Below are links to some useful external websites that offer a variety of web-based or downloadable tools for Proteomics

BioVenn - comparison and visualization of biological lists using area-proportional Venn diagrams

Blast - NCBI Basic Local Alignment Search Tool

ChemCalc - molecular mass calculator

Comet - an open source tandem mass spectrometry (MS/MS) sequence database search tool

Delta Mass - database of protein post-translational modifications

Entrez - NCBI database search and retrieval system

ExPASY - proteomics tools

IonSource - mass spectrometry tools and resources

NEWT - taxonomy database browser

PepNovo - de novo sequencing of low precision MS/MS data

Proteomics Tools - from Institute of systems Biology

ProXL - Analyze, Visualize,& Share Protein Cross-linking Data

Scaffold - download free viewer to read Scaffold (.sfd) files

Skyline – open source software for analysis of SRM/MRM/PRM/DIA/SWATH data

XlinkDB - Database and tools to store, visualize and predict protein interaction topologies

MS contaminant & detergent info:

Common background ions for mass spectrometry

Commonly Observed Background Ions in ESI

CRAPome: a contaminant repository for affinity purification mass spectrometry data