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Frequently Asked Questions

• What is AP/MALDI?
  

  AP/MALDI (atmospheric pressure matrix-assisted laser desorption/ionization) is an atmospheric pressure ionization source used in mass spectrometry. The AP-MALDI technique is also sometimes referred to as API-MALDI. The ion source is easily coupled to ion trap technology or any other MS system equipped with an ESI (electrospray ionization) or nanoESI source.

• How does AP/MALDI work?
  

  AP/MALDI works in a similar manner to vacuum MALDI whereby a UV laser is used to irradiate samples consisting of co-crystallized matrix and analyte. However, with AP/MALDI ions are created at atmospheric pressure instead of under vacuum. By interfacing AP/MALDI onto a mass analyzer with an atmospheric pressure interface (API), ions are transmitted through the API into the vacuum of the MS, and ultimately a simple MALDI-MS instrument is created.

• Why use AP/MALDI instead of traditional MALDI?
  

  There are several advantages afforded by AP/MALDI over vacuum MALDI. Firstly, the fact that AP/MALDI operates at atmospheric pressure offers the opportunity to utilize liquid matrices and matrices that are not vacuum compatible. This makes AP/MALDI a very versatile instrument for a variety of samples. Secondly, the AP/MALDI method has shown indications to be an even "softer" ionization technique than vacuum MALDI due to fast thermalization of the ion internal energy at atmospheric conditions. This feature is important in the analysis of labile biomolecules and non-covalent complexes. Thirdly, AP/MALDI is decoupled from the mass analyzer. This decoupling allows AP/MALDI to be interfaced with ion trap instruments or any other MS system equipped with an API (typically those which use ESI). Ion trap instruments allow MS/MS analysis which is much more powerful and easier to perform than PSD (post-source decay) using TOF instruments. Finally, AP/MALDI is the most cost-effective way to get MS/MS data from MALDI ions.

• How sensitive is AP/MALDI?
  

  It has been reported in the peer-reviewed literature that attomole quantities of peptides can be routinely analyzed using AP/MALDI on an ion trap MS. The signal-to-noise and mass spectra obtained from AP/MALDI are similar to vacuum MALDI. AP/MALDI compensates for the loss of ions going from atmospheric pressure to vacuum, by generating much less fragment ions than compared to vacuum MALDI, typically consuming greater sample quantities, and applying a new pulsed dynamic focusing (PDF) technique (described below) which focuses ions into the vacuum of the mass analyzer. As a result, AP/MALDI sensitivity performance is often the same as those from vacuum MALDI.

• What protocol is recommended for AP-MALDI sample preparation?
  

  Sample protocol for AP-MALDI is not different from that used for vacuum MALDI. Some protocols recommended for analyzing low concentration peptide mixtures are shown here. As in vacuum MALDI, C18 ZipTips can be used for fast cleanup of real samples.

• Is AP/MALDI a high throughput method?
  

  AP/MALDI is definitely much faster than LC-ESI-MS. The rapidity of AP/MALDI depends on the instrument used, but in general with an ion trap, a typical MS analysis can be done within 10 to 20 sec. A data dependent MS/MS analysis can take 30-50 sec. This is still fast enough to complete MS/MS analysis of all samples on a 96-spot target plate in 30-60 minutes using the automated mode of analysis. Furthermore, we have recently introduced "AP/Loader", a multi-plate sampling system, with a magazine capacity of 20 plates, allowing unattended 24 hour operation of 1000s of sample spots. Once again, avoiding the complexity of vacuum and operating at ambient pressure allows the AP/Loader system to be fast and high throughput.

• Can I use my robotics technique for AP/MALDI sample preparation?
  

  MassTech and Agilent 96-spot target plates follow an industry-standard microtiter plate. Thus if your autosampler, liquid dispensing apparatus works with a microtiter format it will accommodate AP/MALDI plates as well. We supply a multi-plate holder which holds 4 of our 96-spot plates for multi-plate sample spotting.

• Can I use my Applied Biosystems (AB) plate or other commercial MALDI plates in AP/MALDI?
  

  We supply different holders for different vendor's plate formats and these holders are easily changed in the AP/MALDI source by a few screws. Thus if you already use AB sample plates, we can supply an AB plate holder. This will allow you to use your ABI plates in both the Voyager and the AP/MALDI instruments. Below is an example of two popular plate types, the AB 100-spot plate and MassTech's 96-spot plate (Part Number P96). Also shown are the plates loaded into MassTech's 2nd generation AP/MALDI-PDF ion sources.

  

  

  

  AB 100-spot, stainless steel MALDI plates (left). MassTech's gold-coated MALDI target plate (P96) (right).

  AB 100-spot plate loaded into the AP/MALDI-PDF 712 source

  MassTech P96 plate loaded into the AP/MALDI-PDF 122 source.

  The Target software (the control software for AP/MALDI) has been preprogrammed to accept Agilent, AB, and DIOS plates, while other plate formats can be custom programmed. Inquire about the plate format you currently use.

• What is Pulsed Dynamic Focusing (PDF)?
  

  Pulsed Dynamic Focusing (PDF) is a new technology introduced by MassTech at ASMS 2004. The PDF technique essentially removes the electric field that exists between the sample plate and API inlet during ionization, at a time just before ions are about to be lost to the walls and tip of the API inlet. Because the electric field is removed in this timely fashion, ions are focused into the MS without losses, thereby enhancing ion transmission and sensitivity.

• How does PDF improve AP/MALDI?
  

  PDF allows better transmission of ions into the API inlet, and thus higher sensitivity. Furthermore, peer-reviewed literature has shown that PDF makes AP/MALDI insensitive to laser misalignments of up to 1.2 mm off-axis, making the source much more robust. We offer these PDF benefits to our existing AP/MALDI users in the form of an external upgrade module. For our new users, we have integrated PDF directly into the ion source housing, and have called the new system "AP/MALDI PDF". In these second generation AP/MALDI PDF systems, we have also made user-interface improvements that include: 1) enhanced image quality, 2) on-screen video capture and sample plate control, 3) faster sample spot changes, 4) new laser safety interlocks, 5) USB connectivity, and 6) full AB plate access.

  

  Modeling results showing ions focused into the API inlet using Pulsed Dynamic Focusing (PDF).

  

  Improved imaging with new, second generation, AP/MALDI PDF ion souces.

• Will AP/MALDI couple to my mass spectrometer?
  

  Currently, MassTech manufactures AP/MALDI ion sources for the following mass spectrometers:

  3D Ion Traps (ITMS):	Thermo Finnigan LCQ series Bruker Esquire series Agilent 1100 LC/MSD series
  Linear Ion Traps (LITs):	Thermo Finnigan LTQ series
  Triple Quad/Linear Ion Trap Hybrids:	AB/MDS SCIEX 4000 Q TRAP
  Time-of-Flight (TOF) MS:	Waters/Micromass Q-Tof series Waters/Micromass LCT series Bruker BioTOF series JEOL AccuTOF Agilent LC/MSD TOF
  Fourier Transform (FT) MS:	IonSpec FTMS with Waters Z-Spray Bruker Apex FTMS Thermo Finnigan LTQ FT

  
  
• Where can I order an AP/MALDI ion source?
  

  Contact MassTech at msms@apmaldi.com or request a quote online.

• Where can I get answers to my other questions?
  

  Contact our technical representative at msms@apmaldi.com or call: +1-(443)-539-1758.