De novo sequencing of peptides using MALDI/TOF-TOF

Yergey, Alfred L.; Coorssen, Jens R.; Backlund, Peter S.; Blank, Paul S.; Humphrey, Glen A.; Zimmerberg, Joshua; Campbell, J. M.; Vestal, Marvin L.

doi:10.1016/s1044-0305(02)00393-8

Cited by 194 publications

(147 citation statements)

References 24 publications

Supporting

Mentioning

145

Contrasting

Unclassified

Order By: Relevance

“…A diode-pumped Nd: YAG laser ( ϭ 355 nm, 15 J) operated at 200 Hz. This mass spectrometer was described previously [16,17]. It should be mentioned that this mass spectrometer was designed for MS/MS studies of peptides and the linear mode was optional.…”

Section: Instrumentationmentioning

confidence: 99%

Protein desolvation in UV matrix-assisted laser desorption/ionization (MALDI)

Sachon

Clodic

Blasco

et al. 2007

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

We describe experiments in MALDI-TOF and MALDI-TOF-TOF showing that the ejection of protein-matrix cluster ions and their partial decay in the source occur in MALDI. The use of radial beam deflection and small size detector in linear mode allows detection of ions with higher time-of-flight and kinetic energy deficit. MALDI-TOF-TOF experiments were carried out by selecting chemical noise ions at m/z higher than that of a free peptide ion. Whatever the selected m/z (up to m/z 300) the molecular peptide ion appeared as the main fragment. The production of protein-matrix clusters and their partial decay in the source was found to increase with the size of the protein (MW from 1000 to 150,000 u), although it decreases with increasing charge state. These effects were observed for different matrices (HCCA and SA) and in a large laser fluence range. Experimental results and calculation highlight that a continuous decay of protein-matrix cluster ions occurs in the source. This decay-desolvation process can account for the high-mass tailing and peak shifting as well as the strong noise/background in the mass spectra of proteins. . This new ionization method allows the production of large intact molecular ions (protein, peptide, DNA, synthetic polymer, etc.) in the gas phase. Intact ions are then analyzed by a mass analyzer, essentially time-of-flights (TOFs).Although MALDI-TOF is now a well-established and powerful method, many questions are still open concerning (1) the conditions of a successful experiment and (2) the main mechanisms involved in the formation of free intact ions [2].Target preparation is a critical step in MALDI. Analyte is often supposed to be co-crystallized with a large excess of matrix. This incorporation of analyte into the small matrix crystals (co-crystallization) remains an open question [3,4]. However, a protein in the target is likely surrounded by matrix molecules.The ejection of material in the very first stage leads to a very dense plume (with a density similar to that of the target) becoming increasingly more diluted (gas) during the plume expansion.The main question is how a free ion is formed from such a dense plume and why analyte-matrix clusters are not the main products. Ejection of matrix-analyte clusters was already found as essential for the analyte ionization in MALDI [5][6][7][8]. Desorption of large clusters was also predicted from molecular dynamics simulations [9,10]. Other authors believe that ionization can be explained by an ion-molecule reaction in the plume [11]. Recent very interesting simulations, including desorption/ablation molecular dynamics and ionization processes modeling, showed that free ions and those in clusters are produced with t t close abundance in the plume [12].The ion analysis through axial-TOF instruments is probably the key point of the main observation of free ions in MALDI. A free ion formed in the source before the delay time is fully accelerated and is detected at a given time forming a resolved peak. The peak width is a function of the initial a...

show abstract

Section: Instrumentationmentioning

confidence: 99%

Protein desolvation in UV matrix-assisted laser desorption/ionization (MALDI)

Sachon

Clodic

Blasco

et al. 2007

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

show abstract

“…The TOF and Q 1 Q 2 Q 3 instruments are typically used in MS 2 (Premstaller & Huber, 2001;Yergey et al, 2002) but not in MS n experiments, whereas IT and FTICR are usually employed for that purpose (Kruppa et al, 2002;Wu et al, 2002). However, it must be emphasized that Q 1 Q 2 Q 3 instruments can produce medium-energy fragmentation (more structural information in the MS 2 spectra), whereas IT gives rise to low-energy fragmentation (it is often necessary to perform MS n analysis to obtain detailed structural information).…”

Section: Tandem Mass Spectrometrymentioning

confidence: 99%

“…Various combinations and arrangements of mass analyzers have been described in order to improve instrumental performance (Chen et al, 1999;Medzihradszky et al, 2000;Collings et al, 2001;Ni & Chan, 2001;Kurahashi et al, 2002;Wattenberg et al, 2002;Yergey et al, 2002). The multiple mass analyzers mainly produced are: IT/TOF, quadrupole/TOF, and TOF/TOF.…”

Section: Multiple Mass Analyzersmentioning

confidence: 99%

Development of new methodologies for the mass spectrometry study of bioorganic macromolecules

Cristoni

Bernardi

2003

Mass Spectrometry Reviews

View full text Add to dashboard Cite

I. Introduction 370 II. Techniques That Are Usually Employed in the Study of Bioorganic Macromolecules 371 A. Proteins and Peptides 371 B. Oligonucleotides 374 C. Oligosaccharides and Glycoconjugates 375 D. Various Complexes (DNA–Protein, Antigen–Antibody, Macromolecules–Metals) 377 III. Common Problems and Developments in the Analysis of Bioorganic Macromolecules by Mass Spectrometry 377 A. Ionization Source Problems and Developments 377 1. Sensitivity 377 2. Problems with Buffers 379 3. Multicharge Effect 381 B. Mass Analyzer Problems and Developments 381 1. Linear Dynamic Range 381 2. Tandem Mass Spectrometry 382 3. Sensitivity 382 4. Resolution 383 5. Mass Accuracy 383 IV. New Promising Technologies 384 A. Interfaces and Ionization Sources 384 1. Improvements in the Coupling of Liquid‐Phase Separation Systems to Mass Spectrometry 384 2. AP‐MALDI 384 3. Deprotonant Agents 385 4. Sonic Spray Ionization 388 5. APCI without Corona Discharge 391 B. Mass Analyzers 393 1. Linear Quadrupole Ion Trap 394 2. TOF Analyzers with New Detectors 395 3. Multiple Mass Analyzers 396 V. Software for Data Treatment 397 VI. Conclusions and Future Developments 399 Acknowledgments 400 References 400 In recent years, mass spectrometry has been increasingly used for the analysis of various macromolecules of biological, biomedical, and biochemical interest. This increase has been made possible by two key developments: the advent of electrospray ionization (ESI) and matrix‐assisted laser desorption ionization (MALDI) sources. The two new techniques produce a significant increase in mass range and in sensitivity that led to the development of new applications and of new analyzer designs, software, and robotics. This review, apart from the description of the status of mass spectrometry in the analysis of bioorganic macromolecules, is mainly devoted to the illustration of the more recent promising techniques and on their possible future evolution. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 22:369–406, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10062

show abstract

“…One of these new analyzers, the MALDI TOF/TOF [20] has unique fragmentation patterns where the tandem spectra are a combination of the products of both high-energy CID and lower-energy PSD. The properties of both these types of fragmentation were previously discussed elsewhere [23]. Detailed analyses of the properties of fragmentation as a function of collision parameters have been completed elsewhere [24].…”

mentioning

confidence: 99%

Fragmentation of leucine enkephalin as a function of laser fluence in a MALDI TOF-TOF

Campbell¹,

Vestal²,

Blank

et al. 2007

J. Am. Soc. Mass Spectrom.

Self Cite

View full text Add to dashboard Cite

The effects of laser fluence on ion formation in MALDI were studied using a tandem TOF mass spectrometer with a Nd-YAG laser and ␣-cyano hydrocinnamic acid matrix. Leucine enkephalin ionization and fragmentation were followed as a function of laser fluence ranging from the threshold of ion formation to the maximum available, that is, about 280 -930 mJ/mm 2 . The most notable finding was the appearance of immonium ions at fluence values close to threshold, increasing rapidly and then tapering in intensity with the appearance of typical backbone fragment ions. The data suggest the presence of two distinct environments for ion formation. One is associated with molecular desorption at low values of laser fluence that leads to extensive immonium ion formation. The second becomes dominant at higher fluences, is associated initially with backbone type fragments, but, at the highest values of fluence, progresses to immonium fragments. This second environment is suggestive of ion desorption from large pieces of material ablated from the surface. Arrhenius rate law considerations were used to estimate temperatures associated with the onset of these two processes. (J Am Soc Mass Spectrom 2007, 18, 607-616)

show abstract

De novo sequencing of peptides using MALDI/TOF-TOF

Cited by 194 publications

References 24 publications

Protein desolvation in UV matrix-assisted laser desorption/ionization (MALDI)

Protein desolvation in UV matrix-assisted laser desorption/ionization (MALDI)

Development of new methodologies for the mass spectrometry study of bioorganic macromolecules

Fragmentation of leucine enkephalin as a function of laser fluence in a MALDI TOF-TOF

Contact Info

Product

Resources

About