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)

MeroX (Gotze Lab)

XlinkX (Heck Lab)

xiSearch (Rappsilber 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 (ASMB)
American society for Mass Spectrometry (ASMS)
Human Proteome Organization (HUPO)

Association of Biomolecular Resource Facilities (ABRF)
American Peptide Society (APS)

American Society of Hematology (ASH)

International Society on Thrombosis and Haemostasis (ISTH)
International Fibrin Research Society (IFRS)

Tissue Engineering and Regenerative Medicine International Society (TERMIS)
Colorado Biological Mass Spectrometry Society

Shock Society

Western Trauma Association

​

Databases

ProteomicsDB

The Human Protein Atlas

MatriNet

MatrixDB

Matrisome Project

ExoCarta

Meltome Atlas

MassIVE

GPMDB

PRIDE

ProteomeXchange

​