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Materials Data on PrSm(Co2Ni3)2 by Materials Project

SmPr(Co2Ni3)2 crystallizes in the orthorhombic Pmmm space group. The structure is three-dimensional. Sm is bonded in a 6-coordinate geometry to six Co and twelve Ni atoms. There are two shorter (2.85 Å) and four longer (2.86 Å) Sm–Co bond lengths. There are eight shorter (3.18 Å) and four longer (3.19 Å) Sm–Ni bond lengths. Pr is bonded in a 6-coordinate geometry to six Co and twelve Ni atoms. All Pr–Co bond lengths are 2.87 Å. There are four shorter (3.19 Å) and eight longer (3.20 Å) Pr–Ni bond lengths. There are two inequivalent Co sites. In the first Co site, Co is bonded in a 12-coordinate geometry to two equivalent Sm, one Pr, and six Ni atoms. There are two shorter (2.46 Å) and four longer (2.47 Å) Co–Ni bond lengths. In the second Co site, Co is bonded in a 12-coordinate geometry to one Sm, two equivalent Pr, and six Ni atoms. There are four shorter (2.46 Å) and two longer (2.47 Å) Co–Ni bond lengths. There are three inequivalent Ni sites. In the first Ni site, Ni is bonded to four equivalent Pr, four equivalent Co, and four equivalent Ni atoms to form NiPr4Co4Ni4 cuboctahedra that share corners with sixteen NiPr2Sm2Co4Ni4 cuboctahedra, edges with ten NiPr2Sm2Co4Ni4 cuboctahedra, and faces with ten NiPr4Co4Ni4 cuboctahedra. All Ni–Ni bond lengths are 2.48 Å. In the second Ni site, Ni is bonded to four equivalent Sm, four equivalent Co, and four equivalent Ni atoms to form NiSm4Co4Ni4 cuboctahedra that share corners with sixteen NiPr2Sm2Co4Ni4 cuboctahedra, edges with ten NiPr2Sm2Co4Ni4 cuboctahedra, and faces with ten NiSm4Co4Ni4 cuboctahedra. All Ni–Ni bond lengths are 2.47 Å. In the third Ni site, Ni is bonded to two equivalent Sm, two equivalent Pr, four Co, and four Ni atoms to form a mixture of edge, face, and corner-sharing NiPr2Sm2Co4Ni4 cuboctahedra. There are one shorter (2.47 Å) and one longer (2.49 Å) Ni–Ni bond lengths.

36 MATERIALS SCIENCE↗

Materials Data on PrSm by Materials Project

SmPr is Magnesium-derived structured and crystallizes in the hexagonal P-6m2 space group. The structure is three-dimensional. Sm is bonded to six equivalent Sm and six equivalent Pr atoms to form SmPr6Sm6 cuboctahedra that share corners with eighteen equivalent SmPr6Sm6 cuboctahedra, edges with six equivalent SmPr6Sm6 cuboctahedra, edges with twelve equivalent PrPr6Sm6 cuboctahedra, faces with eight equivalent SmPr6Sm6 cuboctahedra, and faces with twelve equivalent PrPr6Sm6 cuboctahedra. All Sm–Sm bond lengths are 3.68 Å. All Sm–Pr bond lengths are 3.70 Å. Pr is bonded to six equivalent Sm and six equivalent Pr atoms to form PrPr6Sm6 cuboctahedra that share corners with eighteen equivalent PrPr6Sm6 cuboctahedra, edges with six equivalent PrPr6Sm6 cuboctahedra, edges with twelve equivalent SmPr6Sm6 cuboctahedra, faces with eight equivalent PrPr6Sm6 cuboctahedra, and faces with twelve equivalent SmPr6Sm6 cuboctahedra. All Pr–Pr bond lengths are 3.68 Å.

36 MATERIALS SCIENCE↗

Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection

Generating top-down tandem mass spectra (MS/MS) for complex mixtures of proteoforms has become possible through improvements in fractionation, on-line separation, dissociation, and mass analysis. The algorithms to match tandem mass spectra to sequences have undergone a parallel evolution, with both spectral alignment and peak matching being paired with diverse methods for scoring proteoform-spectral matches (PrSMs). This study assesses state-of-the-art algorithms for top-down identification through three distinct challenges. The first is identifying a large yield of PrSMs while controlling false discovery rate (FDR) in identifying thousands of proteoforms from complex cell lysates via four software workflows: ProSight Proteome Discoverer, TopPIC, Informed Proteomics, and pTop. The second is the deconvolution of data from both Thermo Orbitrap-class and Bruker maXis Q-TOF instruments to produce consistent precursor charge and mass determinations while generating fragment mass lists to optimize identification. The third attempts to detect diverse post-translational modifications (PTMs) in proteoforms from cow milk and human ovarian tissue. The data demonstrate that existing software suites produce admirable sensitivity, in some cases identifying a third of collected tandem mass spectra with FDR controlled below 2%; the overlap in these PrSMs, however, illustrates real value in searching data with multiple search engines. Differences among identification workflows seem to result from each search algorithm incorporating its own deconvolution algorithm. By transmitting deconvolution data from multiple deconvolution routes (Thermo Xtract, Bruker Auto MSn, Mascot Distiller, TopFD, and FLASHDeconv) to the downstream TopPIC search algorithm, we were able to detect common causes of deconvolution disagreement. The detection of PTMs was very inconsistent among search algorithms, with some workflows suggesting as little as 1% of PrSMs from cow’s milk were singly-phosphorylated while other workflows found that 18% of PrSMs were singly-phosphorylated. Taken together, these results make a strong argument for top-down researchers to adopt a standard practice of analyzing each MS/MS experiment with at least two different search engines.

59 BASIC BIOLOGICAL SCIENCES↗