Parsimonious Charge Deconvolution for Native Mass Spectrometry

Abstract

Charge deconvolution infers the mass from mass over charge (m/z) measurements in electrospray ionization mass spectra. When applied over a wide input m/z or broad target mass range, charge-deconvolution algorithms can produce artifacts, such as false masses at one-half or one-third of the correct mass. Indeed, a maximum entropy term in the objective function of MaxEnt, the most commonly used charge deconvolution algorithm, favors a deconvolved spectrum with many peaks over one with fewer peaks. Here we describe a new “parsimonious” charge deconvolution algorithm that produces fewer artifacts. The algorithm is especially well-suited to high-resolution native mass spectrometry of intact glycoproteins and protein complexes. Deconvolution of native mass spectra poses special challenges due to salt and small molecule adducts, multimers, wide mass ranges, and fewer and lower charge states. We demonstrate the performance of the new deconvolution algorithm on a range of samples. On the heavily glycosylated plasma properdin glycoprotein, the new algorithm could deconvolve monomer and dimer simultaneously and, when focused on the m/z range of the monomer, gave accurate and interpretable masses for glycoforms that had previously been analyzed manually using m/z peaks rather than deconvolved masses. On therapeutic antibodies, the new algorithm facilitated the analysis of extensions, truncations, and Fab glycosylation. The algorithm facilitates the use of native mass spectrometry for the qualitative and quantitative analysis of protein and protein assemblies.

Functional diversification of hybridoma produced antibodies by CRISPR/HDR genomic engineering

“…To assess sortase-mediated conjugation a small nucleophilic peptide (GGGCK(FAM)) was Orbitrap instrument with extend mass range (EMR) as described before (42). Intact Mass software was used for zero-charge deconvolution of the spectra to determine the antibody mass (43).…”

Deconvolution in mass spectrometry based proteomics

“…Recently, parsimony was used in a charge deconvolution algorithm for the native MS of intact protein and glycoprotein complexes. The algorithm divided the deconvolution process into two sub‐problems as charge inference and peak sharpening …”

“…The algorithm divided the deconvolution process into two sub-problems as charge inference and peak sharpening. 48…”

FLASHDeconv: Ultrafast, high-quality feature deconvolution for top-down proteomics

“…Due to the high mass of the analytes, however, in mass spectrometry (MS)-based TD approach (TD-MS), a single protein species can result in multiple MS features with different charge states and isotopic envelopes, making the signal structure highly complex and, in turn, the accurate determination of proteoform masses challenging 9 . Feature deconvolution (i.e., the determination of intact proteoform masses) is thus an essential step for TD data analysis 10,11 .…”

“…Quality is another issue of these approaches. Mass artifacts and limitations with respect to mass or charge ranges reduce the methods' applicability 10,11,13 .…”