Fetch isotopic images

%matplotlib inline
from matplotlib import pyplot as plt
import pandas as pd
import numpy as np
from metaspace import SMInstance
import getpass
sm = SMInstance()
sm

This notebook illustrates how to pull ion images for annotations from METASPACE. It will obtain and display all the isotope images for a set of annotations.

Enter your API Key (only required for private datasets)

To access private datasets on METASPACE, generate an API key from your account page and enter it when prompted below. This step can be skipped for accessing public datasets.

# This will prompt you to enter your API key if needed and it will save it to a config file.
# Note that API keys should be kept secret like passwords.
sm.save_login()

Analysis

Whilst the API does support access by dataset name, it’s most reliable to query using the dataset id. A quick hack to grab this through the web app is to filter the dataset then check the url:

The id for the selected dataset(s) can be copied from here e.g.

ht​tp.://metaspace2020.eu/#/annotations?ds=2016-09-22_11h16m17s&sort=-msm

ds = sm.dataset(id="2016-09-22_11h16m17s")
results = ds.results()
annotations = results[results.fdr <= 0.1][['msm']]
annotations.head()

		msm
formula	adduct
C40H80NO8P	+K	0.991456
C43H76NO7P	+Na	0.987877
C42H84NO8P	+K	0.987600
C37H71O8P	+K	0.987128
C44H86NO8P	+K	0.976368

Download and plot all isotopic images for the first 5 annotations

limit = 5 # number of annotations to get
plt.figure(figsize=(20, 16))
for ii in range(limit):
    row = results.iloc[ii]
    (sf, adduct) = row.name
    images = ds.isotope_images(sf, adduct)
    for j, im in enumerate(images):
        plt.subplot(limit, 4, ii * 4 + j + 1)
        plt.title("[{}{}]+ m/z {}".format(sf, adduct, images.peak(index=j)))
        plt.imshow(images[j], cmap='viridis')
plt.show()

Bulk-download one image per annotation and calculate the pearson correlation between images

isotope_image_sets = ds.all_annotation_images(fdr=0.10, only_first_isotope=True, scale_intensity=False)

# Convert images into the format NumPy expects: a 2D array where each row
# is one annotation's pixels / each column is one pixel across all annotations
images = np.array([imgs[0].flatten() for imgs in isotope_image_sets])
labels = [(imgs.formula, imgs.adduct) for imgs in isotope_image_sets]
corr = np.corrcoef(images)
corr_df = pd.DataFrame(corr, index=labels, columns=labels)
corr_df

	(C40H80NO8P, +K)	(C43H76NO7P, +Na)	(C42H84NO8P, +K)	(C37H71O8P, +K)	(C44H86NO8P, +K)	(C41H83N2O6P, +K)	(C45H80NO7P, +Na)	(C40H80NO8P, +Na)	(C42H82NO8P, +K)	(C40H80NO8P, +H)	...	(C20H38O2, +H)	(C43H84NO8P, +H)	(C42H78NO8P, +H)	(C44H82NO8P, +H)	(C43H87N2O6P, +K)	(C42H83O10P, +Na)	(C8H20NO6P, +K)	(C48H84NO8P, +K)	(C16H16O11S, +K)	(C45H78NO8P, +K)
(C40H80NO8P, +K)	1.000000	1.000000	0.952897	0.967237	0.245976	0.833225	0.952896	0.982682	0.848139	0.921046	...	-0.007426	0.851782	0.982674	0.933620	0.382377	0.952055	0.152810	0.490398	0.289137	0.636388
(C43H76NO7P, +Na)	1.000000	1.000000	0.952897	0.967237	0.245976	0.833225	0.952896	0.982682	0.848139	0.921046	...	-0.007426	0.851782	0.982674	0.933620	0.382377	0.952055	0.152810	0.490398	0.289137	0.636388
(C42H84NO8P, +K)	0.952897	0.952897	1.000000	0.928603	0.265837	0.769453	1.000000	0.958757	0.843311	0.878954	...	-0.004923	0.818077	0.958749	0.976383	0.477978	0.998177	0.155859	0.561101	0.287036	0.665877
(C37H71O8P, +K)	0.967237	0.967237	0.928603	1.000000	0.311083	0.826645	0.928601	0.959579	0.874272	0.867523	...	-0.006511	0.879146	0.959580	0.900842	0.381378	0.929519	0.212115	0.543898	0.413908	0.725554
(C44H86NO8P, +K)	0.245976	0.245976	0.265837	0.311083	1.000000	0.315141	0.265828	0.282098	0.663409	0.230023	...	0.008136	0.491154	0.282133	0.213727	0.259783	0.265818	0.740538	0.636748	0.721979	0.514660
(C41H83N2O6P, +K)	0.833225	0.833225	0.769453	0.826645	0.315141	1.000000	0.769453	0.841931	0.799991	0.750975	...	-0.004867	0.801050	0.841924	0.760261	0.308824	0.766656	0.340360	0.448071	0.326168	0.593814
(C45H80NO7P, +Na)	0.952896	0.952896	1.000000	0.928601	0.265828	0.769453	1.000000	0.958756	0.843308	0.878951	...	-0.004923	0.818067	0.958748	0.976380	0.477895	0.998177	0.155857	0.561080	0.287023	0.665875
(C40H80NO8P, +Na)	0.982682	0.982682	0.958757	0.959579	0.282098	0.841931	0.958756	1.000000	0.856468	0.915175	...	-0.007160	0.859451	0.999993	0.955873	0.427682	0.957449	0.168905	0.517190	0.305991	0.645559
(C42H82NO8P, +K)	0.848139	0.848139	0.843311	0.874272	0.663409	0.799991	0.843308	0.856468	1.000000	0.752610	...	0.000489	0.889056	0.856479	0.780084	0.430843	0.843408	0.501314	0.777492	0.593308	0.833599
(C40H80NO8P, +H)	0.921046	0.921046	0.878954	0.867523	0.230023	0.750975	0.878951	0.915175	0.752610	1.000000	...	-0.000408	0.863759	0.915163	0.896570	0.369670	0.876900	0.058189	0.408694	0.193200	0.515406
(C36H75N, +H)	-0.009600	-0.009600	-0.006478	-0.007373	0.011932	-0.007958	-0.006478	-0.008536	0.001118	-0.008468	...	0.932312	-0.004992	-0.008534	-0.008279	-0.000601	-0.007299	0.009374	0.008436	0.011921	-0.006137
(C45H91N2O6P, +Na)	-0.052784	-0.052784	-0.066423	-0.045096	0.051254	-0.037897	-0.066523	-0.039045	-0.035051	-0.026981	...	-0.001376	-0.001272	-0.039039	-0.048234	0.679391	-0.067202	0.015372	0.046015	0.081648	-0.064650
(C44H86NO8P, +H)	0.245644	0.245644	0.244563	0.266167	0.853654	0.283919	0.244544	0.275143	0.547783	0.368546	...	0.009352	0.519933	0.275162	0.244955	0.238411	0.243413	0.522728	0.414717	0.519774	0.297139
(C41H77O8P, +K)	0.210762	0.210762	0.221701	0.299568	0.978221	0.284668	0.221688	0.247133	0.620025	0.197050	...	0.008431	0.479948	0.247174	0.177315	0.229913	0.222255	0.737555	0.590756	0.764812	0.493705
(C44H86NO8P, +Na)	0.374057	0.374057	0.394609	0.436303	0.955099	0.466513	0.394577	0.427371	0.741378	0.382486	...	0.007935	0.629556	0.427405	0.365155	0.402833	0.394298	0.679352	0.667214	0.688418	0.572253
(C35H66O4, +H)	0.913117	0.913117	0.883293	0.973004	0.303228	0.791940	0.883290	0.920476	0.830891	0.847750	...	-0.005603	0.897092	0.920478	0.874707	0.376022	0.885332	0.172918	0.526275	0.401639	0.727048
(C45H78NO7P, +Na)	0.848139	0.848139	0.843311	0.874272	0.663409	0.799991	0.843308	0.856468	1.000000	0.752610	...	0.000489	0.889056	0.856479	0.780084	0.430843	0.843408	0.501314	0.777492	0.593308	0.833599
(C42H84NO8P, +H)	0.863766	0.863766	0.887750	0.801698	0.240099	0.672882	0.887751	0.876120	0.716219	0.955765	...	0.002122	0.820121	0.876103	0.914706	0.430544	0.885567	0.054280	0.438330	0.166587	0.489774
(C45H91N2O6P, +H)	-0.046544	-0.046544	-0.057529	-0.039530	0.046183	-0.033571	-0.057667	-0.036520	-0.029975	-0.017688	...	-0.001129	0.006288	-0.036515	-0.039828	0.641025	-0.058414	0.006987	0.045510	0.078993	-0.055700
(C42H84NO8P, +Na)	0.933645	0.933645	0.976458	0.900813	0.213180	0.760246	0.976458	0.955848	0.779990	0.896295	...	-0.006614	0.808984	0.955838	0.999879	0.471518	0.975507	0.091025	0.468234	0.221518	0.567425
(C46H90NO10P, +H)	-0.158368	-0.158368	-0.146483	-0.075452	0.844551	-0.098018	-0.146478	-0.128755	0.270007	-0.129845	...	0.012548	0.118463	-0.128715	-0.186785	-0.007145	-0.145936	0.599686	0.371394	0.639227	0.209528
(C44H80NO8P, +K)	0.712669	0.712669	0.634190	0.763761	0.545115	0.771138	0.634164	0.711596	0.866938	0.596540	...	-0.005017	0.777400	0.711613	0.557933	0.329890	0.634538	0.455223	0.700800	0.534026	0.815117
(C42H82NO8P, +Na)	0.881005	0.881005	0.872070	0.896388	0.603782	0.838684	0.872061	0.908116	0.970683	0.823794	...	-0.001476	0.927534	0.908125	0.853167	0.469023	0.871687	0.423398	0.707348	0.523192	0.764953
(C37H71O8P, +Na)	0.954757	0.954757	0.934630	0.978277	0.311323	0.830642	0.934629	0.971658	0.857565	0.884022	...	-0.007087	0.879542	0.971660	0.932100	0.418883	0.934401	0.192368	0.534684	0.378283	0.689998
(C40H79O10P, +Na)	0.999347	0.999347	0.951841	0.966621	0.237472	0.830904	0.951840	0.981573	0.842813	0.922001	...	-0.007330	0.850054	0.981564	0.933843	0.379390	0.951060	0.144795	0.482258	0.282528	0.630409
(C46H84NO8P, +K)	0.598949	0.598949	0.541537	0.656881	0.633622	0.766413	0.541488	0.615919	0.814744	0.505041	...	-0.001309	0.726755	0.615941	0.479559	0.389002	0.540876	0.567930	0.670072	0.565501	0.743202
(C28H33O14, +Na)	0.025906	0.025906	0.013698	0.039182	0.048013	0.029408	0.013688	0.034824	0.030510	0.046188	...	-0.001915	0.066998	0.034829	0.028291	0.222509	0.012846	0.017974	0.013835	0.053694	-0.017291
(C45H91N2O6P, +K)	-0.078443	-0.078443	-0.090400	-0.068159	0.138939	-0.060259	-0.090502	-0.062721	-0.018367	-0.045871	...	-0.002302	-0.000804	-0.062710	-0.073268	0.677184	-0.091331	0.070271	0.066088	0.131005	-0.071368
(C46H84NO8P, +H)	0.374061	0.374061	0.394577	0.436341	0.954995	0.466528	0.394545	0.427361	0.741312	0.382491	...	0.007937	0.629565	0.427395	0.365127	0.402726	0.394267	0.679322	0.667131	0.688433	0.572273
(C41H82NO8P, +H)	0.938958	0.938958	0.888678	0.932395	0.197604	0.797989	0.888675	0.935026	0.777460	0.948548	...	-0.007908	0.914281	0.935018	0.897701	0.361409	0.888487	0.058150	0.441738	0.209431	0.617771
(C41H83N2O6P, +Na)	0.790232	0.790232	0.750700	0.794648	0.335099	0.979850	0.750699	0.829114	0.781973	0.715908	...	-0.005648	0.779169	0.829108	0.757378	0.343047	0.747780	0.348768	0.454985	0.335521	0.583238
(C42H82NO8P, +H)	0.617407	0.617407	0.600632	0.612815	0.753103	0.571425	0.600625	0.637339	0.804308	0.721005	...	0.006482	0.813286	0.637345	0.590777	0.354026	0.599305	0.440937	0.609404	0.509301	0.556482
(C46H80NO8P, +K)	0.610930	0.610930	0.657352	0.659183	0.597602	0.491470	0.657343	0.628072	0.838353	0.517155	...	-0.002591	0.699062	0.628089	0.562409	0.462758	0.659030	0.410232	0.951021	0.553891	0.907534
(C37H68O4, +H)	0.680584	0.680584	0.684260	0.791282	0.715124	0.670272	0.684249	0.710134	0.897573	0.616228	...	0.001152	0.866172	0.710160	0.639643	0.390156	0.687006	0.505569	0.758991	0.696927	0.851164
(C39H75O8P, +K)	0.877262	0.877262	0.934213	0.925133	0.472458	0.738031	0.934212	0.896959	0.907352	0.783411	...	-0.003472	0.852741	0.896970	0.892038	0.490283	0.935419	0.330791	0.710169	0.520290	0.811476
(C42H82NO6P, +K)	-0.057401	-0.057401	-0.071163	-0.047388	0.066776	-0.040896	-0.071303	-0.044335	-0.032253	-0.029844	...	-0.001480	0.000079	-0.044328	-0.052903	0.682871	-0.072057	0.030825	0.043389	0.112792	-0.068358
(C26H30O12, +Na)	0.010865	0.010865	-0.001546	0.025708	0.026594	0.017037	-0.001561	0.018531	0.014167	0.026144	...	-0.001465	0.050583	0.018534	0.011355	0.186877	-0.002215	0.005312	0.005111	0.039767	-0.017069
(C39H79N2O6P, +K)	-0.023062	-0.023062	-0.050788	-0.019007	0.115662	0.058220	-0.050867	-0.003415	0.014955	0.005829	...	-0.002467	0.041734	-0.003408	-0.025108	0.598397	-0.052413	0.101190	0.012588	0.146437	-0.080461
(C39H73O8P, +K)	0.668030	0.668030	0.673405	0.760046	0.786346	0.662500	0.673399	0.688299	0.935355	0.568486	...	0.001652	0.810951	0.688329	0.599187	0.388371	0.675261	0.612481	0.824019	0.758521	0.870343
(C48H91NO8, +K)	-0.158368	-0.158368	-0.146483	-0.075452	0.844551	-0.098018	-0.146478	-0.128755	0.270007	-0.129845	...	0.012548	0.118463	-0.128715	-0.186785	-0.007145	-0.145936	0.599686	0.371394	0.639227	0.209528
(C10H7NO3, +K)	0.427481	0.427481	0.428150	0.554429	0.796830	0.470626	0.428135	0.455527	0.724911	0.369360	...	0.008353	0.604125	0.455564	0.372570	0.326230	0.428474	0.671104	0.654067	0.884128	0.674531
(C20H38O2, +H)	-0.007426	-0.007426	-0.004923	-0.006511	0.008136	-0.004867	-0.004923	-0.007160	0.000489	-0.000408	...	1.000000	-0.002736	-0.007158	-0.006625	0.000142	-0.005837	0.006002	0.007444	0.008340	-0.005509
(C43H84NO8P, +H)	0.851782	0.851782	0.818077	0.879146	0.491154	0.801050	0.818067	0.859451	0.889056	0.863759	...	-0.002736	1.000000	0.859456	0.809514	0.407435	0.818763	0.276569	0.625656	0.394536	0.744101
(C42H78NO8P, +H)	0.982674	0.982674	0.958749	0.959580	0.282133	0.841924	0.958748	0.999993	0.856479	0.915163	...	-0.007158	0.859456	1.000000	0.955863	0.427685	0.957441	0.168933	0.517213	0.306024	0.645578
(C44H82NO8P, +H)	0.933620	0.933620	0.976383	0.900842	0.213727	0.760261	0.976380	0.955873	0.780084	0.896570	...	-0.006625	0.809514	0.955863	1.000000	0.477581	0.975415	0.091060	0.468987	0.222420	0.567233
(C43H87N2O6P, +K)	0.382377	0.382377	0.477978	0.381378	0.259783	0.308824	0.477895	0.427682	0.430843	0.369670	...	0.000142	0.407435	0.427685	0.477581	1.000000	0.476365	0.169598	0.500062	0.268338	0.374949
(C42H83O10P, +Na)	0.952055	0.952055	0.998177	0.929519	0.265818	0.766656	0.998177	0.957449	0.843408	0.876900	...	-0.005837	0.818763	0.957441	0.975415	0.476365	1.000000	0.154454	0.561858	0.289387	0.669347
(C8H20NO6P, +K)	0.152810	0.152810	0.155859	0.212115	0.740538	0.340360	0.155857	0.168905	0.501314	0.058189	...	0.006002	0.276569	0.168933	0.091060	0.169598	0.154454	1.000000	0.473728	0.738939	0.402623
(C48H84NO8P, +K)	0.490398	0.490398	0.561101	0.543898	0.636748	0.448071	0.561080	0.517190	0.777492	0.408694	...	0.007444	0.625656	0.517213	0.468987	0.500062	0.561858	0.473728	1.000000	0.567532	0.863574
(C16H16O11S, +K)	0.289137	0.289137	0.287036	0.413908	0.721979	0.326168	0.287023	0.305991	0.593308	0.193200	...	0.008340	0.394536	0.306024	0.222420	0.268338	0.289387	0.738939	0.567532	1.000000	0.559128
(C45H78NO8P, +K)	0.636388	0.636388	0.665877	0.725554	0.514660	0.593814	0.665875	0.645559	0.833599	0.515406	...	-0.005509	0.744101	0.645578	0.567233	0.374949	0.669347	0.402623	0.863574	0.559128	1.000000

51 rows × 51 columns