1. Evaluated Reference MS/MS Spectra Libraries Current and Future NIST Programs

2. NIST/EPA/NIH Library of EI Mass Spectra Search Program/Algorithms Archive Program Computer Assisted Evaluation

3. NIST MS/MS Library June 2005 - 5,191 Spectra –1,920 Precursor ions (incl. 292 Anions) From NIST, Contributors and literature Ion trap, Triple Quad, … New data structure/software –Energy and precursor ion variations –Evaluation/Search logic –Range of Energies (collision cell)

4. Archive Program – MS/MS Mode

5. Archive Program + MS Interpreter

6. NIST MS Search Program – MS/MS Library MW / Formula / Name / Conditions Levels

7. NIST Library of Peptide Ion Fragmentation Spectra Peptide sequences are used to infer proteins – from protein digests Derived from ‘Shotgun’ proteomics –Identifications originate from sequence-based search method Human, Yeast, Selected Proteins, … –90,000 Consensus spectra Ion trap and qtof spectra (tof/tof soon) of ESI and MALDI generated ions

8. Processing Pipeline From Raw data to Identified Proteins –Complex series of data transformations –Peptide sequences are identified by matching m/z values against all possible sequences Consensus spectra extracted from pipeline –New QA/QC methods Library re-inserted to pipeline for faster, more reliable, more sensitive IDs

9. Input list Matching peptide and probability scores Reference spectrum and annotation Query MS/MS Head to tail sample and reference spectra comparison

10. Fragmentation depends on energy/time FT-ICR –Lowest energies (SORI, IRMPD, SID, …) Ion Trap –Allows multiple stages of fragmentation Collision cell (Low E) –Dissociation increases with energy PSD –Low energy, limited energy/time Collision cell (High E) –Single collision, wide E distribution