Mass spectra for Deep learning algorithms, spectra knowleagebase

[ypriverol]

Here is a list of interesting projects that would be nice to have identified because they have been previously used in deep-learning training algorithms:

DDA datasets:

• PXD008034: 12
• PXD000269: 79
• PXD024364: Global detection of human variants and isoforms by deep proteome sequencing
• PXD004977: 42
• PXD001608: 60
• PXD002549: 89
• PXD002452: 179
• PXD001636: 60
• PXD004087: 72
• PXD001695: 234
• PXD002785: 22
• PXD000955: 196
• PXD003472: 36
• PXD001865: 144
• PXD002607: 36 (De novo PTM Peaks)
• PXD002908: 40
• MSV000085230
• PXD031812: 32
• PXD003002: 24
• PXD004276: 136
• PXD003189: 64
• PXD003583: 30
• PXD004321: 42
• PXD005126: 45
• PXD002912: 90

DeepMass Manuscript:

• PXD002908: 40
• PXD002912: 90
• PXD003668: 101
• PXD001608: 60
• PXD004977: 42
• PXD002549: 89
• PXD002452: 179
• PXD000955: 196
• PXD001865: 144
• PXD001695: 234
• PXD026436: 3
• PXD039809: 36
• PXD019483: 128

Prosit:

• PXD010871: 8 (This dataset do not contains spectra DDA)
• PXD034056: 6 (This dataset do not contains spectra)
• PXD004732: 1460
• PXD010595: 888
• PXD021013: 1865

ProteomeTools:

• PXD009449: 100
• PXD000138: 193

Ion mobility:

• PXD019086: 16

PTMs - ubiquitinome:

• PXD019854: 296

### PTMs - phospho:

• PXD019347: 36
• PXD021318: 8 (timsTOFF)
• PXD029545: 18
• PXD026805: 24
• PXD026824: 18

DIA- Pposphoproteomics:

• PXD014525: 426
• PXD017476: 20

DIA:

• PXD010012: 9 (timsTOFF)

### Single cell dataset:

• PXD019958: 9

HLA Datasets:

• PXD015489: 18
• MSV000084442
• PXD031709: 9
• PXD006939: 121
• PXD021398: 566
• MSV000087743
• MSV000084442
• MSV000084172
• PXD005231: 41
• PXD020011: 239
• PXD012308: 131
• PXD015408: 9
• PXD009925: 30
• PXD033868: 15
• PXD004894: 140
• PXD011628: 38
• PXD000394: 41
• PXD003790: 60
• PXD009738: 66
• PXD009531: 85
• PXD007635: 275
• PXD025655: 13 (https://www.mcponline.org/action/showPdf?pii=S1535-9476%2821%2900096-7)
• PXD017448: 6
• PXD013649: 85
• MSV000080527

Tumor, Cell line dataset:

• PXD003668: 101
• PXD004452: 1023

### Big datasets, tissue, species proteome:

• PXD010154: 1809
• PXD001250: 270
• PXD005485: 1104
• PXD014877: 366
• PXD005041: 48