Statement of Specs ONLY (Salient Characteristics).docx

Statement of Specifications

Salient/Key Requirements:

1) Acceptable size dimensions of no more than 275 cm in length x 100 cm in width x 260 cm in height for the equipment, potential key add-ons, and other key components combined. These dimensions are hard limits due to the physical size constraints of the space.

2) Power requirements. No more than 2x 220V plugs due to the power constraints of the lab.

3) Imaging mass spectrometer. We require the ability perform imaging mass spectrometry to look at molecules in 2D space.

4) Trapped ion mobility separation (TIMS).

a. We require the ability to assess the substance’s 3D shape in space (known as collisional cross section; CCS). Program needs to use this ability to measure CCS to distinguish between specific lipid isoforms, separate isobaric peptides, and identify unknown small molecules.

b. The equipment must be able to use the ion mobility with MALDI imaging.

c. The equipment must be able to use ion mobility with MALDI.

d. The equipment must be able to use the ion mobility with ESI and nanoESI.

e. The MS instrument must contain a dual trapped ion mobility spectrometry (TIMS) analyzer that delivers high ion mobility resolution with parallel accumulation– these features allow for samples to be sorted by CCS prior to time of flight (TOF) analysis while the next batch of ions is loaded. This will assure ion mobility can be performed with 100% duty cycle without losing sensitivity.

f. We require that the CCS and m/z be calibrated with the same calibrant reagent (e.g. one calibration compound(s) for both CCS and m/z), and that both of these calibrations can be applied across all compounds regardless of class.

5) High resolution QTOF.

a. TOF analysis must be high resolution with a resolving power greater than or equal to 60000 with full sensitivity resolution at m/z 1222.

b. We require that the instrument provide mass accuracy of <0.8ppm internally and 2 ppm externally calibrated. Coupled with CCS information from ion mobility, this will assure molecules are identified correctly.

c. The TOF analyzer must be able to acquire at equal to or greater than 300 Hz.

6) First-pass identification. We require mass spectrometer capable of first-pass identification that doesn’t require follow up evaluations in order to increase sample throughput. This first pass ID ability via ion mobility techniques allows high throughput screening of at least 20 true square pixels per seconds. First pass identification via ion mobility is required for high throughput that is needed for this project. We require the ability to run a lot of samples while being sure of the findings on the first run without requiring numerous second, more targeted runs relying on tandem mass spec.

7) Tandem mass spectrometry collision cell.

a. This instrument must have the ability to fragment ions in a collision cell.

b. Fragmenting ions is used as an additional identification parameter and is necessary for many mass spectrometry-based analyses.

c. Collision cell must be after ion mobility (TIMS) separation, so that mobility-separated ions can be fragmented and identified.

d. The quadrupole in front of the collision cell must be able to isolate ions with m/z values up to 3000, and pass ions up to m/z 40,000 without isolation.

8) MALDI laser specifications. We require that the MALDI laser:

a. Have a minimum laser spot size of 20 mm or smaller.

b. Have a square pixel for MALDI imaging, which prevents overlap/oversampling of the sample.

c. Have the ability to operate at greater than or equal to 10 kHz at its minimum focus (≤20 mm). This allows for high-throughput mass spectrometry analysis.

9) MALDI source specifications. We require that the MALDI source:

a. Allow for rapid switching between ESI and MALDI (<30 seconds), without physical hardware changes or venting of instrument. Venting the instrument delays instrument use and decreases sample throughput.

b. Have the ability to analyze a MALDI target with ≥1536 sample spots. We anticipate using MALDI for high-throughput analyses so a MALDI target with a large number of spots is necessary.

10) Bottom-up proteomics. We extensively use bottom-up proteomics and require that the mass spectrometer meet or exceed current bottom-up proteomics capabilities.

a. We require that the mass spectrometer should be able to identify >40,000 unique peptides in a single run from a complex mixture in order to perform bottom-up proteomics experiments.

b. This spec can be shown in a publication.

11) Native ESI. We require that the ability to perform native ESI experiments.

12) Include ultra-performance liquid chromatography instrument.

a. The UPLC must include an autosampler, pumps, column oven, and UV detector.

13) Nanospray Source.

a. The mass spectrometer must include a nanospray source to improve instrument sensitivity.

14) Compatible with Waters M-class HPLC.

a. The new MS instrument must provide software (not contact-closure) control of previously purchased and currently in use Waters M-class UPLC.

b. Coupled with the nanospray source, this allows for nano-scale separations.

15) The mass spectrometer software must provide.

a. Data format output that is compatible with third party software (Byos) to seamlessly integrate into current workflows.

b. Data analysis software that allows manual interpretation of mass spectrometry data.

c. Maximum Entropy deconvolution (or equivalent).

16) Real-time bottom-up proteomics data processing. We require that the instrument include software that allows real-time processing (e.g. data is processed while being acquired) of bottom-up proteomics data. This increases sample throughput by eliminating the need to manually set up and run data analysis.