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1 2 3 4 Measuring Masses of Large Biomolecules and Bioparticles 5 6 7 Using Mass Spectrometric Techniques 8 9 Wen Ping Peng *, Szu Wei Chou, Avinash A. Patil 10 11 12 Department of Physics, National Dong Hwa University, Shoufeng, Hualien, 97401, 13 Taiwan, R.O.C. 14 15 16 * To whom correspondence should be addressed, e mail: [email protected] 17 18 19 Contract/grant sponsor: NSC 102 2112 M 259 003 MY3 20 21 Prepared for the Analyst (review article) 22 23 24 25 26 27 Manuscript 28 29 30 31 32 33 34 35 36
37 Accepted 38 39 40 41 42 43 44 45 Analyst 46 47 48 49 50 51 Keywords: large protein complexes, bioparticles, ion source, mass analyzer, detectors, 52 mass measurement, mass assignment, mass resolution 53 54 55 56 57 58 59 60 Analyst Page 2 of 51
1 2 3 4 Abstract 5 6 7 Large biomolecules and bioparticles play a vital role in biology, chemistry, biomedical 8 9 10 science, and physics. Mass is a critical parameter for characterization of large 11 12 13 biomolecules and bioparticles. To achieve mass analysis, choosing a suitable ion 14 15 source is the first step and the instruments of detecting ions, mass analyzers and 16 17 18 detectors, should also be considered. Abundant mass spectrometric techniques have 19 20 21 been proposed to determine the masses of large biomolecules and bioparticles, and 22 23 24 these techniques can be divided into two categories: The first category is to measure 25 26
27 the mass (or size) of intact particles, including single particle quadrupole ion trap Manuscript 28 29 30 mass spectrometry, cell mass spectrometry, charge detection mass spectrometry, and 31 32 33 differential mobility mass analysis; the second category aims to measure the mass and 34 35 36 tandem mass of biomolecular ions, including quadrupole ion trap mass spectrometry,
37 Accepted 38 39 time of flight mass spectrometry, quadrupole orthogonal time of flight mass 40 41 42 spectrometry and orbitrap mass spectrometry. Moreover, algorithms for mass and 43 44
45 stoichiometry assignment of electrospray mass spectra are developed to obtain Analyst 46 47 accurate structure information and subunit combinations. 48 49 50 51 52 53 54 55 56 57 58 59 60 Page 3 of 51 Analyst
1 2 3 4 1. Introduction 5 6 7 Mass spectrometric techniques can be applied to acquire masses and fragment of 8 9 10 large biomolecules and of bioparticles which facilitate the study of biological process, 11 12 1 3 13 interaction of biomolecules, and their structures and functions. The size of large 14 15 16 biomolecules and bioparticles are in the range from 1 nm to 100 µm. Those large 17 18 biomolecules and bioparticles include protein complexes, viruses, bacteria and cells. 19 20 21 So far, it is still a challenge to detect bioparticles with sizes from 20 nm to 100 nm. 4, 5 22 23 24 Many research groups have tried to develop mass spectrometers to detect the masses 25 26
27 of these sizes. In general, a mass spectrometer includes an ion source, a mass analyzer Manuscript 28 29 30 and a detector and therefore selecting ion sources and designing workable mass 31 32 6 33 analyzers and detectors are a necessity. 34 35 36 Ions are a primary issue for mass analysis. The ion sources used in mass
37 Accepted 38 7 39 spectrometry (MS) for large ions include electrospray ionization (ESI) , 40 41 8, 9 42 matrix assisted laser desorption/ionization (MALDI) and laser induced acoustic 43 44 10 12 45 desorption (LIAD) . With ESI ion source, proteins, protein complexes and viral Analyst 46 47 capsids are generated in air and kept intact in vacuum. 13 17 ESI ion source can produce 48 49 50 multiple charged ions with mass to charge ratio (m/z) below 100000. However, when 51 52 53 the particle size becomes large, particles gain higher charges on the surfaces (typically 54 55 56 > 50+) and cause highly overlapping ion series, making charge assignment 57 58 59 60 Analyst Page 4 of 51
1 2 3 18 20 4 difficult. By contrast, the MALDI ion source mostly generates singly, doubly 5 6 7 charged peaks which could be easily assigned. Intact ions can be produced by laser 8 9 10 irradiation on matrix crystal. When analyzing large ions, formation of particles is 11 12 13 found in the size range from 10 nm to 1000 nm by irradiating MALDI matrix 14 15 samples. 21, 22 The matrix particles will interfere with viral particles (the size range 16 17 18 from 20 nm to 300 nm) during laser desorption process and thus hinder the analysis of 19 20 21 large bioparticles. Moreover, when the particle mass becomes large (>100 kDa), its 22 23 24 ion velocity is low, making high mass ion detection very challenging.23 25 Besides, 25 26
27 tandem mass analysis of MALDI ions is helpful to acquire the structure information, Manuscript 28 29 30 but it is not well studied yet for m/z > 12000. 26 The LIAD ion source is favorable in 31 32 12, 27, 33 generating particles with the size greater than 50 nm by means of acoustic waves. 34 35 28 36 Multiple pre charged ions can be generated without matrix interference and fitted to
37 Accepted 38 12, 27 39 single particle analysis with both optical and charge detection. The drawback of 40 41 42 LIAD ion source is low ion generation efficiency. 43 44
45 After ions are generated, they must be transported and guided to the mass Analyst 46 47 analyzers for mass analysis. Typically, by reducing the guiding quadrupole driving 48 49 50 frequency and increasing the buffer gas pressure, high mass ions can be cooled down 51 52 53 and guided to mass analyzers. 29 33 Mass analyzers can be divided into ion trap and 54 55 56 time of flight categories. Ion trap mass analyzers such as two dimensional 34 37 and 57 58 59 60 Page 5 of 51 Analyst
1 2 3 38, 39 40 31, 32, 4 three dimensional quadrupole ion trap (QIT) , DC gate ion trap and orbitrap 5 6 41 7 show good trapping efficiency of large particles. Time of flight (TOF) mass 8 9 10 analyzers can be run in linear, reflectron, and orthogonal modes and coupled with 11 12 29, 30 13 quadrupole for mass selection, ion activation and isolation. Moreover, no mass 14 15 analyzers can fully cover the whole size ranges of nanoparticles. If the particle density 16 17 18 is known, the particle size can be converted to particle mass. Therefore, differential 19 20 21 mobility analysis (DMA) coupled with electrospray ion source offers an alternative 22 23 24 approach to measure the effective particle sizes and thus characterize large 25 26
27 biomolecules and nanoparticles ranging from a few nanometers to several hundred Manuscript 28 29 30 nanometers.42 44 31 32 33 Detectors are incorporated with mass analyzers to detect ions. The main reason 34 35 36 that the conventional mass spectrometers cannot detect high mass ions is the use of a
37 Accepted 38 39 secondary electron detector, such as an electron multiplier and multi channel plates 40 41 42 (MCP) which cause low secondary electron yields of high mass ions. New detectors 43 44 27, 40 45, 46 45 including a charge detector , a nanomembrane detector , a secondary ion Analyst 46 47 detector 47, 48 , an active pixel detector 49 , and a cryodetector 50 are therefore designed 48 49 50 and incorporated with mass analyzers to overcome that problem. 46, 47, 51, 52 51 52 53 In general, when determining the masses of large biomolecules and bioparticles, 54 55 56 we could divide mass spectrometric techniques into two categories. The first category 57 58 59 60 Analyst Page 6 of 51
1 2 3 4 aims to measure the masses of intact particles including single particle quadrupole ion 5 6 12, 28, 53 27, 54 7 trap mass spectrometry , cell mass spectrometry , charge detection mass 8 9 40, 55, 56 42, 43 10 spectrometry and differential mobility mass analysis . In single quadrupole 11 12 13 ion trap mass spectrometry and cell mass spectrometry, detectors such as light 14 15 scattering, laser induced fluorescence, a charge detector and an electron multiplier are 16 17 18 developed to overcome the detection limit of large biomolecules and bioparticles. 19 20 21 Charge detection mass spectrometry adopts a non destructive charge detector to sense 22 23 24 the image charge of particles. Differential mobility mass analysis employs the 25 26
27 condensation particle counters (CPCs) to optically detect nanoparticles. The second Manuscript 28 29 30 category focuses on the mass and tandem mass measurement of biomolecular ions 31 32 57 59 33 including quadrupole ion trap mass spectrometry , time of flight mass 34 35 23, 24, 46 29, 30 36 spectrometry , quadrupole orthogonal time of flight mass spectrometry and
37 Accepted 38 31, 32, 41 39 orbitrap mass spectrometry . Quadrupole ion trap mass spectrometry uses an 40 41 42 electron multiplier to acquire mass spectra of large proteins. Time of flight mass 43 44
45 spectrometry couples with several detectors including a microchannel plate detector, a Analyst 46 47 secondary ion detector, a cryogenic detector, a nanomembrane detector, and a charge 48 49 50 detector to extend the detection limit of large proteins. Quadrupole orthogonal 51 52 53 time of flight mass spectrometry and orbitrap mass spectrometry can perform tandem 54 55 56 mass analysis and high mass resolution analysis. 57 58 59 60 Page 7 of 51 Analyst
1 2 3 4 Quadruople orthogonal time of flight MS and orbitrap MS now play important 5 6 1 7 roles in native mass spectrometry. Large viral capsids, such as hepatitis B virus 8 9 19, 10 capsids and their fragmental ions are acquired with quadrupole orthogonal TOF MS. 11 12 60 13 Orbitrap MS is now able to analyze large protein complexes up to 1 MDa and its 14 15 tandem MS ability achieves MS 3 with high mass resolution. 31, 32 The high quality 16 17 18 mass spectra enable high throughput study of large ESI ions. To streamline the 19 20 21 identification of mass, stoichiometry and interactions of different subunits, new 22 23 24 algorithms, such as AutoMass 19 and Massign, 20 are developed. 25 26
27 Manuscript 28 29 30 2. Ion Sources 31 32 33 2.1 Electrospray ionization 34 35 36 Dole et al . developed electrospray ionization to generate molecular beam of
37 Accepted 38 61 39 macroions. Polystyrene macroions of molecular weight up to 411000 weight ‐ 40 41 42 average amu appear mostly to be multiply charged single species. An important 43 44
45 milestone was hit by Fenn et al. who applied ESI technique to generate Analyst 46 47 oligonucleotides and proteins and proteins with molecular weights up to 130000 Da 48 49 50 were obtained. 7 Robinson et al. performed impressive mass measurement of 51 52 53 bacteriophage MS2 viral capsid ions up to 2.5 ×10 6 Da and with a charge state of 54 55 56 ~113. 62 Bacteriophage MS2 viral capsids remained intact during their flight and were 57 58 59 60 Analyst Page 8 of 51
1 2 3 4 dissociated to monomeric subunits. Benner and Siuzdak et al. used ESI to generate 5 6 14 7 tobacco mosaic viruses (TMV) in the gas phase with charges up to several hundred. 8 9 60 63 64 10 Hepatitis B virus (HBV) , norwalk virus and bacteriophage HK97 viruses with 11 12 13 molecular weight of few MDa were generated by ESI and analyzed by modified 14 15 Q TOF instrument by Heck et al. The above studies demonstrated that ESI ion source 16 17 18 coupled with mass spectrometry is a powerful analytical technique to generate 19 20 21 macroions and obtain the structure information of ions. 22 23 24 2.2 Matrix assisted laser desorption ionization 25 26
27 Tanaka et al. first generated polymer and proteins up to m/z 100000 with soft Manuscript 28 29 30 laser desorption/ionization of nanogold powder dispersed in glycerol and acquired the 31 32 8 33 mass spectra. Karas and Hillenkamp reported matrix assisted laser desorption 34 35 9 36 ionization by ultraviolet irradiation could obtain mass spectra of proteins.
37 Accepted 38 39 Hillenkamp et al. further used infrared laser to acquire mass spectra of synthetic DNA, 40 41 42 restriction enzyme fragments of plasmid DNA, and RNA transcripts up to a size of 43 44 25 45 2180 nucleotides. Li et al. generated polymers up to 1.5 MDa and detected the Analyst 46 47 doubly charged ion signals. 23 Not only polymers and proteins can be generated by 48 49 50 MADLI ion source, but also nanomaterials can be formed in the gas phase, ZnS 65 and 51 52 53 Pt66 nanoparticles were detected with a TOF mass spectrometer. Low charge states of 54 55 56 MALDI ions make the mass assignment simple and straight forward. 57 58 59 60 Page 9 of 51 Analyst
1 2 3 4 2.3 Laser induced acoustic desorption 5 6 7 Laser induced acoustic desorption (LIAD) can generate large ions. Chen et al. 8 9 10 adopted LIAD to desorb 20 µm size Al 2O3 particles and cyctocrome C protein from 11 12 10 13 sapphire substrate. In addition, surface acoustic waves can detach particles from 14 15 sample substrate surface and improves cleaning effectiveness as shown by 16 17 18 Kolomenskii et al. 67 Viral particles, bacteria and cells are desorbed by LIAD with 19 20 21 quadrupole ion trap mass spectrometry. 12, 27, 28 22 23 24 25 26
27 3. Instrumentation Manuscript 28 29 30 3.1 Quadrupole ion trap mass spectrometry and linear ion trap mass spectrometry 31 32 33 Quadrupole ion trap (QIT) is a suitable ion trap device for non destructive mass 34 35 36 measurement of single, trapped nanoparticles and for destructive mass measurement
37 Accepted 38 68 39 of large ions. The non destructive mass measurement can be traced to 1950s. Single 40 41 42 microparticles were trapped and analyzed by light scattering, laser induced 43 44
45 fluorescence, and charge detection methods. The destructive mass measurement is Analyst 46 47 done with an electron multiplier and a charge detector. To eject ions, “mass selective 48 49 50 instability” mode is applied in a quadrupole ion trap. Either rf amplitude or frequency 51 52 53 must be scanned to acquire the mass spectra. Frequency scan employs the wideband 54 55 56 power amplifier, so it can easily cover wide mass range. Voltage scan needs a power 57 58 59 60 Analyst Page 10 of 51
1 2 3 4 amplifier to boost a transformer to several thousand volts. Due to high Q factor of a 5 6 7 transformer, it is very difficult to cover wide mass range with voltage scan. Therefore, 8 9 54, 57, 69 10 frequency scan is superior to voltage scan. 11 12 n 34, 13 The advantage of linear ion trap (LIT) is its high ion capacity and MS ability. 14 15 38 LIT is favorable to store more ions and allows tandem analysis of trapped ions. An 16 17 18 electron multiplier and high buffer gas pressure would affect bioparticle detection 19 20 21 with LIT. 70 High buffer gas is needed to cool down ions when the size of ions 22 23 24 becomes larger, but an electron multiplier could not be operated in this condition. 25 26
27 Typically conversion dynode voltage must be set high enough (> 10kV) to get high Manuscript 28 29 30 gain of ion signals, but high buffer gas pressure will cause discharging of an electron 31 32 33 multiplier. A charge detector coupled with LIT MS can work at high pressure 34 35 36 condition without discharging problem and thus enhance the detection of high mass
37 Accepted 38 39 ion signals. 40 41 42 43 44
Analyst 45 3.1.1 Electron multiplier 46 47 The sensitivity of a secondary electron detector (e.g. an electron multiplier and 48 49 50 microchannel plates) decreases as ν 4.4 , where ν is the velocity of the incident ion. 45, 46 51 52 53 This velocity relation leads to a remarkable decrease in sensitivity of those detectors 54 55 56 for large and heavy ions. To detect high mass MALDI ions with an electron multiplier, 57 58 59 60 Page 11 of 51 Analyst
1 2 3 4 Schlunegger et al . firstly adopted three dimensional QIT with frequency scan method 5 6 57 7 to cover high mass range. By using low frequencies (below 100 kHz) and low 8 9 10 amplitudes (below 200 V), high mass singly charged bovine serum albumin (BSA) 11 12 13 and immunoglobulin G (IgG) ions are trapped and analyzed by frequency sweep 14 15 method. The instrument shows good sensitivity, signal to noise ratios (10:1), and a 16 17 18 mass resolution of 70. Ding et al . proposed using a frequency scan digital ion trap 19 20 21 coupled with electrospray ionization (ESI) and atmospheric pressure matrix assisted 22 23 24 laser desorption/ionization (AP MALDI) sources to demonstrate the capability of the 25 26 69 27 digital method. AP MALDI mass spectra of singly charged horse heart myoglobin Manuscript 28 29 30 ions (17 000 Th) were generated using a trapping voltage of only 1000 V and a mass 31 32 33 resolution of 2100 is reached. Recently, McLuckey et al . developed mass selective 34 35 36 instability analysis by scanning a direct current (dc) voltage applied to the end cap
37 Accepted 38 59 39 electrodes while holding the radio frequency (rf) potential at a fixed value in a QIT. 40 41 42 They ejected ions along the ß z = 0 instability line in the direction from high 43 44
45 mass to charge (m/z) to low m/z. Doubly charged pyruvate kinase ions were observed Analyst 46 47 at m/z ∼ 131 000. The combination of QIT and an electron multiplier detector suffers 48 49 50 from poor ion secondary electron conversion efficiency and low ion ejection velocity 51 52 53 and therefore the ion detection efficiency of high mass ions is poor. 54 55 56 Commercial LIT MS operated in the frequency of ~1 MHz can detect mass 57 58 59 60 Analyst Page 12 of 51
1 2 3 4 range up to m/z ~4,000. In order to extend mass range of LIT MS, Chen et al . 5 6 7 developed a home made frequency scan LIT mass spectrometer with low rf driving 8 9 10 frequency. They adopted frequency scan method to cover the wide mass range and 11 12 13 raised the conversion dynode voltage up to 30 kV to increase secondary electron 14 15 signals. Singly charged secretory immunoglobulin A (385 kDa) ions were detected. 16 17 18 Reilly et al . demonstrated singly charged, intact proteins in the range of 10 to 200 19 20 21 kDa and 1.5 MDa urea particles can be detected by a linear quadrupole ion trap. 22 23 24 3.1.2 Light scattering 25 26
27 Photon is a fundamental light particle and used by light scattering method to Manuscript 28 29 30 detect ions because of its high sensitivity. Millikan’s oil drop experiment is the first 31 32 71 33 one to measure charges of microparticles by light scattering method. Wuerker et al . 34 35 36 demonstrated the capability of trapping and detection of single microparticles using a
37 Accepted 38 68 39 QIT mass spectrometer. Hars and Tass further proposed measuring the star like ion 40 41 42 motion in the radial plane to determine the mass of a single particle in the range of 43 44 9 12 3 72 45 10 10 Da with accuracy of 10 ; however, changes in charge states are not obvious Analyst 46 47 because of multi particle clumping during the injection of ions. Schlemmer et al . 48 49 50 developed fast Fourier transform technique to measure the single particle mass at r z 51 52 53 73, 74 plane. 500 nm SiO 2 particles were trapped in an ion trap with resolution (mass 54 55 56 deviation) of 10 4 in a 10 s measurement. Cai et al . further used QIT to trap and eject 57 58 59 60 Page 13 of 51 Analyst
1 2 3 75, 76 4 microparticles, and ions were detected via light scattering method. Single particle 5 6 7 mass spectra were acquired in mass selective instability mode. But absolute charge 8 9 10 states of trapped particles were not known in this study. Peng et al . observed a 11 12 13 stationary star pattern by fine tuning driving frequency to resonate with the radial 14 15 secular frequency in a QIT and obtained an analytical formula of secular frequency 16 17 18 that is valid for q <0.8.12, 53 Intact single Escherichia coli cells were generated by 19 z 20 21 MALDI ion source and their absolute mass was measured. 53 Besides, with laser 22 23 24 induced acoustic desorption (LIAD) ion source, viruses, bacteria, and mammalian 25 26
27 whole cells can be generated without confusion caused by MALDI clusters. The m/z Manuscript 28 29 30 of a particle can be measured with very high precision up to 10 4.77, 78 The QIT MS 31 32 33 adopted an averaging peak to peak voltage detector to measure rf amplitude which is 34 35 36 traced to a standard rf source and therefore QIT MS can be used as particle mass
37 Accepted 38 78 39 standard measurement with the particle size greater than 300 nm. 40 41 42 Trevitt et al . combined the secular frequency measurement with Mie scattering 43 44
45 measurement of single particle and found small uncertainties in secular frequency Analyst 46 47 measurement resulted in significant errors in the absolute mass and charges. But the 48 49 50 79 misalignment of QIT electrodes is small and trap parameter z 0 is appropriate. To 51 52 53 overcome low light collecting efficiency of QIT, Nie et al . used a cylindrical ion trap 54 55 56 (CIT) to replace the end cap electrodes by an electrically conductive glass plate that 57 58 59 60 Analyst Page 14 of 51
1 2 3 4 enables collection >10% of light radiating from the trapped particle. They 5 6 7 successfully detected recombinant human adenovirus type 5 (Ad5), grouper iridovirus 8 9 28 10 (GIV), and vaccinia virus (VV) with sizes range from 80 to 300 nm. 11 12 13 14 15 3.1.3 Laser induced fluorescence 16 17 18 Laser induced fluorescence (LIF) is widely used in flow cytometry to measure 19 20 21 the size distribution of nanoparticles. Cai et al . firstly attempted to integrate the LIF 22 23 24 with QIT to confine single particles with mass larger than 5 MDa in a trap. 80 They 25 26
27 successfully observed individual fluorescent 27 nm nanospheres which contains 180 Manuscript 28 29 30 fluorescein dye equivalents and an average signal to noise ratio of 10 has been 31 32 33 achieved. Moreover, they adopted another QIT to cool nanoparticles inside the QIT 34 35 58, 36 and monitor LIF of trapped particles to acquire the mass spectra of single particles.
37 Accepted 38 80 5 5 39 This configuration extended the mass analysis of nanoparticles with m/z > 10 . 40 41 42 Recently, Talbot et al . used LIF to visualize populations of gaseous ions stored in a 43 44
45 quadrupole ion trap (QIT) mass spectrometer. This technique might help understand Analyst 46 47 the collective ion motion and the ejection behavior of high mass ions under high 48 49 50 buffer gas pressure. 81 51 52 53 54 55 56 3.1.4 Charge detector 57 58 59 60 Page 15 of 51 Analyst
1 2 3 4 Single particle QIT mass spectrometry can measure intact bioparticles, including 5 6 4 7 viruses, bacteria, and whole mammalian cells with high precision. But it takes about 8 9 10 15–30 minutes to determine the absolute mass of each trapped particle. Peng et al . 11 12 13 first proposed charge monitoring laser induced acoustic desorption mass spectrometry 14 15 (CMS) for rapid mass measurement of cells and microparticles. 27, 54 The CMS 16 17 18 simultaneously measure both the mass to charge ratio (m/z) and total charges (z) of a 19 20 21 particle. Typically more than 5 particles with S/N ratio of 10 are acquired in one 22 23 24 second. The background noise of the charge detector is about 500 e. CMS 25 26 + 27 successfully measured different types of mononuclear cells (CD3 lymphocytes and Manuscript 28 29 30 CD14 + monocytes) and cancer cells. Nie et al . followed this approach to acquire mass 31 32 33 and mass distributions of different red blood cells.82 Mass resolution of ∼100 and 34 35 83 36 mass accuracy of ∼1% can be achieved with this frequency scan CMS. Chen et al.
37 Accepted 38 39 measured the mass distribution of sinapinic acid matrix clusters from monomer to 40 41 22 42 MDa region with a CMS. In CMS, harmonic interference noises from an AC power 43 44
45 source and rf voltage interference noise from rf field affect the detection of a charge Analyst 46 47 detector. Chou et al. proposed an orthogonal wavelet packet decomposition (OWPD) 48 49 50 filtering approach to denoise interference from the acquired mass spectra. Mass 51 52 53 spectra of microparticles and Escherichia coli are obtained without rf interference. 84 54 55 56 When rf is applied on a QIT in high pressure condition (~80 mTorr), undesired arcing 57 58 59 60 Analyst Page 16 of 51
1 2 3 4 is produced; therefore, Xiong et al. adopted rectangular and triangular waveforms to 5 6 7 reduce the onset voltage and found their mass resolution is the same as that of 8 9 85 10 conventional sinusoidal waveform. Moreover, rectangular waveform technique can 11 12 69 13 detect large ions with a digital ion trap, which fosters the development of miniature 14 15 instrument with switching circuits instead of power amplifier. The power of CMS 16 17 18 instrument can be greatly reduced. To reduce the size of ion trap, Nie et al. have 19 20 21 shown that a miniature cylindrical ion trap mass spectrometer (CIT MS) equipped 22 23 24 with a mechanical pump can measure the masses of cells and microparticles.86 25 26
27 In applications, CMS is used to measure the quantity of nano /microparticles as Manuscript 28 29 30 efficient carriers for drug delivery. 87, 88 Quantitative measurement of the cellular 31 32 33 uptake of nano /microparticles is of great importance for the elucidation of the 34 35 36 mechanisms of cell endocytosis and exocytosis. We found CMS coulb be used to
37 Accepted 38 39 measure not only the cellular uptake of metal nanoparticles but also that of nonmetal 40 41 42 nano /microparticles and greatly reduced analysis time as compared to conventional 43 44
45 approaches such as inductively coupled plasma mass spectrometry (ICP MS) which Analyst 46 47 limits to metal nanoparticles. Nie et al. used CMS to characterize the column packing 48 49 50 materials in high performance liquid chromatography (HPLC). 89 The mass deviation 51 52 53 of the silica particles after modification by different length of alkyl chains can also be 54 55 56 determined using CMS. The specific surface area, carbon load, and size distribution 57 58 59 60 Page 17 of 51 Analyst
1 2 3 4 of packing materials are characterized simultaneously too. Nie et al. showed CMS can 5 6 7 be incorporated with an ambient desorption source to measure masses of 8 9 90 10 microparticles. The ambient desorption method exploited the discontinuous 11 12 13 atmospheric pressure interface (DAPI) to generate and desorb microparticles under 14 15 atmospheric pressure with a pulsed airflow as shown in Figure 1. Bacteria, cells, 16 17 18 polystyrenes, synthetic diamonds, and silica particles can be directly desorbed in 19 20 21 ambient condition. 22 23 24 Furthermore, a charge detector can measure the quantity of molecules. Peng et al. 25 26 27 27 first measured the C 60 signals with a QIT MS. Chen et al. measured IgG and IgM Manuscript 28 29 30 ions. 91 To increase the number of ions and ion signal, a possible way is to incorporate 31 32 33 a charge detector with LIT MS. 34 35 36
37 Accepted 38 39 3.2 Time of flight mass spectrometry 40 41 42 MALDI ion source is frequently coupled with time of flight (TOF) mass 43 44 92 45 spectrometer. The mass range of TOF MS should be unlimited in theory; however, Analyst 46 47 its mass range is limited by the sensitivity of a detector in practice. Conventional 48 49 50 secondary electron detectors, e.g. MCP are incorporated with TOF MS and the 51 52 53 detection limit is < 1 MDa. Secondary ion detectors, cryogenic detectors, and 54 55 56 nanomembrane detectors are proposed to overcome the detection limit of TOF MS 57 58 59 60 Analyst Page 18 of 51
1 2 3 4 and now are able to detect ions with mass > 1 MDa. 5 6 7 8 9 10 3.2.1 Microchannel plates 11 12 13 The microchannel plate detector is widely used in TOF MS. Detection of human 14 15 IgM at m/z approximately 1 MDa is achieved by Williams et al .24 Li et al. further 16 17 18 demonstrated the detection of doubly charged polystyrene signals with molecular 19 20 21 weight up to 1.5 million.23 But the signal to noise ratio is poor and close to upper 22 23 24 limit of a MCP detector. To enhance the sensitivity of a MCP detector, Heeren et al. 25 26
27 developed an active pixel detector (MCP based detection system). The S/N ratio can Manuscript 28 29 30 be improved to a factor of ~4 in detecting IgA molecules. 49 31 32 33 34 35 36 3.2.2 Secondary ion detector
37 Accepted 38 39 A Daly detector is a gas ion detector which consists of a metal doorknob, a 40 41 93 42 scintillator (phosphor screen) and a photomultiplier. It was widely used in mass 43 44
45 spectrometers. Zenobi et al. collected the photons produced by the impact of ion Analyst 46 47 packets with a scintillator and demonstrated that an ion to photon detector showed 48 49 50 about 10 times higher signals than the MCP for heavy ions (150 kDa).48 Wang et al. 51 52 53 further developed a bipolar ion detector (BID) to detect secondary ions rather than 54 55 56 secondary electrons with a conversion dynode voltage at 25 kV. For ions with m/z ~ 57 58 59 60 Page 19 of 51 Analyst
1 2 3 47 4 90 000, the sensitivity of the BID is 1.4 14.4 times that of the MCP. 5 6 7 8 9 10 3.2.3 Cryogenic detector 11 12 13 Phonons are elementary excitations of crystal lattice. When ions impinge the 14 15 cryogenic detector, heats are generated and transferred to collective vibrations on 16 17 18 normalinsulator superconductor (NIS) microcalorimeter device near absolute zero 19 20 21 temperature. 94 A very small change in temperature resulting from interaction of NIS 22 23 24 microcalorimeter device and a particle leads to a significant change in resistance. The 25 26
27 junction current is measured by a high speed low noise series array superconducting Manuscript 28 29 30 quantum interference device (SQUID) preamplifier. Measuring the phonons is 31 32 33 therefore dependent on the energy not on particle masses and velocity of ions. Frank 34 35 36 et al. introduced a low temperature calorimetric detector to measure kinetic energy of
37 Accepted 38 95, 96 39 individual incident ions irrespective of their masses or charge state. Cryogenic 40 41 42 microcalorimeters and superconducting tunnel junctions are velocity independent and 43 44
45 phonon of ions at temperatures lower than hundred millikelvin are measured. Analyst 46 47 Recently, Zenobi et al. showed a 16 element superconducting tunnel junction (STJ) 48 49 50 detector coupled with a fully adjustable gimbal mounted ion source/focusing region 51 52 53 can allow unparalleled sensitivity for detection of singly charged immunoglobulin M 54 55 56 ions (~1MDa).97 Bier et al . further used the same 16 STJs detector and detected 57 58 59 60 Analyst Page 20 of 51
1 2 3 98, 99 4 polystyrene ions and virus capsids up to 2 MDa and 13 MDa, respectively. These 5 6 7 cryogenic particle detectors show good mass sensitivity at high mass range, but the 8 9 10 drawbacks of cryogenic detectors are expensive cryogenic cooling unit, low active 11 12 13 detection areas and long response time, and thus restrict their practical use. 14 15
16 17 18 3.2.4 Nanomembrane detector 19 20 21 A nanomembrane detector based on mechanical deformation and vibration of a 22 23 24 nanomembrane is developed to overcome the detection of high mass ions by Blick et 25 26 45, 46 27 al. Figure 2 shows the schematic design of nanomembrane detector with TOF MS. Manuscript 28 29 30 Mechanical vibrations of the nanomembrane excited by ion bombardment translate 31 32 33 into corresponding oscillations in the field emission current. The modulated field 34 35 36 emission current is amplified by the microchannel plate (MCP). High mass proteins
37 Accepted 38 39 such as IgG and IgM are measured with high mass resolution of 129±44 and 250±48. 40 41 45 42 In the right inset of Figure 2, the mass resolution (m/ m) becomes better as 43 44
45 molecular mass is increasing, which is because the rise time and decay constant are Analyst 46 47 highly independent on both mass and kinetic energy of the ion, and the time 48 49 50 resolution is highly dependent on the effective cooling of the silicon nanomembrane 51 52 53 via field emission. 54 55 56 57 58 59 60 Page 21 of 51 Analyst
1 2 3 4 3.2.5 Charge detector 5 6 7 Hillenkamp et al. developed a charge detector for ion detection in MALDI TOF 8 9 10 instruments. The charge detector comprises a 18 mm diameter metal electrode as a 11 12 13 Faraday charge collector and a charge sensitive FET preamplifier. A net charge of 14 15 4 16 1.8 ×10 is required for S/N ratio of 2. IgG ions can be detected with S/N ratio > 10. 17 18 With rise time of 25 ns, mass resolution for MALDI ion detection is not restricted to a 19 20 21 charge detector. To increase the sensitivity of a charge detector, Bouyjou et al. 22 23 24 developed a16 channel low power CMOS device and reached an equivalent noise 25 26 100 27 charge of 318 e . Manuscript 28 29 30 31 32 33 3.3 Charge detection mass spectrometry 34 35 36 Charge detection mass spectrometry (CDMS) measures the image charge of ions.
37 Accepted 38 39 Image charge detection of microparticles was first reported in 1960 by Shelton et al ., 40 41 42 who used pairs of conducting metal plates inside a shielded cylinder to detect charged 43 44 101 45 iron spheres in a high voltage accelerator system. With known time of flight of ions, Analyst 46 47 absolute masses of ions thus can be calculated. To measure the absolute masses of 48 49 50 particles accurately, two types of measurement were developed to increase the 51 52 53 signal to noise ratio. First is the recirculating trap which allows multiple paths of ions 54 55 56 in an electrostatic DC ion trap. 40 Second is the linear array which can extend the 57 58 59 60 Analyst Page 22 of 51
1 2 3 4 detection limit by √2 with multiple sensing stages. 56 5 6 7 8 9 10 3.3.1 Recirculating trap 11 12 13 Benner designed a gated electrostatic ion trap that can repetitiously measure the 14 15 charge and m/z of large electrospray ions. 40 The schematic design of this instrument is 16 17 18 shown in Figure 3. Once a single ion passing through the detector tube, the detector 19 20 21 displays an amplifier noise of 50 electrons. After averaging, noise can be reduced to 5 22 23 24 electrons. Jarrold et al . showed cooling of the JFET can increase its transconductance 25 26 55 27 and lower thermal noise, and thus improve the signal to noise (S/N) ratio. Single Manuscript 28 29 30 ions with 9 elementary charges have been detected while ADH monomer ions with 32 31 32 33 to 43 charges were trapped over 1500 cycles and the measured image charge is around 34 35 36 2.2 electrons. With CDMS, Jarrold et al. further measured the mass (23.6 MDa) and
37 Accepted 38 102 39 charge (427e) of bacteriophage P22 procapsids and detected intermediates of 40 41 103 42 hepatitis B virus capsids . 43 44
45 3.3.2 Linear array Analyst 46 47 Another thought to reduce noise is to arrange charge detectors in series. In Figure 48 49 50 4, Gamero Castano et al . showed the design and carefully calculated its charge 51 52 53 detection limit. 56 The detection limit and standard error of the charge measurement 54 55 56 can be reduced by factors of √2 and √ . Measurement of a droplet with time of 57 58 59 60 Page 23 of 51 Analyst
1 2 3 4 flight of 493 µs and charge noise of ~100 electrons were demonstrated. 5 6 7 8 9 10 3.4 Differential mobility analysis 11 12 13 Differential mobility analysis (DMA) is a routine analysis method used to 14 15 rapidly characterize viruses and virus like particles.42, 44 A DMA device is composed 16 17 18 of four major elements: a gas flow, a neutralizer, an electric field which is generated 19 20 21 by two flat electrodes and perpendicular to the gas flow, and a condensation particle 22 23 24 counter (CPC) placed at the end of one electrode for particle detection as depicted in 25 26 43 27 Figure 5. In a DMA device, a charged particle is driven by two forces, drag force Manuscript 28 29 30 (related to gas flow, particle drift, and particle size) and electric force (generated by 31 32 33 the interaction between electric field and particle charge). Specific particles can drift 34 35 36 into CPC in exact conditions; therefore, DMA is capable of separating charged
37 Accepted 38 42 39 particle based on their m/z or gas phase electrical mobility. Unlike typical MS 40 41 42 analyzers, drag force provides a big effect on particle motion because DMA is 43 44
45 operated at near atmospheric pressure with gas flow. So, the information of particle Analyst 46 47 sizes can be offered by DMA analysis. 48 49 50 Charge reduced electrospray differential mobility analysis (ES DMA) can 51 52 53 quantitatively analyze particle sizes from 0.7 to 800 nm. The notable precision of 24 54 55 56 nm particles separated by ES DMA is 1.2 nm (standard derivation). 104 The ES DMA 57 58 59 60 Analyst Page 24 of 51
1 2 3 4 is suitable for size analysis of whole viruses and virus fragments. For instance, S. 5 6 7 Guha et al . measured the PR772 and PR7 with ES DMA, and the mean sizes were 8 9 105 10 determined to be 62.1 ± 0.4 nm and 23.0 ± 0.3 nm, respectively. Hogan et al . also 11 12 13 analyzed bacteriophage MS2 and found its diameter was 24.13 ± 0.06 nm while the 14 15 capsid heads of large bacteriophages T2 and T4 88.32 nm ± 1.02 nm and 87.03 ± 0.18 16 17 18 nm, respectively. 43 Besides, ES DMA has capability of measuring the concentration 19 20 21 of virus in solution. Cole et al . determined the particle concentration of three 22 23 24 bacteriophages MS2, PP7, and ϕX174 which were similar to amino acid analysis in 25 26 106 27 most cases. Manuscript 28 29 30 31 32 33 3.5 Quadrupole orthogonal time of flight mass spectrometry 34 35 36 Using nanoflow electrospray with time of flight mass analysis, Robinson et al .
37 Accepted 38 39 showed that it is possible to obtain definitive charge states in the spectra of large 40 41 107 42 multiprotein complexes. In Figure 6a, GroEL complex shows a series of peaks 43 44
45 centered at m/z 10000. Next, bacteriophage MS2 was proved to maintain the intact Analyst 46 47 capsid in vacuum and had undergone collision induced dissociation (CID) with 48 49 50 neutral gas molecules and the CID mass spectrum was shown in Figure 6b.62 Heck et 51 52 53 al . further modified the Q TOF 1 instrument including the introduction of enhanced 54 55 56 pressure and altered electronics (e.g. quadrupole frequency, collision energy and TOF 57 58 59 60 Page 25 of 51 Analyst
1 2 3 4 pusher frequency), as well as specialized detectors to improve transmission and 5 6 30 7 measurement of very large ions. The instrument design is shown in Figure 7. HBV 8 9 10 capsids of 90 and of 120 dimers with masses of 3 and of 4 MDa were determined 11 12 60, 108 13 from m/z 20000 to 30000. The measured precision of both capsids is within 14 15 0.1%. 10.1 MDa norwalk virus like particles were measured as a function of solution 16 17 18 pH, ionic strength, and capsid protein concentration. 63 Figure 8 shows the intact 18 19 20 21 MDa capsids of bacteriophage HK97 measured with modified Q TOF 1 instrument 22 23 24 with a charge number of 350.64 It is noted that incomplete desolvation of specimen 25 26
27 causes the peak separation and overlapping around 40 GDa which limits the detection Manuscript 28 29 30 of large protein complexes from GDa to MDa. 31 32 33 34 35 36 3.6 Orbitrap mass spectrometry
37 Accepted 38 39 With an orbitrap mass analyzer, intact protein assemblies with molecular weight 40 41 41 31, 109 42 approaching one million Daltons were measured by Cooks and Heck et al. 43 44
45 Since the introduction of the first orbitrap based mass spectrometer in 2006, this mass Analyst 46 47 analyzer has become increasingly popular. 110 112 The orbitrap mass spectrometers are 48 49 50 used to analyze small molecules and peptides, but now these instruments can be 51 52 53 modified to analyze very large native protein assemblies. Shown in Figure 9 is a 54 55 56 dedicated instrumental modifications of an Exactive Plus instrument (ThermoFisher 57 58 59 60 Analyst Page 26 of 51
1 2 3 4 Scientific) with a higher energy collision induced dissociation (HCD) option. Briefly, 5 6 7 the modifications include altering software to allow detection of ions at higher m/z 8 9 10 range, tuning radiofrequency voltages of transport multipoles and altering the pressure 11 12 13 in the HCD cell. CsI clusters up to m/z of 18,000 were detected and a resolution of 14 15 25,000 was achieved at m/z of 5,000 and a resolution of 16,000 was obtained at m/z of 16 17 18 10,000. The full width at half maximum (FWHM) resolution of GroEL peaks (68+ to 19 20 21 77+ at m/z of 10,000 to 12,000) was close to 4,000, and the experimental molecular 22 23 24 weight was close to 1 MDa . Moreover, glycoforms for an antibody based construct 25 26 109 27 with a very heterogeneous glycan pattern were resolved and assigned. A few Manuscript 28 29 30 femtomoles of samples were required and data acquisition of single mass spectrum 31 32 33 was in few seconds. A resolution up to 12000 at m/z 6000 could be achieved with 34 35 36 high mass accuracy (~0.001%), thus allowing the assignment of modified antibodies.
37 Accepted 38 39 Kelleher and Makarov et al. further modified the Q Exactive plus instrument with 40 41 42 orthogonal ion injection interface, two ion funnels, a quadrupole filter and a high 43 44 2 32 45 pressure HCD cell (10 mbar). The signal to noise ratio can be enhanced with Analyst 46 47 orthogonal ion injection and ion funnels and the injection time was greatly reduced. 48 49 50 The ion transmission was extended to m/z 20000 and ions can be mass selected in this 51 52 53 mass range. Isolation window was about 70 in the m/z range exceeding 10000 Th. 54 55 56 Tandem MS analysis of large protein complexes, such as phosporylase B (194 kDa), 57 58 59 60 Page 27 of 51 Analyst
1 2 3 3 4 pyruvate kinase (232 kDa), and GroEL (801 kDa) can be reached to MS . 5 6 7 8 9 10 4. Algorithms 11 12 13 Electrospray ionization coupled to native mass spectrometry (MS) has evolved as 14 15 an important tool in structural biology to decipher the composition of protein 16 17 18 complexes. 1, 20, 113 Commercial MS software was successfully developed to 19 20 21 investigate and assign mass spectra of proteins or peptides. It is proper for the 22 23 24 identification of charge state series of protein complexes as the charge state series are 25 26
27 sufficiently separated. However, overlapping charge state distributions, fine structure Manuscript 28 29 30 and peak broadening of heterogeneous samples hamper mass analysis. To facilitate 31 32 33 mass analysis, theory development and automation in the pre processing of raw mass 34 35 36 spectra, assigning peaks to ion series and deciphering the subunit compositions are
37 Accepted 38 39 discussed as below. 40 41 42 43 44
45 4.1 Theory Analyst 46 47 Conventional approach to assign ESI mass spectra of proteins was first invented 48 49 50 by Mann et al . They developed the first averaging and deconvolution algorithm to 51 52 53 assign charge states in ESI mass spectra of protein complexes. 114 The “averaging 54 55 56 algorithm”, assigns charge numbers to the ions associated with the m/z value for each 57 58 59 60 Analyst Page 28 of 51
1 2 3 4 peak and averages the resulting masses to give a best estimate of the molecular 5 6 7 masses. The “deconvolution algorithm”, transforms several peaks of multiply charged 8 9 10 ion into one peak corresponding to a singly charged ion as shown in Figure 10. 11 12 13 Moreover, maximum entropy approaches are often used to find the best assignment 14 15 and reduce the complexity in the spectra based on deconvolution algorithm. 115 120 16 17 18 These approaches are useful to analyze proteins of intermediate masses, but are not 19 20 21 able to correctly assign charge states of larger protein complexes, e.g. viral capsids or 22 23 24 nano /microparticles. Peng et al . introduced an LeastMass algorithm which is able to 25 26 18 27 achieve the charge states assignment of very high mass ions created by ESI. This Manuscript 28 29 30 algorithm searches a series of m/z peaks which can match the charge ratio as input 31 32 33 and the molecular mass are obtained by taking into account all possible charge states. 34 35 36 The plot of S/
37 Accepted 38 39 and
45 standard deviation theory, in which a harmonic oscillation indicates a correct charge Analyst 46 47 state assignment. Shown in Figure 11 is the analysis of HBV capsids. The periodic 48 49 50 pattern is observed in T=3 and T=4 ions when the correct charge is matched. 51 52 53 However, a selection of mixture peaks of T=3 and T=4 ions results in the loss of 54 55 56 periodicity. LeastMass can also help assign the correct charge states of single plasmid 57 58 59 60 Page 29 of 51 Analyst
1 2 3 4 DNA and PEG ions analyzed by Fourier transform ion cyclotron resonance (FTICR) 5 6 121, 122 7 mass spectrometer and 18 MDa capsids of bacteriophage HK97 by QTOF 1 8 9 64 10 instrument . 11 12 13 14 15 4.2 Raw data processing 16 17 18 Raw data processing is of importance to reduce analysis time. An algorithm that 19 20 21 can handle noisy raw mass spectra is necessary. The data pre processing requires 22 23 24 thorough smoothing, background subtraction, and an automatic threshold 25 26
27 determination. This is especially challenging when the signals are highly deformed Manuscript 28 29 30 and mixed with noises. 19 The automatic pre processing software can greatly reduce 31 32 33 analysis time and keep fidelity of acquired mass spectra. 34 35 36
37 Accepted 38 39 4.3 Search engine 40 41 42 A search engine, AutoMass, was developed by Peng et al . to automatically assign 43 44 19 45 ion series to peaks by game theory. AutoMass can define the correct boundary Analyst 46 47 between different distributions to yield accurate masses. It helps analyze the masses 48 49 50 and the boundary of heterogeneous protein assemblies with overlapping charge state 51 52 53 distributions, fine structure, and peak broadening. The boundaries of ion series in the 54 55 56 well resolved tandem mass spectra of the hepatitis B virus (HBV) capsids and those 57 58 59 60 Analyst Page 30 of 51
1 2 3 4 of the mass spectrum from CRISPR related cascade protein complex are accurately 5 6 7 assigned. In Figure 12, complicated tandem mass spectra derived from intact HBV 8 9 10 capsids at high collision energy conditions are analyzed. The generated HBV tandem 11 12 13 mass spectra of T = 3 and of T = 4 precursor ions with an accelerating voltage of 400 14 15 V are depicted in Figure 12a,c, and tandem mass analysis by AutoMass are shown in 16 17 18 Figure 12b,d, respectively. The deviation of the predicted and the measured oligomer 19 20 21 masses is less than 0.03%, far less than a single protein subunit. Moreover, less 22 23 24 well resolved mass spectra, for example, the norovirus capsid mass spectra at 25 26
27 different levels of desolvation are analyzed as well. Manuscript 28 29 30 31 32 33 4.4 Subunit complexes assignment 34 35 36 Morgner et al . introduced Massign to optimize data analysis by reducing spectra
37 Accepted 38 39 size, smoothing and subtracting background, identifying peaks, assigning ion series 40 41 42 and the number of possible subunit combinations by integrating information from 43 44 20 45 multiple sources. By adding connectivity and stoichiometry restraints into the Analyst 46 47 software, Massign reduces the number of potential complexes to one or two as shown 48 49 50 in Figure 13. In practice, the ion boundary has to be manually refined and potential 51 52 53 mass range, m/z range, and maximum possible charge are needed to be inputted 54 55 56 manually. Benesch et al . developed CHAMP software which can estimate the 57 58 59 60 Page 31 of 51 Analyst
1 2 3 123 4 distribution of different stoichiometries from overlapping and unresolved peaks. It 5 6 120 7 is similar to SOMMS but is more user friendly. Thalassinos et al . developed the 8 9 124 10 Amphitrite software, which is favorable to analyze ion mobility data and is 11 12 13 comparable to CHAMP and SOMMS in peak assignment. It can retrieve or compare 14 15 different ion shapes from very complex samples. 16 17 18 19 20 21 5. Choice of mass spectrometer 22 23 24 The mass spectrometric techniques are summarized in table 1. In the following, 25 26
27 we will discuss how to choose a proper mass spectrometric technique. Firstly, to Manuscript 28 29 30 measure masses of microparticles (e.g. cells), a quadrupole ion trap with a charge 31 32 33 detector would be favorable because it can measure masses and mass distribution of 34 35 27 36 cells in a short period of time. Besides, it can measure mass difference before and
37 Accepted 38 39 after cellular uptake of nanoparticles and adhesion of moleclues on microparticle 40 41 87, 89 42 surfaces and columns. Secondly, a quadrupole ion trap with light scattering can 43 44 12, 53 45 measure masses of single virus, bacteria and cells with high precision. With this Analyst 46 47 technique, changes in mass due to adhesion of molecules on single 48 49 50 nano /microparticles in vacuum can be studied. Thirdly, charge detection mass 51 52 53 spectrometry can measure the masses of viruses; 14, 103 however, multiple charge nature 54 55 56 of ESI causes wide mass distribution of ions and limits its application. Fourthly, ESI 57 58 59 60 Analyst Page 32 of 51
1 2 3 4 differential mobility analysis (DMA) is an alternative instrument to acquire the size 5 6 43 31, 41 7 distribution of nanoparticles rapidly. Fifthly, orbitrap and orthogonal quadrupole 8 9 62, 64 10 time of flight mass analyzers allow mass analysis of intact virus capsids and large 11 12 31 13 proteins. Tandem mass analysis offers the structure information. But when particle 14 15 size becomes larger, higher energy is required to activate and dissociate those 16 17 18 bioparticles . During activation and dissociation of nanoparticles, trapping frequency 19 20 21 in an ion trap device is not able to cover a board range. Tandem in space is therefore 22 23 24 favored than tandem in time technique. 125, 126 Mann et al. showed that dual linear ion 25 26 127 27 trap orbitrap instrument can increase sequence speed in proteomics research. Dual Manuscript 28 29 30 ion traps provide a possible solution to dissociate large ions to fragments by 31 32 58, 128 33 combining both tandem in time and tandem in space techniques. Sixthly, with the 34 35 36 help of AutoMass and Massign programs, analysis time of complicated ESI mass
37 Accepted 38 39 spectra can be greatly reduced. However, automated data preprocessing is required to 40 41 42 minimize the effect of deformed mass spectra of heterogeneous protein complexes, 43 44
45 reduce the size of data and speed up the analysis time. Seventhly, pulse nature of Analyst 46 47 MALDI ion source is suitable to couple with time of flight mass analyzer to acquire 48 49 50 simple mass spectra. TOF MS with a cryogenic detector, an active pixel detector and 51 52 53 a nanomembrane detector can now extend mass detection from hundred kDa to MDa. 54 55 56 But tandem mass analysis of high mass ions in a TOF TOF instrument and low 57 58 59 60 Page 33 of 51 Analyst
1 2 3 4 ionization efficiency of MALDI ion source in detecting large bioparticles (>100 kDa) 5 6 7 are still very challenging. The use of a charge detector with TOF MS and quadrupole 8 9 10 ion trap MS can help understand quantity of ions and examine the possible ionization 11 12 13 mechanism. Finally, mass resolution in high mass range and isotopic analysis of high 14 15 mass biomolecules 129 are still challenging for both FTICR and orbitrap mass 16 17 18 analyzers. 19 20 21 22 23 24 6. Conclusions and Future Outlook 25 26
27 Single particle quadrupole mass spectrometry approach provides accurate mass Manuscript 28 29 30 measurement with particle sizes from 80 nm to 10 m.4 But it is not suitable for high 31 32 33 speed analysis. Cell mass spectrometry offers destructive measurement of cells with 34 35 27 36 sizes from 700 nm to 30 m. It offers high speed analysis of cells. Charge detection
37 Accepted 38 39 mass spectrometry proposed non destructive determination of particle charges. The 40 41 42 signal to noise can be enhanced with increasing multiple paths of ions. The use of a 43 44 98 45 cryogenic detector in TOF MS can extend the detection limit up to 2 MDa. With Analyst 46 47 nanomembrane detectors, IgM molecules can be detected with TOF MS with a 48 49 50 resolution of ~250. 45 Differential mobility analysis (DMA) is now available to rapidly 51 52 53 characterize viruses and virus like particles. 18 MDa viral particles with charges up to 54 55 56 350 are explored.64 The mass resolution has reached the instrumental limit of 57 58 59 60 Analyst Page 34 of 51
1 2 3 4 quadrupole orthogonal TOF MS. Orbitrap MS might be a promising solution to 5 6 32 7 improve mass resolution in analyzing large bioparticles to MDa mass range. The 8 9 10 AutoMass, a game theory based search engine, can successfully assign the very 11 12 19 13 complicated tandem mass spectra of HBV capsids with m/z from 40000 to 80000. 14 15 Moreover, Massign can simplify the assignment of different subunit combinations in 16 17 18 large heterogeneous systems. 20 Overall, mass spectrometric techniques are powerful 19 20 21 tools and continuing to provide valuable mass and structure information of large 22 23 24 biomolecules and bioparticles. 25 26
27 Manuscript 28 29 30 DISCLOSURE STATEMENT 31 32 33 The author is not aware of any affiliations, memberships, funding, or financial 34 35 36 holdings that might be perceived as affecting the objectivity of this review.
37 Accepted 38 39 40 41 42 ACKNOWLEDGMENTS 43 44
45 The author thanks National Dong Hwa University (NSC 102 2112 M 259 003 MY3) Analyst 46 47 and the National Science Council of Taiwan, Republic of China, for continuous 48 49 50 support of his work over the past six years. 51 52 53 54 55 56 57 58 59 60 Page 35 of 51 Analyst
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37 74. S. Schlemmer, S. Wellert, F. Windisch, M. Grimm, S. Barth and D. Gerlich, Accepted 38 Appl Phys A , 2004, 78 , 629 636. 39 75. Y. Cai, W. P. Peng, S. J. Kuo, Y. T. Lee and H. C. Chang, Anal. Chem. , 2001, 40 41 74 , 232 238. 42 76. Y. Cai, W. P. Peng, S. J. Kuo and H. C. Chang, International Journal of Mass 43 44 Spectrometry , 2002, 214 , 63 73. 45 77. W. P. Peng, Y. C. Yang, C. W. Lin and H. C. Chang, Anal. Chem. , 2005, 77 , Analyst 46 47 7084 7089. 48 78. W. P. Peng, Y. T. Lee, J. W. Ting and H. C. Chang, Review of Scientific 49 50 Instruments , 2005, 76 , 023108. 51 79. A. J. Trevitt, P. J. Wearne and E. J. Bieske, International Journal of Mass 52 Spectrometry , 2007, 262 , 241 246. 53 54 80. Y. Cai, W. P. Peng, S. J. Kuo, S. Sabu, C. C. Han and H. C. Chang, Anal. 55 Chem. , 2002, 74 , 4434 4440. 56 57 81. F. Talbot, S. Sciuto and R. Jockusch, Journal of The American Society for 58 59 60 Page 39 of 51 Analyst
1 2 3 Mass Spectrometry , 2013, 24 , 1823 1832. 4 5 82. Z. Nie, F. Cui, Y. K. Tzeng, H. C. Chang, M. Chu, H. C. Lin, C. H. Chen, H. H. 6 Lin and A. L. Yu, Anal. Chem. , 2007, 79 , 7401 7407. 7 8 83. Z. Nie, F. Cui, M. Chu, C. H. Chen, H. C. Chang and Y. Cai, International 9 Journal of Mass Spectrometry , 2008, 270 , 8 15. 10 84. S. W. Chou, G. R. Shiu, H. C. Chang and W. P. Peng, Journal of The 11 12 American Society for Mass Spectrometry , 2012, 23 , 1855 1864. 13 85. C. Xiong, G. Xu, X. Zhou, J. Wang, Y. Tang, R. Chen, W. P. Peng, H. C. 14 15 Chang and Z. Nie, Analyst , 2012, 137 , 1199 1204. 16 86. Z. Zhu, C. Xiong, G. Xu, H. Liu, X. Zhou, R. Chen, W. P. Peng and Z. Nie, 17 18 Analyst , 2011, 136 , 1305 1309. 19 87. H. C. Lin, H. H. Lin, C. Y. Kao, A. L. Yu, W. P. Peng and C. H. Chen, Angew 20 21 Chem Int Edit , 2010, 49 , 3460 3464. 22 88. W. P. Peng, C. H. Chen and A. L. Yu, G.I.T. Laboratory Journal , 2010, 9-10 , 23 32 35. 24 25 89. C. Q. Xiong, X. Y. Zhou, R. Chen, Y. M. Zhang, W. P. Peng, Z. X. Nie, H. C. 26 Chang, H. W. Liu and Y. Chen, Anal. Chem. , 2011, 83 , 5400 5406. 27 Manuscript 28 90. C. Xiong, X. Zhou, J. Wang, N. Zhang, W. P. Peng, H. C. Chang and Z. Nie, 29 Anal. Chem. , 2013, 85 , 4370 4375. 30 31 91. C. H. Chen, J. L. Lin, M. L. Chu and C. H. Chen, Anal. Chem. , 2010, 82 , 32 10125 10128. 33 34 92. K. G. Standing, International Journal of Mass Spectrometry , 2000, 200 , 35 597 610. 36
37 93. N. R. Daly, Review of Scientific Instruments , 1960, 31 , 264 267. Accepted 38 94. G. C. Hilton, J. M. Martinis, D. A. Wollman, K. D. Irwin, L. L. Dulcie, D. 39 Gerber, P. M. Gillevet and D. Twerenbold, Nature , 1998, 391 , 672 675. 40 41 95. M. Frank, S. E. Labov, G. Westmacott and W. H. Benner, Mass Spectrometry 42 Reviews , 1999, 18 , 155 186. 43 44 96. M. Frank, C. A. Mears, S. E. Labov, W. H. Benner, D. Horn, J. M. Jaklevic 45 and A. T. Barfknecht, Rapid Communications in Mass Spectrometry , 1996, 10 , Analyst 46 47 1946 1950. 48 97. R. J. Wenzel, U. Matter, L. Schultheis and R. Zenobi, Anal. Chem. , 2005, 77 , 49 50 4329 4337. 51 98. A. A. Aksenov and M. E. Bier, Journal of the American Society for Mass 52 Spectrometry , 2008, 19 , 219 230. 53 54 99. M. E. Bier, Flexible Package Conf. of the Society of Plastics Engineers , 2008, 55 Feb. 24 27th. 56 57 100. F. Bouyjou, H. Tap Beteille, J. Sauvaud, R. Molina and C. Aoustin, Integration 58 59 60 Analyst Page 40 of 51
1 2 3 of a 16 channel low power cmos instrumentation chain for electron and 4 5 charged particle detection in astrophysics, 2010. 6 101. H. Shelton, C. D. Hendricks and R. F. Wuerker, Journal of Applied Physics , 7 8 1960, 31 , 1243 1246. 9 102. D. Z. Keifer, E. E. Pierson, J. A. Hogan, G. J. Bedwell, P. E. Prevelige and M. 10 F. Jarrold, Rapid Communications in Mass Spectrometry , 2014, 28 , 483 488. 11 12 103. E. E. Pierson, D. Z. Keifer, L. Selzer, L. S. Lee, N. C. Contino, J. C. Y. Wang, 13 A. Zlotnick and M. F. Jarrold, Journal of the American Chemical Society , 14 15 2014, 136 , 3536 3541. 16 104. R. Anumolu, J. A. Gustafson, J. J. Magda, J. Cappello, H. Ghandehari and L. F. 17 18 Pease, ACS Nano , 2011, 5, 5374 5382. 19 105. S. Guha, L. F. Pease Iii, K. A. Brorson, M. J. Tarlov and M. R. Zachariah, 20 21 Journal of Virological Methods , 2011, 178 , 201 208. 22 106. K. D. Cole, L. F. Pease Iii, D. H. Tsai, T. Singh, S. Lute, K. A. Brorson and L. 23 Wang, Journal of Chromatography A , 2009, 1216 , 5715 5722. 24 25 107. A. A. Rostom and C. V. Robinson, Journal of the American Chemical Society , 26 1999, 121 , 4718 4719. 27 Manuscript 28 108. C. Uetrecht, C. Versluis, N. R. Watts, P. T. Wingfield, A. C. Steven and A. J. R. 29 Heck, Angewandte Chemie International Edition , 2008, 47 , 6247 6251. 30 31 109. S. Rosati, R. J. Rose, N. J. Thompson, E. van Duijn, E. Damoc, E. Denisov, A. 32 Makarov and A. J. R. Heck, Angewandte Chemie International Edition , 2012, 33 34 51 , 12992 12996. 35 110. A. Makarov, E. Denisov, A. Kholomeev, W. Balschun, O. Lange, K. Strupat 36
37 and S. Horning, Anal. Chem. , 2006, 78 , 2113 2120. Accepted 38 111. A. Makarov, Anal. Chem. , 2000, 72 , 1156 1162. 39 112. M. Hardman and A. A. Makarov, Anal. Chem. , 2003, 75 , 1699 1705. 40 41 113. A. R. McKay, B. T. Ruotolo, L. L. Ilag and C. V. Robinson, Journal of the 42 American Chemical Society , 2006, 128 , 11433 11442. 43 44 114. M. Mann, C. K. Meng and J. B. Fenn, Anal. Chem. , 1989, 61 , 1702 1708. 45 115. R. Winkler, Rapid Communications in Mass Spectrometry , 2010, 24 , 285 294. Analyst 46 47 116. J. J. Hagen and C. A. Monnig, Anal. Chem. , 1994, 66 , 1877 1883. 48 117. B. Reinhold and V. Reinhold, Journal of the American Society for Mass 49 50 Spectrometry , 1992, 3, 207 215. 51 118. H. Zheng, P. C. Ojha, S. McClean, N. D. Black, J. G. Hughes and C. Shaw, 52 Rapid Communications in Mass Spectrometry , 2003, 17 , 429 436. 53 54 119. A. Almudaris, D. Ashton, C. Beddell, D. Cooper, S. Craig and R. Oliver, 55 European Journal of Mass Spectrometry , 1996, 2, 57 67. 56 57 120. B. van Breukelen, A. Barendregt, A. J. R. Heck and R. H. H. van den Heuvel, 58 59 60 Page 41 of 51 Analyst
1 2 3 Rapid Communications in Mass Spectrometry , 2006, 20 , 2490 2496. 4 5 121. J. E. Bruce, X. Cheng, R. Bakhtiar, Q. Wu, S. A. Hofstadler, G. A. Anderson 6 and R. D. Smith, Journal of the American Chemical Society , 1994, 116 , 7 8 7839 7847. 9 122. X. Cheng, D. G. Camp, Q. Wu, R. Bakhtiar, D. L. Springer, B. J. Morris, J. E. 10 Bruce, G. A. Anderson, C. G. Edmonds and R. D. Smith, Nucleic Acids 11 12 Research , 1996, 24 , 2183 2189. 13 123. F. Stengel, A. J. Baldwin, M. F. Bush, G. R. Hilton, H. Lioe, E. Basha, N. Jaya, 14 15 E. Vierling and J. L. P. Benesch, Chem Biol , 2012, 19 , 599 607. 16 124. G. N. Sivalingam, J. Yan, H. Sahota and K. Thalassinos, International Journal 17 18 of Mass Spectrometry , 2013, 345–347 , 54 62. 19 125. M. Yang, J. M. Dale, W. B. Whitten and J. M. Ramsey, Anal. Chem. , 1995, 67 , 20 21 1021 1025. 22 126. J. V. Johnson, R. A. Yost, P. E. Kelley and D. C. Bradford, Anal. Chem. , 1990, 23 62 , 2162 2172. 24 25 127. J. V. Olsen, J. C. Schwartz, J. Griep Raming, M. L. Nielsen, E. Damoc, E. 26 Denisov, O. Lange, P. Remes, D. Taylor, M. Splendore, E. R. Wouters, M. 27 Manuscript 28 Senko, A. Makarov, M. Mann and S. Horning, Mol Cell Proteomics , 2009, 8, 29 2759 2769. 30 31 128. Y. F. Hsu, J. L. Lin, M. L. Chu and C. H. Chen, Analyst , 2013, 138 , 32 4823 4829. 33 34 129. L. Fornelli, J. Parra, R. Hartmer, C. Stoermer, M. Lubeck and Y. Tsybin, Anal 35 Bioanal Chem , 2013, 405 , 8505 8514. 36
37 130. H. Koizumi, W. B. Whitten and P. T. A. Reilly, Journal of the American Accepted 38 Society for Mass Spectrometry , 2008, 19 , 1942 1947. 39 131. H. Koizumi, X. Wang, W. B. Whitten and P. T. A. Reilly, Journal of the 40 41 American Society for Mass Spectrometry , 2010, 21 , 242 248. 42 132. J. Lee, H. Chen, T. Liu, C. E. Berkman and P. T. Reilly, Anal. Chem. , 2011, 83 , 43 44 9406 9412.
45 Analyst 46 47 48 49 50 51 52
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1 2 3 Figure Captions: 4 5 6 Figure 1(a) Experimental setup of an ambient desorption CMS which consists an AD 7 8 ion source, a QIT mass analyzer, and a charge detector. (b) Schematic of ambient 9 desorption process. The microparticles are desorbed by aerodynamic force and 10 inhaled into the mass spectrometer when discontinuous atmospheric 11 12 interface (DAPI) was open. Reprinted with permission from ref. 90. 13 14 15 Figure 2 A nanomembrane detector. (a) Schematic of the detector coupled to a 16 MALDI-TOF mass spectrometer. (b) Detailed illustration of the operation principle of 17 18 the detector. (c) Schematic of the detector configuration, consisting of a trilayer made 19 of Al/Si3N4/Al, an extraction gate, MCP, and an anode. The right inset is the MALDI 20 21 TOF mass spectrum of IgM with a nanomembrane detector (a) IgM mass spectrum. 22 Inset: histogram of IgM. (b) The FWHM mass resolution of the detector. Reprinted 23 from ref. 45 and ref. 46 with permission. 24 25 26 Figure 3 The gated electrostatic ion trap. Trapping plates on the left and right sides of 27 Manuscript 28 the detector module define the potential field that forces ions to cycle back and forth 29 through the detector tube. A support arm, attached to the bottom of the detector block, 30 31 holds the detector assembly rigidly to minimize vibrations and shields an internal FET 32 from rf noise. Reprinted with permission from ref. 40. 33 34 35 Figure 4 Induction charge detector with multiple sensing stages. Reprinted with 36
37 permission from ref. 56. Accepted 38 39 Figure 5 Schematic of the different components of the electrospray–differential 40 41 mobility analysis (ES–DMA) system. Reprinted with permission from ref. 43. 42 43 44 Figure 6 (a) Mass spectrum of GroEL. (b) CID mass spectrum of MS2 virus capsid 45 ions. Reprinted from ref. 107 and ref. 62 with permission. Analyst 46 47 48 Figure 7 Schematic layout of the modified Q-TOF 1 instrument (Micromass, U.K.). 49 50 Items in dark blue are modifications relative to the standard Q-TOF 1 configuration. 51 Reprinted with permission from ref. 30. 52
53 54 Figure 8 The assembly of HK97 capsids analyzed with native ESI-MS. a) Assembly 55 and maturation pathway of HK97. b) Free capsomers with penton signal in blue and 56 57 hexon signal in red. c) Intact Prohead-1 particle. Reprinted with permission from ref. 58 59 60 Page 43 of 51 Analyst
1 2 3 64. 4 5 6 Figure 9 Schematic of the modified Exactive Plus instrument with HCD option. 7 8 Reprinted with permission from ref. 31. 9 10 Figure 10 (a) Deconvolution of the cytochrome c (M = 12360) mass spectrum. The 11 12 theoretical positions of the first side peaks are marked by dark triangles. (b) "Zoom" 13 expansion of the spectrum in (a) for the mass range between 10 000 and 14 000. 14 15 Reprinted with permission from ref. 114. 16 17 18 Figure 11 (a) Mass spectrum of HBV ions. Analysis of HBV capsids (b) T = 3 ions, (c) 19 T = 4 ions, and (d) mixture of T = 3 and T = 4 ions in the overlapping m/z region. The 20 21 insert shows the selected m/z peaks for the analysis in part d. Reprinted with 22 permission from ref. 18. 23
24 25 Figure 12 AutoMass analysis of CID tandem mass spectra of HBV capsids at an 26 accelerating voltage of 400 V. (a) CID mass spectrum of T = 3 ions, (b) the AutoMass 27 Manuscript 28 analysis of (a), (c) CID mass spectrum of T = 4 ions, (d) the AutoMass analysis of (c). 29 N0 denotes the number of proteins in the oligomers. Reprinted with permission from 30 31 ref. 19. 32 33 34 Figure 13 Massign assignment of subunit complexes 5, 2, 3, and 4 are shown in (A), 35 (B), (C), and (D) respectively. Final assignment for all 4 complexes to the series is 36
37 shown in (E). Reprinted with permission from ref. 20. Accepted 38 39 40 41 42 43 44 45 Analyst 46 47 48 49 50 51 52
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1 2 3 Figure 1 4 5 6 7 8 9 10 11 12 13 14 15 16 Figure 2 17 18 19 20 21 22 23 24 25 26
27 Manuscript 28 29 30 31 32 33 34 Figure 3 35 36
37 Accepted 38 39 40 41 42 43 44
45 Analyst 46 47 48 49 50 51 52
53 54 55 56 57 58 59 60 Page 45 of 51 Analyst
1 2 3 Figure 4 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 Figure 5 20 21 22 23
24 25 26 27 Manuscript 28 29 30 31 32 33 34 35 36
37 Accepted 38 Figure 6 39 40 41 42 43 44
45 Analyst 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Analyst Page 46 of 51
1 2 3 Figure 7 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
24 25 26 Figure 8 27 Manuscript 28 29 30 31 32 33 34 35 36
37 Accepted 38 39 40 41 42 Figure 9 43 44 45 Analyst 46 47 48 49 50 51 52
53 54 55 56 57 58 59 60 Page 47 of 51 Analyst
1 2 3 Figure 10 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
24 25 26 27 Manuscript 28 29 30 31 32 33 34 35 36
37 Accepted 38 39 40 41 42 43 44 45 Analyst 46 47 48 49 50 51 52
53 54 55 56 57 58 59 60 Analyst Page 48 of 51
1 2 3 Figure 11 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
27 Manuscript 28 29 Figure 12 30 31 32 33 34 35 36
37 Accepted 38 39 40 41 42 43 44
45 Analyst 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Page 49 of 51 Analyst
1 2 3 Figure 13 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
27 Manuscript 28 29 30 31 32 33 34 35 36
37 Accepted 38 39 40 41 42 43 44 45 Analyst 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Analyst Page 50 of 51
1 2 3 Table 1. Comparison of physical mass spectrometric techniques available for large 4 5 biomolecules and bioparticles 6 7 Mass Analytes Analyzer/ detector Particle Particle Mass Mass Refs. 8 9 spectrometry Size (nm) mass resolution accuracy 10 techniques (Da) (m/∆m) 11 6 3 57,69 12 Quadrupole ion Micro particles, secondary electron <10 <10 10 10 13 trap mass nanodiamond, light scattering 10 10 3 <10 12 10 10 4 12, 28, 53, 68, 1% 14 spectrometry nanoparticles, bacteria/ 72 75, 77 79 15 16 viruses/cells laser induced 10 10 2 <10 5 5, 58, 80 17 fluorescence 18 19 charge detector 10 10 4 <10 16 ~10 2 1% 4, 27, 54, 82 85, 20 87 90 21 22 Linear ion trap protein, protein secondary electron, <10 1 <10 6 ~10 2 70, 130, 131 23 24 mass complexes, organic charge detector 25 spectrometry compounds 26
27 Time of flight protein, protein secondary electron, 10 10 2 <10 6 10 10 3 1% 23, 24, 45 48, Manuscript 28 95, 96 29 (TOF) mass complexes, organic cryogenic detector, 30 spectrometry compounds, polymer, nanomembrane, 31 nanoparticles charge detector 32 33 Charge detection micro particles, charge detector, 10 10 4 <10 12 10 10 2 40, 55, 56, 102 34 mass nanoparticles, protein, linear array, 35 36 spectrometry protein complex, viruses recirculating trap Accepted 37 38 39 Differential nanoparticles, DMA 10 10 4 10 9 10 12 10 10 2 43, 44, 104 106 40 41 mobility mass microparticles, bacteria/ 42 Spectrometry viruses 43 44 (DMA) Analyst 45 Quadrupole Protein, protein TOF, secondary 10 10 2 <10 6 10 10 3 0.1% 30, 60, 62 64, 46 47 orthogonal complexes, virus capsids electron 108, 132 48 time of flight 49 50 mass 51 spectrometry
52 2 6 4 31, 32, 41, 109 53 Orbitrap mass antibodies, viral cell, orbitrap 10 10 <10 ~10 0.001% 54 spectrometry protein, protein 55 Complexes 56 57 58 59 60 Page 51 of 51 Analyst
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
27 Manuscript 28 29 30 31 32 33 34 35 36
37 Accepted 38 39 40 41 42 43 44
45 Analyst 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60