Deep learning the collisional cross sections of the peptide universe from a million training samples

ABSTRACTThe size and shape of peptide ions in the gas phase are an under-explored dimension for mass spectrometry-based proteomics. To explore the nature and utility of the entire peptide collisional cross section (CCS) space, we measure more than a million data points from whole-proteome digests of five organisms with trapped ion mobility spectrometry (TIMS) and parallel accumulation – serial fragmentation (PASEF). The scale and precision (CV <1%) of our data is sufficient to train a deep recurrent neural network that accurately predicts CCS values solely based on the peptide sequence. Cross section predictions for the synthetic ProteomeTools library validate the model within a 1.3% median relative error (R > 0.99). Hydrophobicity, position of prolines and histidines are main determinants of the cross sections in addition to sequence-specific interactions. CCS values can now be predicted for any peptide and organism, forming a basis for advanced proteomics workflows that make full use of the additional information.

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Deep learning the collisional cross sections of the peptide universe from a million experimental values

Nature Communications ◽

10.1038/s41467-021-21352-8 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 2

Author(s):

Florian Meier ◽

Niklas D. Köhler ◽

Andreas-David Brunner ◽

Jean-Marc H. Wanka ◽

Eugenia Voytik ◽

...

Keyword(s):

Cross Section ◽

Cross Sections ◽

Peptide Sequence ◽

Peptide Ions ◽

Additional Information ◽

Deep Recurrent Neural Network ◽

Collisional Cross Section ◽

Data Points ◽

Main Determinants ◽

Experimental Values

AbstractThe size and shape of peptide ions in the gas phase are an under-explored dimension for mass spectrometry-based proteomics. To investigate the nature and utility of the peptide collisional cross section (CCS) space, we measure more than a million data points from whole-proteome digests of five organisms with trapped ion mobility spectrometry (TIMS) and parallel accumulation-serial fragmentation (PASEF). The scale and precision (CV < 1%) of our data is sufficient to train a deep recurrent neural network that accurately predicts CCS values solely based on the peptide sequence. Cross section predictions for the synthetic ProteomeTools peptides validate the model within a 1.4% median relative error (R > 0.99). Hydrophobicity, proportion of prolines and position of histidines are main determinants of the cross sections in addition to sequence-specific interactions. CCS values can now be predicted for any peptide and organism, forming a basis for advanced proteomics workflows that make full use of the additional information.

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A METHOD FOR EXTRACTING THE RESONANCE PARAMETERS FROM EXPERIMENTAL CROSS-SECTIONS

International Journal of Modern Physics E ◽

10.1142/s0218301313500328 ◽

2013 ◽

Vol 22 (05) ◽

pp. 1350032 ◽

Cited By ~ 5

Author(s):

S. A. RAKITYANSKY ◽

N. ELANDER

Keyword(s):

Experimental Data ◽

Cross Section ◽

Cross Sections ◽

Single Channel ◽

Analytic Structure ◽

Resonance Parameters ◽

S Matrix ◽

Analytic Expressions ◽

Data Points ◽

Pseudo Data

Within the proposed method, a set of experimental data points are fitted using a multi-channel S-matrix. Then the resonance parameters are located as its poles on an appropriate sheet of the Riemann surface of the energy. The main advantage of the method is that the S-matrix is constructed in such a way that it has proper analytic structure, i.e. for any number of two-body channels, the branching at all the channel thresholds is represented via exact analytic expressions in terms of the channel momenta. The way the S-matrix is constructed makes it possible not only to locate multi-channel resonances but also to extract their partial widths as well as to obtain the scattering cross-section in the channels for which no data are available. The efficiency of the method is demonstrated by two model examples of a single-channel and a two-channel problems, where known resonance parameters are rather accurately reproduced by fitting the pseudo-data artificially generated using the corresponding potentials.

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Can We Extract Production Cross-Sections from Thick Target Yield Measurements? A Case Study Using Scandium Radioisotopes

Instruments ◽

10.3390/instruments3020029 ◽

2019 ◽

Vol 3 (2) ◽

pp. 29 ◽

Cited By ~ 1

Author(s):

Mateusz Sitarz ◽

Jerzy Jastrzębski ◽

Férid Haddad ◽

Tomasz Matulewicz ◽

Katarzyna Szkliniarz ◽

...

Keyword(s):

Cross Section ◽

Cross Sections ◽

Production Cross ◽

Thick Target ◽

Cross Section Data ◽

Thick Target Yield ◽

Section Data ◽

Target Yield ◽

Data Points

In this work, we present an attempt to estimate the reaction excitation function based on the measurements of thick target yield. We fit a function to experimental data points and then use three fitting parameters to calculate the cross-section. We applied our approach to 43Ca(p,n)43Sc, 44Ca(p,n)44gSc, 44Ca(p,n)44mSc, 48Ca(p,2n)47Sc and 48Ca(p,n)48Sc reactions. A general agreement was observed between the reconstructions and the available cross-section data. The algorithm described here can be used to roughly estimate cross-section values, but it requires improvements.

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Electron Irradiation Effects in Polyoxymethylene Crystals Grown Inside Trioxane Crystals

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010006444x ◽

1971 ◽

Vol 29 ◽

pp. 78-79

Author(s):

J. P. Colson ◽

D. H. Reneker

Keyword(s):

Cross Section ◽

Cross Sections ◽

Detailed Examination ◽

The Other ◽

Electron Micrograph ◽

Irradiation Effects ◽

Threefold Axis ◽

Typical Sample ◽

Polymer Crystals ◽

Chain Axis

Polyoxymethylene (POM) crystals grow inside trioxane crystals which have been irradiated and heated to a temperature slightly below their melting point. Figure 1 shows a low magnification electron micrograph of a group of such POM crystals. Detailed examination at higher magnification showed that three distinct types of POM crystals grew in a typical sample. The three types of POM crystals were distinguished by the direction that the polymer chain axis in each crystal made with respect to the threefold axis of the trioxane crystal. These polyoxymethylene crystals were described previously.At low magnifications the three types of polymer crystals appeared as slender rods. One type had a hexagonal cross section and the other two types had rectangular cross sections, that is, they were ribbonlike.

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A quantitative approach to inner shell losses

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010010977x ◽

1978 ◽

Vol 36 (1) ◽

pp. 526-527 ◽

Cited By ~ 2

Author(s):

R.D. Leapman ◽

P. Rez ◽

D.F. Mayers

Keyword(s):

Energy Transfer ◽

Cross Section ◽

Cross Sections ◽

Accurate Determination ◽

Background Intensity ◽

Core Excitation ◽

Quantitative Basis ◽

Cross Section Differential ◽

Bound Electrons

Microanalysis by EELS has been developing rapidly and though the general form of the spectrum is now understood there is a need to put the technique on a more quantitative basis (1,2). Certain aspects important for microanalysis include: (i) accurate determination of the partial cross sections, σx(α,ΔE) for core excitation when scattering lies inside collection angle a and energy range ΔE above the edge, (ii) behavior of the background intensity due to excitation of less strongly bound electrons, necessary for extrapolation beneath the signal of interest, (iii) departures from the simple hydrogenic K-edge seen in L and M losses, effecting σx and complicating microanalysis. Such problems might be approached empirically but here we describe how computation can elucidate the spectrum shape.The inelastic cross section differential with respect to energy transfer E and momentum transfer q for electrons of energy E0 and velocity v can be written as

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Oxygen K near edge structures studied with multiple scattering calculations

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100104583 ◽

1988 ◽

Vol 46 ◽

pp. 504-505

Author(s):

Xudong Weng ◽

Peter Rez

Keyword(s):

Cross Section ◽

Cross Sections ◽

Partial Cross Section ◽

Energy Window ◽

Edge Structure ◽

Fine Structures ◽

Hydrogenic Model ◽

Electron Energy Loss ◽

Quantitative Chemical

In electron energy loss spectroscopy, quantitative chemical microanalysis is performed by comparison of the intensity under a specific inner shell edge with the corresponding partial cross section. There are two commonly used models for calculations of atomic partial cross sections, the hydrogenic model and the Hartree-Slater model. Partial cross sections could also be measured from standards of known compositions. These partial cross sections are complicated by variations in the edge shapes, such as the near edge structure (ELNES) and extended fine structures (ELEXFS). The role of these solid state effects in the partial cross sections, and the transferability of the partial cross sections from material to material, has yet to be fully explored. In this work, we consider the oxygen K edge in several oxides as oxygen is present in many materials. Since the energy window of interest is in the range of 20-100 eV, we limit ourselves to the near edge structures.

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Absolute inner-shell cross section determination for EELS analysis

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010010473x ◽

1988 ◽

Vol 46 ◽

pp. 534-535

Author(s):

P.A. Crozier

Keyword(s):

Cross Section ◽

Cross Sections ◽

Absolute Cross Section ◽

Specimen Thickness ◽

Mass Thickness ◽

Scattering Cross ◽

Before And After ◽

Estimated Error ◽

Scattering Cross Sections ◽

Electron Microscopist

Absolute inelastic scattering cross sections or mean free paths are often used in EELS analysis for determining elemental concentrations and specimen thickness. In most instances, theoretical values must be used because there have been few attempts to determine experimental scattering cross sections from solids under the conditions of interest to electron microscopist. In addition to providing data for spectral quantitation, absolute cross section measurements yields useful information on many of the approximations which are frequently involved in EELS analysis procedures. In this paper, experimental cross sections are presented for some inner-shell edges of Al, Cu, Ag and Au.Uniform thin films of the previously mentioned materials were prepared by vacuum evaporation onto microscope cover slips. The cover slips were weighed before and after evaporation to determine the mass thickness of the films. The estimated error in this method of determining mass thickness was ±7 x 107g/cm2. The films were floated off in water and mounted on Cu grids.

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A technique for preparing semiconductor cross sections for both TEM and SEM analysis

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100155530 ◽

1989 ◽

Vol 47 ◽

pp. 712-713

Author(s):

Stanley J. Klepeis ◽

J.P. Benedict ◽

R.M Anderson

Keyword(s):

Sample Preparation ◽

Cross Section ◽

Cross Sections ◽

Sem Analysis ◽

Preparation Technique ◽

Ion Milling ◽

Tem Analysis ◽

Polished Cross Section ◽

Area Of Interest ◽

Polished Side

The ability to prepare a cross-section of a specific semiconductor structure for both SEM and TEM analysis is vital in characterizing the smaller, more complex devices that are now being designed and manufactured. In the past, a unique sample was prepared for either SEM or TEM analysis of a structure. In choosing to do SEM, valuable and unique information was lost to TEM analysis. An alternative, the SEM examination of thinned TEM samples, was frequently made difficult by topographical artifacts introduced by mechanical polishing and lengthy ion-milling. Thus, the need to produce a TEM sample from a unique,cross-sectioned SEM sample has produced this sample preparation technique.The technique is divided into an SEM and a TEM sample preparation phase. The first four steps in the SEM phase: bulk reduction, cleaning, gluing and trimming produces a reinforced sample with the area of interest in the center of the sample. This sample is then mounted on a special SEM stud. The stud is inserted into an L-shaped holder and this holder is attached to the Klepeis polisher (see figs. 1 and 2). An SEM cross-section of the sample is then prepared by mechanically polishing the sample to the area of interest using the Klepeis polisher. The polished cross-section is cleaned and the SEM stud with the attached sample, is removed from the L-shaped holder. The stud is then inserted into the ion-miller and the sample is briefly milled (less than 2 minutes) on the polished side. The sample on the stud may then be carbon coated and placed in the SEM for analysis.

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Experimental Studies Of Multilayer Glass Structures On Compression, Compression With Bending And Simple Bending

Promyshlennoe i Grazhdanskoe Stroitel stvo ◽

10.33622/0869-7019.2019.01.22-30 ◽

2019 ◽

pp. 22-30

Keyword(s):

Cross Section ◽

Cross Sections ◽

Applied Load ◽

Experimental Studies ◽

Strength Properties ◽

Research Topic ◽

Normative Values ◽

Laminated Glass ◽

The Cross ◽

Experimental Values

The work of multilayer glass structures for central and eccentric compression and bending are considered. The substantiation of the chosen research topic is made. The description and features of laminated glass for the structures investigated, their characteristics are presented. The analysis of the results obtained when testing for compression, compression with bending, simple bending of models of columns, beams, samples of laminated glass was made. Overview of the types and nature of destruction of the models are presented, diagrams of material operation are constructed, average values of the resistance of the cross-sections of samples are obtained, the table of destructive loads is generated. The need for development of a set of rules and guidelines for the design of glass structures, including laminated glass, for bearing elements, as well as standards for testing, rules for assessing the strength, stiffness, crack resistance and methods for determining the strength of control samples is emphasized. It is established that the strength properties of glass depend on the type of applied load and vary widely, and significantly lower than the corresponding normative values of the strength of heat-strengthened glass. The effect of the connecting polymeric material and manufacturing technology of laminated glass on the strength of the structure is also shown. The experimental values of the elastic modulus are different in different directions of the cross section and in the direction perpendicular to the glass layers are two times less than along the glass layers.

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