Proteomic Search Tools
Fragpipe (Nesvizhskii Lab)

Protein Prospector (UCSF)
Mascot (Matrix Science)
MaxQuant (Cox Lab)
Scaffold (Proteome Software)
Proteome Discoverer (Thermo Fisher)
pFind (He Lab)
MetaMorpheus (Smith Lab)

Data Independent Acquisition (DIA) Tools
Skyline (MacCoss Lab)
DIA-NN (Dr. Demichev, Ralser lab)

Spectronaut (Bionosys)
EncyclopeDIA (MacCoss Lab)

Cross-linking MS (CL-MS) Tools
pLink (He Lab)
XlinkX (Heck Lab)
ProXL (Davis Lab)

Proteome Processing and Analysis Tools
NormalyzerDE (Jakob Willforss)
Metaboanalyst (Xia Lab)
Morpheus (Broad Institute)
Jvenn (J.C. Oliveros)
Perseus (Cox Lab)
Panther Gene Ontology

Professional Societies
American society for Matrix Biology
American society for Mass Spectrometry
Human Proteome Organization
American Peptide Society
International Fibrin Research Society
Tissue Engineering and Regenerative Medicine International Society
Colorado Biological Mass Spectrometry Society

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Databases

ProteomicsDB

The Human Protein Atlas

MatrixDB

Matrisome Project

ExoCarta

Meltome Atlas

MassIVE

GPMDB

PRIDE

ProteomeXchange

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