Wolfram Language Paclet Repository

Community-contributed installable additions to the Wolfram Language

YingyingJin/ IMMSATD

Tools for plotting IM-MS ATD (Arrival TIme Distribution)

Contributed by: Yingying Jin

A Mathematica package for reading, processing, and visualizing Ion Mobility–Mass Spectrometry (IM-MS) Arrival Time Distributions (ATDs), with special tools to analyze and model oligomer behavior based on known monomer CCS. Ideal for biophysical researchers or mass spectrometry analysts studying oligomeric assemblies, especially in amyloid aggregation pathways where predicting and resolving complex arrival time distributions is crucial.

Installation Instructions

To install this paclet in your Wolfram Language environment, evaluate this code:
PacletInstall["YingyingJin/IMMSATD"]


To load the code after installation, evaluate this code:
Needs["YingyingJin`IMMSATD`"]

Details

Read and Smooth ATDs Supports .Mcs and .csv file formats using mcsreadatd and SmoothKernelDistribution, creating smoothed probability density functions from raw IM-MS data.
Peak Fitting Based on Known Monomer CCS Calculates theoretical arrival times of oligomers using a custom function IsoDriftTime, given parameters such as: Monomer CCS, Molecular weight,Charge,Drift voltage, pressure, temperature, and tube length
Arrival Time Prediction & Visualization -Plots predicted oligomer arrival times overlaid on experimental ATDs. -Labels peaks corresponding to specific oligomer orders (e.g., monomer, dimer, trimer). -Computes FWHM (full width at half max) of arrival time peaks, scaled by oligomer size.
Mobility Transformation & Plotting -Converts arrival times to inverse ion mobility (1/K₀) using InverseIonMobilityGraph -Plots ATDs in both time and mobility space with custom styling and color coding for different oligomers.

Examples

Basic Examples (3) 

Read MCS file and Plot the ATD (Note if input is CSV file, Use SmoothKernelDistribution[mIonCount[Import[XXX,"CSV"], with file formating as {{m/z, intensity},{m/z, intensity}…}):

In[1]:=
atd = SmoothKernelDistribution[InterpretationBox[FrameBox[TagBox[TooltipBox[PaneBox[GridBox[List[List[GraphicsBox[List[Thickness[0.0025`], List[FaceForm[List[RGBColor[0.9607843137254902`, 0.5058823529411764`, 0.19607843137254902`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3]]], List[List[List[205.`, 22.863691329956055`], List[205.`, 212.31669425964355`], List[246.01799774169922`, 235.99870109558105`], List[369.0710144042969`, 307.0436840057373`], List[369.0710144042969`, 117.59068870544434`], List[205.`, 22.863691329956055`]], List[List[30.928985595703125`, 307.0436840057373`], List[153.98200225830078`, 235.99870109558105`], List[195.`, 212.31669425964355`], List[195.`, 22.863691329956055`], List[30.928985595703125`, 117.59068870544434`], List[30.928985595703125`, 307.0436840057373`]], List[List[200.`, 410.42970085144043`], List[364.0710144042969`, 315.7036876678467`], List[241.01799774169922`, 244.65868949890137`], List[200.`, 220.97669792175293`], List[158.98200225830078`, 244.65868949890137`], List[35.928985595703125`, 315.7036876678467`], List[200.`, 410.42970085144043`]], List[List[376.5710144042969`, 320.03370475769043`], List[202.5`, 420.53370475769043`], List[200.95300006866455`, 421.42667961120605`], List[199.04699993133545`, 421.42667961120605`], List[197.5`, 420.53370475769043`], List[23.428985595703125`, 320.03370475769043`], List[21.882003784179688`, 319.1406993865967`], List[20.928985595703125`, 317.4896984100342`], List[20.928985595703125`, 315.7036876678467`], List[20.928985595703125`, 114.70369529724121`], List[20.928985595703125`, 112.91769218444824`], List[21.882003784179688`, 111.26669120788574`], List[23.428985595703125`, 110.37369346618652`], List[197.5`, 9.87369155883789`], List[198.27300024032593`, 9.426692008972168`], List[199.13700008392334`, 9.203690528869629`], List[200.`, 9.203690528869629`], List[200.86299991607666`, 9.203690528869629`], List[201.72699999809265`, 9.426692008972168`], List[202.5`, 9.87369155883789`], List[376.5710144042969`, 110.37369346618652`], List[378.1179962158203`, 111.26669120788574`], List[379.0710144042969`, 112.91769218444824`], List[379.0710144042969`, 114.70369529724121`], List[379.0710144042969`, 315.7036876678467`], List[379.0710144042969`, 317.4896984100342`], List[378.1179962158203`, 319.1406993865967`], List[376.5710144042969`, 320.03370475769043`]]]]], List[FaceForm[List[RGBColor[0.5529411764705883`, 0.6745098039215687`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[44.92900085449219`, 282.59088134765625`], List[181.00001525878906`, 204.0298843383789`], List[181.00001525878906`, 46.90887451171875`], List[44.92900085449219`, 125.46986389160156`], List[44.92900085449219`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6627450980392157`, 0.803921568627451`, 0.5686274509803921`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[355.0710144042969`, 282.59088134765625`], List[355.0710144042969`, 125.46986389160156`], List[219.`, 46.90887451171875`], List[219.`, 204.0298843383789`], List[355.0710144042969`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6901960784313725`, 0.5882352941176471`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[200.`, 394.0606994628906`], List[336.0710144042969`, 315.4997024536133`], List[200.`, 236.93968200683594`], List[63.928985595703125`, 315.4997024536133`], List[200.`, 394.0606994628906`]]]]]], List[Rule[BaselinePosition, Scaled[0.15`]], Rule[ImageSize, 10], Rule[ImageSize, 15]]], StyleBox[RowBox[List["mIonCount", " "]], Rule[ShowAutoStyles, False], Rule[ShowStringCharacters, False], Rule[FontSize, Times[0.9`, Inherited]], Rule[FontColor, GrayLevel[0.1`]]]]], Rule[GridBoxSpacings, List[Rule["Columns", List[List[0.25`]]]]]], Rule[Alignment, List[Left, Baseline]], Rule[BaselinePosition, Baseline], Rule[FrameMargins, List[List[3, 0], List[0, 0]]], Rule[BaseStyle, List[Rule[LineSpacing, List[0, 0]], Rule[LineBreakWithin, False]]]], RowBox[List["PacletSymbol", "[", RowBox[List["\"YingyingJin/IMMSATD\"", ",", "\"YingyingJin`IMMSATD`mIonCount\""]], "]"]], Rule[TooltipStyle, List[Rule[ShowAutoStyles, True], Rule[ShowStringCharacters, True]]]], Function[Annotation[Slot[1], Style[Defer[PacletSymbol["YingyingJin/IMMSATD", "YingyingJin`IMMSATD`mIonCount"]], Rule[ShowStringCharacters, True]], "Tooltip"]]], Rule[Background, RGBColor[0.968`, 0.976`, 0.984`]], Rule[BaselinePosition, Baseline], Rule[DefaultBaseStyle, List[]], Rule[FrameMargins, List[List[0, 0], List[1, 1]]], Rule[FrameStyle, RGBColor[0.831`, 0.847`, 0.85`]], Rule[RoundingRadius, 4]], PacletSymbol["YingyingJin/IMMSATD", "YingyingJin`IMMSATD`mIonCount"], Rule[Selectable, False], Rule[SelectWithContents, True], Rule[BoxID, "PacletSymbolBox"]][ mcsreadatd[ BinaryReadList[ "/Users/yingyingjin/Box Sync/ESI_2023/120123/A315T_5uM/a1332a.Mcs"]]], 1.5]
Out[1]=

Plot the PDF:

In[2]:=
atdplot = Plot[PDF[atd, x], {x, 400, 1000}, Frame -> True, FrameStyle -> Black, PlotRange -> {0, 0.02}, FrameStyle -> Black, AspectRatio -> 1, PlotStyle -> {Black, Thick}, PlotRange -> All, ImageSize -> Small]
Out[2]=

Fitting the peaks base on isotropic drift time of known monomer CCS:

In[3]:=
nmer = {12, 8, 6, 4, 3, 2, 1};
In[4]:=
Clear[L]
In[5]:=
Atd1 = IsoDriftTime[{280, 1332, 1}, n -> #, T -> 303.5(*Kelvin*), P -> 5(*torr*), dV -> 90.2, t0 -> 240] & /@ nmer Atd = Atd1;
Out[5]=
In[6]:=
ShowATD = Show[ListPlot[{Atd[[#]], PDF[atd, Atd[[#]]]} & /@ Range[Length[Atd]], Filling -> Axis, PlotStyle -> {Red, FontSize -> 30}, PlotRange -> {{400, 1200}, {0, 0.04}}, Frame -> {{False, False}, {True, False}}, FrameStyle -> Black, AspectRatio -> 1, FrameLabel -> {Style["ATD (µs)", FontSize -> 14, Bold]}, ImageSize -> Small], atdplot]
Out[6]=

Details and Options (1) 

Color Coding the Peaks and converting arrival time distribution (ATD) into mobiligram (MG):

In[7]:=
mercolor = {{RGBColor[0.8, 0.31, 0.31], Dashing[{Small, Small}]}, {RGBColor[0.5, 0.69, 0.74], Dashing[{Small, Small}]}, {RGBColor[1, 0.5, 0], Dashing[{Small, Small}]}, {RGBColor[1., 0.85, 0.49], Dashing[{Small, Small}]}, {RGBColor[0.5, 0, 0.5], Dashing[{Small, Small}]}, {RGBColor[0.66, 0.71, 0.5], Dashing[{Small, Small}]}, {RGBColor[1, 0.5, 0.5], Dashing[{Small, Small}]}};
In[8]:=
mobilitygraph = ListLinePlot[ Table[{InverseIonMobilityGraph[x, dV -> 90.2, t0 -> 240], PDF[atd, x]}, {x, 300, 1200}], PlotRange -> {{0.1, 0.6}, {0, 0.03}}, Axes -> {True, False}, AspectRatio -> 1, PlotStyle -> {Black, Thick}, ImageSize -> Small, Frame -> True, FrameStyle -> Black, AspectRatio -> 1, FrameLabel -> {Style[ "1/\!\(\*SubscriptBox[\(K\), \(0\)]\) (\!\(\*FractionBox[\(Vs\), SuperscriptBox[\(cm\), \(2\)]]\))", FontSize -> 14, Bold]}]
Out[8]=
In[9]:=
ss = (FWHM[{Atd[[#]], 1}]*(nmer[[#]])^0.5)/5000 & /@ Range[1, Length[nmer]] NpeakMobility = {InverseIonMobilityGraph[Atd[[#]], t0 -> 240], PDF[atd, Atd[[#]]]} & /@ Range[1, Length[nmer]] A315T5uM15minIE20 = showMobilityATD[NpeakMobility, mobilitygraph, ss, 1, mercolor, 5]
Out[9]=
Out[4]=
Out[5]=

Scope (2) 

Calculate and plot the CCS based on the ATD data:

In[10]:=
ccs = CCSpoint[{Atd[[#]], 1332, 1}, t0 -> 240, T -> 303, P -> 5, n -> nmer[[#]]] & /@ Range[1, Length[nmer]]; ccsPlot = Table[{nmer[[i]], ccs[[i]]}, {i, 1, Length[nmer]}] listISOmer = Table[{i, 265*i^(2/3)}, {i, 1, 13}]; plistISOmer = ListLinePlot[listISOmer, AspectRatio -> 1, PlotRange -> {0, 1800}, Frame -> True, FrameStyle -> Black, FrameLabel -> {Style["Oligomeric State", Bold, FontSize -> 14], Style["CCS(\[Angstrom]2)", Bold, FontSize -> 14]}, ImageSize -> Small]; A315T5uM15minIE40CCS = Show[plistISOmer, ListPlot[ccsPlot, PlotStyle -> Red, PlotMarkers -> {"OpenMarkers", Medium}]]
Out[8]=
Out[5]=

Plot ATDs on step-field experiments:

In[11]:=
atd1 = "/Users/yingyingjin/Box Sync/ESI_2023/091223/a315t/b1332a.Mcs"; atd2 = "/Users/yingyingjin/Box Sync/ESI_2023/091223/a315t/b1332b.Mcs"; atd3 = "/Users/yingyingjin/Box Sync/ESI_2023/091223/a315t/b1332c.Mcs"; atd4 = "/Users/yingyingjin/Box Sync/ESI_2023/091223/a315t/b1332d.Mcs";
In[12]:=
Atd = {atd1, atd2, atd3, atd4};
In[13]:=
dist = SmoothKernelDistribution[InterpretationBox[FrameBox[TagBox[TooltipBox[PaneBox[GridBox[List[List[GraphicsBox[List[Thickness[0.0025`], List[FaceForm[List[RGBColor[0.9607843137254902`, 0.5058823529411764`, 0.19607843137254902`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3]]], List[List[List[205.`, 22.863691329956055`], List[205.`, 212.31669425964355`], List[246.01799774169922`, 235.99870109558105`], List[369.0710144042969`, 307.0436840057373`], List[369.0710144042969`, 117.59068870544434`], List[205.`, 22.863691329956055`]], List[List[30.928985595703125`, 307.0436840057373`], List[153.98200225830078`, 235.99870109558105`], List[195.`, 212.31669425964355`], List[195.`, 22.863691329956055`], List[30.928985595703125`, 117.59068870544434`], List[30.928985595703125`, 307.0436840057373`]], List[List[200.`, 410.42970085144043`], List[364.0710144042969`, 315.7036876678467`], List[241.01799774169922`, 244.65868949890137`], List[200.`, 220.97669792175293`], List[158.98200225830078`, 244.65868949890137`], List[35.928985595703125`, 315.7036876678467`], List[200.`, 410.42970085144043`]], List[List[376.5710144042969`, 320.03370475769043`], List[202.5`, 420.53370475769043`], List[200.95300006866455`, 421.42667961120605`], List[199.04699993133545`, 421.42667961120605`], List[197.5`, 420.53370475769043`], List[23.428985595703125`, 320.03370475769043`], List[21.882003784179688`, 319.1406993865967`], List[20.928985595703125`, 317.4896984100342`], List[20.928985595703125`, 315.7036876678467`], List[20.928985595703125`, 114.70369529724121`], List[20.928985595703125`, 112.91769218444824`], List[21.882003784179688`, 111.26669120788574`], List[23.428985595703125`, 110.37369346618652`], List[197.5`, 9.87369155883789`], List[198.27300024032593`, 9.426692008972168`], List[199.13700008392334`, 9.203690528869629`], List[200.`, 9.203690528869629`], List[200.86299991607666`, 9.203690528869629`], List[201.72699999809265`, 9.426692008972168`], List[202.5`, 9.87369155883789`], List[376.5710144042969`, 110.37369346618652`], List[378.1179962158203`, 111.26669120788574`], List[379.0710144042969`, 112.91769218444824`], List[379.0710144042969`, 114.70369529724121`], List[379.0710144042969`, 315.7036876678467`], List[379.0710144042969`, 317.4896984100342`], List[378.1179962158203`, 319.1406993865967`], List[376.5710144042969`, 320.03370475769043`]]]]], List[FaceForm[List[RGBColor[0.5529411764705883`, 0.6745098039215687`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[44.92900085449219`, 282.59088134765625`], List[181.00001525878906`, 204.0298843383789`], List[181.00001525878906`, 46.90887451171875`], List[44.92900085449219`, 125.46986389160156`], List[44.92900085449219`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6627450980392157`, 0.803921568627451`, 0.5686274509803921`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[355.0710144042969`, 282.59088134765625`], List[355.0710144042969`, 125.46986389160156`], List[219.`, 46.90887451171875`], List[219.`, 204.0298843383789`], List[355.0710144042969`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6901960784313725`, 0.5882352941176471`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[200.`, 394.0606994628906`], List[336.0710144042969`, 315.4997024536133`], List[200.`, 236.93968200683594`], List[63.928985595703125`, 315.4997024536133`], List[200.`, 394.0606994628906`]]]]]], List[Rule[BaselinePosition, Scaled[0.15`]], Rule[ImageSize, 10], Rule[ImageSize, 15]]], StyleBox[RowBox[List["mIonCount", " "]], Rule[ShowAutoStyles, False], Rule[ShowStringCharacters, False], Rule[FontSize, Times[0.9`, Inherited]], Rule[FontColor, GrayLevel[0.1`]]]]], Rule[GridBoxSpacings, List[Rule["Columns", List[List[0.25`]]]]]], Rule[Alignment, List[Left, Baseline]], Rule[BaselinePosition, Baseline], Rule[FrameMargins, List[List[3, 0], List[0, 0]]], Rule[BaseStyle, List[Rule[LineSpacing, List[0, 0]], Rule[LineBreakWithin, False]]]], RowBox[List["PacletSymbol", "[", RowBox[List["\"YingyingJin/IMMSATD\"", ",", "\"YingyingJin`IMMSATD`mIonCount\""]], "]"]], Rule[TooltipStyle, List[Rule[ShowAutoStyles, True], Rule[ShowStringCharacters, True]]]], Function[Annotation[Slot[1], Style[Defer[PacletSymbol["YingyingJin/IMMSATD", "YingyingJin`IMMSATD`mIonCount"]], Rule[ShowStringCharacters, True]], "Tooltip"]]], Rule[Background, RGBColor[0.968`, 0.976`, 0.984`]], Rule[BaselinePosition, Baseline], Rule[DefaultBaseStyle, List[]], Rule[FrameMargins, List[List[0, 0], List[1, 1]]], Rule[FrameStyle, RGBColor[0.831`, 0.847`, 0.85`]], Rule[RoundingRadius, 4]], PacletSymbol["YingyingJin/IMMSATD", "YingyingJin`IMMSATD`mIonCount"], Rule[Selectable, False], Rule[SelectWithContents, True], Rule[BoxID, "PacletSymbolBox"]][ mcsreadatd[BinaryReadList[Atd[[#]]]]]] & /@ Range[1, Length[Atd]]; atd1332plot = Plot[PDF[dist[[#]], x], {x, 310, 950}, Frame -> True, FrameStyle -> Black, PlotRange -> {0, 0.02}, FrameStyle -> Black, AspectRatio -> 1, PlotStyle -> {Black, Thick}, PlotRange -> All] & /@ Range[1, Length[Atd]]
Out[14]=

Publisher

Yingying Jin

Compatibility

Wolfram Language Version 14

Version History

  • 1.0.6 – 19 August 2025
  • 1.0.5 – 19 August 2025
  • 1.0.4 – 04 August 2025
  • 1.0.3 – 04 August 2025
  • 1.0.2 – 03 August 2025
  • 1.0.1 – 03 August 2025
  • 1.0.0 – 03 August 2025

License Information

MIT License

Paclet Source

Source Metadata

  • Citation:
    • 1.Mason, E. A. & McDaniel, E. W. Transport Properties of Ions in Gases. 551–560 (1988) doi:10.1002/3527602852.indsub.
      2.Wyttenbach, T., Kemper, P. R. & Bowers, M. T. Design of a new electrospray ion mobility mass spectrometer. Int J Mass Spectrom 212, 13–23 (2001).
      3. Marchand, A., Livet, S., Rosu, F. & Gabelica, V. Drift Tube Ion Mobility: How to Reconstruct Collision Cross Section Distributions from Arrival Time Distributions? Anal Chem 89, 12674–12681 (2017).