[feature request] mgf-fused compatibility with other tools

Adafede commented 3 years ago

Hi again,

Would it be feasible to obtain a fused-mgf with isotopic pattern and MS1 correlated ions written in it, as it is done for SIRIUS?

It would be really nice and I think that having thee clique correlations in it could be highly useful!

Would it be possible to have incremental values starting with 1 for the MS2SCANS (all MS1 to -1)? This would help for generating spectral networks as in GNPS or spec2vec.

Hereafter an example of the lines of such an MGF (generated by MZmine > export to Sirius)

BEGIN IONS
FEATURE_ID=68
PEPMASS=439.1789996172761
CHARGE=1
RTINSECONDS=72.315714
SPECTYPE=CORRELATED MS
MSLEVEL=1
FILENAME=210629_AR_12_bramble_8_1_pos;210629_AR_09_bramble_0_2_pos;210629_AR_11_bramble_7_1_pos;210629_AR_08_bramble_5_1_pos;210629_AR_13_bramble_0_3_pos;210629_AR_06_bramble_2_1_pos;210629_AR_10_bramble_6_1_pos;210629_AR_05_bramble_1_1_pos;210629_AR_04_bramble_0_1_pos;210629_AR_07_bramble_4_1_pos
SCANS=-1
439.1789996172761 2.5E7
440.1822573225499 4.5E6
441.18412023556925 9.5E5
442.1870353137215 1.3E5
END IONS

BEGIN IONS
FEATURE_ID=68
PEPMASS=439.1789996172761
CHARGE=1
RTINSECONDS=72.315714
MSLEVEL=2
FILENAME=210629_AR_12_bramble_8_1_pos;210629_AR_10_bramble_6_1_pos;210629_AR_05_bramble_1_1_pos;210629_AR_11_bramble_7_1_pos;210629_AR_08_bramble_5_1_pos;210629_AR_06_bramble_2_1_pos;210629_AR_07_bramble_4_1_pos
SCANS=68
MERGED_SCANS=658,678,646,642,666,642,639,663,637,661,635,659
MERGED_STATS=12 / 18 (6 removed due to low quality, 0 removed due to low cosine).
50.08512878417969 3.1E3
50.83534240722656 5.6E3
51.242713928222656 7.1E3
52.01398849487305 4.6E3
52.196685791015625 6.5E3
52.59766387939453 1.1E4
53.12872314453125 5.2E3
53.36445617675781 5.6E3
53.5899658203125 3.3E3
54.181121826171875 5.4E3
54.3321418762207 6.0E3
55.380760192871094 5.0E3
55.401729583740234 5.6E3
55.63516616821289 3.2E3
55.743064880371094 5.8E3
56.86734390258789 3.1E3
57.74196243286133 7.1E3
57.98003005981445 4.5E3
58.278072357177734 8.1E3
58.3421630859375 3.3E3
59.03913497924805 4.5E3
59.68634033203125 7.2E3
60.24223327636719 6.6E3
62.29823684692383 5.0E3
62.578800201416016 5.6E3
66.48686981201172 6.0E3
66.98571014404297 1.6E4
66.995849609375 6.5E3
67.1788101196289 1.6E4
67.99356842041016 5.3E3
71.47051239013672 3.5E3
72.276611328125 3.2E3
73.03571319580078 7.5E3
74.00833892822266 7.7E3
74.88280487060547 5.0E3
74.99490356445312 1.6E4
75.29606628417969 3.7E3
75.64757537841797 3.9E3
77.38615417480469 1.3E4
77.78624725341797 6.0E3
78.04827880859375 1.8E4
78.43748474121094 1.5E4
78.82537078857422 4.5E3
79.4976577758789 3.4E3
80.95541381835938 3.5E3
81.20062255859375 3.6E3
86.91014099121094 1.5E4
87.80812072753906 1.8E4
90.08291625976562 5.0E3
92.7730484008789 3.6E3
95.45011138916016 3.6E3
95.8768310546875 1.5E4
97.4272232055664 7.4E3
98.03407287597656 6.4E3
98.97550964355469 1.5E4
102.05142211914062 3.8E3
103.26054382324219 4.0E3
107.02253723144531 1.3E4
107.49016571044922 6.3E3
109.41071319580078 6.1E3
111.3140640258789 6.1E3
111.49977111816406 1.7E4
111.63798522949219 1.8E4
121.30016326904297 3.3E3
124.32919311523438 1.5E4
127.08543395996094 6.5E3
127.39874267578125 6.7E3
128.52391052246094 5.5E3
138.9855499267578 3.8E3
142.14781188964844 5.7E3
147.9310760498047 3.8E3
149.5344696044922 6.8E3
150.7562713623047 6.5E3
153.61341857910156 1.3E4
156.45423889160156 9.7E3
158.99514770507812 7.8E3
161.59744262695312 3.6E3
162.15785217285156 5.4E3
165.04714965820312 3.7E3
165.92715454101562 4.9E3
169.04818725585938 1.4E4
170.99710083007812 5.5E3
175.23463439941406 6.0E3
177.74778747558594 1.9E4
178.13275146484375 3.9E3
185.0416800407578 4.5E5
189.0068359375 6.8E3
189.4669647216797 8.5E3
200.28623962402344 4.2E3
201.9659423828125 4.3E3
205.7871856689453 1.5E4
208.00393676757812 3.7E3
209.40072631835938 4.8E3
219.01901245117188 6.4E3
222.53546142578125 4.1E3
224.6581573486328 7.7E3
227.36868286132812 4.0E3
229.3699188232422 6.2E3
231.08353890137707 3.3E7
232.08691988826865 2.9E5
238.91880798339844 6.5E3
245.8209228515625 5.1E3
247.4027099609375 4.4E3
249.00186157226562 8.7E3
262.6654968261719 4.2E3
265.0605346562779 2.0E4
275.1733093261719 9.8E3
278.6474304199219 7.8E3
280.5945739746094 4.0E3
290.86163330078125 4.1E3
296.39398193359375 6.2E3
299.88836669921875 3.9E3
314.1477966308594 2.1E4
330.30450439453125 5.2E3
333.08392333984375 9.1E3
346.6341857910156 7.9E3
354.96868896484375 9.3E3
371.0360412597656 1.7E4
392.9235534667969 2.4E4
398.16815185546875 4.0E3
398.21429443359375 6.7E3
404.3261413574219 5.8E3
407.2449035644531 4.4E3
410.5480651855469 7.4E3
431.23883056640625 6.0E3
436.6654968261719 8.7E3
448.4732360839844 4.9E3
452.3183898925781 4.8E3
460.8016052246094 1.0E4
END IONS

Hope it makes sense, best!

adelabriere commented 3 years ago

Hi, thanks for the suggestion about the first point, I actually never had any issue with GNPS on the SLAW generated MGF but I guess it would be easier to use this way. I ll change that.

For the inclusion of correlated ion that is a good point, I will add it. However I think that keeping an option where the MGF contains only MS2 is also a good practice. I will probably add a "format" parameter class which would allow to choose which kind of output you want of SLAW eg: MGF: MS2 or MGF: MS2+MS1.

Best, Alexis

Adafede commented 3 years ago

However I think that keeping an option where the MGF contains only MS2 is also a good practice.

100% agree, wonderful, can't wait!

Adafede commented 2 years ago

Closing it here since the repo moved, if a repost on the other repo is needed happy to do! :)

adelabriere / SLAW

[feature request] mgf-fused compatibility with other tools #3