formed by fragmentation of "hydrogen-abundant" peptide radicals during MALDI-ISD processes and a and y' ions formation cannot be explained by the N-C α bond cleavage model alone. Although the mechanism of a and y' ions formation is not fully understood, the yield of these ions is related to the proton affinity of the matrix used. [5] Since the protonated analytes are generated by proton transfer from the protonated matrix to the analyte, the internal energy of analyte ions increases as the matrix proton affinity decreases. [5] Therefore, a matrix with a low proton affinity gives more internal energy to the peptide by proton transfer reaction and thereby favors the formation of a and y' ions. [5] This indicates the thermochemistry of peptide ionization to be important in the MALDI-ISD process. On the other hand, MALDI mass spectrometry has also been used for the analysis of glycans. [6] 2,5-Dihydroxybenzoic acid is emerging as the good matrix for this purpose [6] and it works as a hydrogen radical donor during the MALDI-ISD process [1]. However, the formation
MALDI Imaging Mass Spectrometry
NATO Science for Peace and Security Series A: Chemistry and Biology, 2014
In-Source Decay and Pseudo-MS3of Peptide and Protein Ions Using Liquid AP-MALDI
Journal of the American Society for Mass Spectrometry, 2016
Atmospheric pressure MALDI on a Q-Exactive instrument was optimized for in-source decay and pseudo-MS 3. The dependence of AP-MALDI ISD on the MALDI liquid matrix was investigated for peptides and proteins. The liquid matrices enabled long-life ISD signal, and exhibited high fragment ion yield and signal stability. Extensive a-, b-, c-, y-, and z-type fragment series were observed depending on the matrix used but were most extensive with 2,5-DHB. Complete sequence coverage of small peptide and intact protein-terminus sequence tags were obtained and confirmed using HCD as a pseudo-MS 3 method.
$$ {{\text{C}}_{\alpha }} - {\text{C}} $$ Bond Cleavage of the Peptide Backbone in MALDI In-Source Decay Using Salicylic Acid Derivative Matrices
Journal of The American Society for Mass Spectrometry, 2011
The use of 5-formylsalicylic acid (5-FSA) and 5-nitrosalicylic acid (5-NSA) as novel matrices for in-source decay (ISD) of peptides in matrix-assisted laser desorption/ionization (MALDI) is described. The use of 5-FSA and 5-NSA generated a-and x-series ions accompanied by oxidized peptides [M-2 H + H] +. The preferential formation of a-and x-series ions was found to be dependent on the hydrogen-accepting ability of matrix. The hydrogen-accepting ability estimated from the ratio of signal intensity of oxidized product [M-2 H + H] + to that of nonoxidized protonated molecule [M + H] + of peptide was of the order 5-NSA95-FSA95aminosalicylic acid (5-ASA) ≒ 2,5-dihydroxyl benzoic acid (2,5-DHB) ≒ 0. The results suggest that the hydrogen transfer reaction from peptide to 5-FSA and 5-NSA occurs during the MALDI-ISD processes. The hydrogen abstraction from peptides results in the formation of oxidized peptides containing a radical site on the amide nitrogen with subsequent radical-induced cleavage at the C a À C bond, leading to the formation of a-and x-series ions. The most significant feature of MALDI-ISD with 5-FSA and 5-NSA is the specific cleavage of the C a À C bond of the peptide backbone without degradation of side-chain and post-translational modifications (PTM). The matrix provides a useful complementary method to conventional MALDI-ISD for amino acid sequencing and site localization of PTMs in peptides.
The quest for improved reproducibility in MALDI mass spectrometry
Mass Spectrometry Reviews, 2016
I. Introduction II. Standard MALDI sample Preparations A. Seeding Method B. Crystal doping method C. Rapid crystallisation D. Sandwich method E. Co-Mixing method F. Electrospray method III. Properties of different matrices A. Organic acid matrices B. Ionic liquid matrices C. Proton stripping matrices D. Inorganic matrices IV. Matrix Dopants and additives V.
Timeframe Dependent Fragment Ions Observed in In-Source Decay Experiments with β-Casein Using MALDI MS
Journal of the American Society for Mass Spectrometry, 2015
The fragment ions observed with time-of-flight (TOF) and quadrupole ion trap (QIT) TOF mass spectrometers (MS) combined with matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) experiments of phosphorylated analytes β-casein and its model peptide were compared from the standpoint of the residence timeframe of analyte and fragment ions in the MALDI ion source and QIT cell. The QIT-TOF MS gave fragment c-, z'-, z-ANL, y-, and b-ions, and further degraded fragments originating from the loss of neutrals such as H2O, NH3, CH2O (from serine), C2H4O (from threonine), and H3PO4, whereas the TOF MS merely showed MALDI source-generated fragment c-, z'-, z-ANL, y-, and w-ions. The fragment ions observed in the QIT-TOF MS could be explained by the injection of the source-generated ions into the QIT cell or a cooperative effect of a little internal energy deposition, a long residence timeframe (140 ms) in the QIT cell, and specific amino acid effects on low-energy CID...
Locating and identifying posttranslational modifications by in‐source decay during MALDI‐TOF mass spectrometry
Protein Science, 1999
A technique is described for identifying and locating posttranslational modifications~PTMs! in peptides and proteins of known sequence by interpretation of c n ion signals generated by in-source decay during delayed ion extraction in matrix-assisted laser desorption0ionization time-of-flight mass spectrometry. Sites of phosphorylation in seven synthetic peptides were determined, as was the location of both the heme group and N, N, N-trimethyllysine in yeast cytochrome c. A semi-automated data analysis process facilitates the identification of segments of the sequence on each side of the PTM, permitting its placement at the junction of the segments and definition of the added mass. A graphical display facilitates illustration of both the location and mass of the PTM.
ARES - a spectrometer for the investigation of rare particle decays and rare nuclear processes
Nuclear Instruments & Methods in Physics Research Section A-accelerators Spectrometers Detectors and Associated Equipment, 1994
A magnetic spectrometer intended for a wide range of investigations of rare particle and nuclear processes is described. The spectrometer consists of cylindrical proportional chambers (˜ 15000 signal wires) with gas supply and gas leakage systems, cylindrical scintillation hodoscopes, a magnet, electronics with power supplies, and a data acquisition system. Basic characteristics of the spectrometer are discussed and results of first physics experiments are presented.
Loading Preview
Sorry, preview is currently unavailable. You can download the paper by clicking the button above.