Our responsibilities:<\/p>\n
- \n
- Providing you with comprehensive advice before you start your experiment, including clear assessments of costs and any risks associated with the analysis.<\/li>\n
- Giving facility inductions and training where required.<\/li>\n
- Providing a comprehensive protocol and all relevant reagents and consumables (some are chargeable).<\/li>\n
- Providing support during the experimental procedures where required.<\/li>\n
- Ensuring that analytical systems are functioning correctly and that the data produced is an accurate representation of the sample provided.<\/li>\n
- Providing feedback on the results, identifying issues if they occur and suggesting ways to address the issues if possible.<\/li>\n
- Providing access to the relevant data analysis software and providing training and advice where required.<\/li>\n
- Providing data analysis services where available and required (at extra cost)<\/li>\n<\/ul>\n
Factors effecting success<\/h2>\n
- \n
- The samples have an unusual composition. This may be the presence of a high level of contamination such as lipids or polymers, a high level of a subset of proteins or unusual mechanical properties such as a high fibrous content.<\/li>\n
- Inadequate choice of control whereby it is significantly different to the samples it compares to.<\/li>\n
- The availability of a reference protein sequence library. You ideally need to working in a biological system that has a full protein library or has a closely related species that does. Please note we require a protein sequence library (proteome) \u2013 a sequenced genome is not sufficient as the translation from genetic sequence to protein sequence is non-trivial.<\/li>\n<\/ul>\n
Protocol<\/h2>\n
The latest comprehensive protocol is available in the facility.<\/p>\n
Methods involved<\/h2>\n
Covaris disruption of protein samples before S-Trap sample preparation<\/u><\/p>\n
S-Trap based sample preparation for protein analysis<\/u><\/p>\n
Mass spectrometry based quantitative analysis of peptides samples<\/u><\/p>\n
Quantitative analysis of peptide based mass spectrometry data using Proteome Discoverer<\/u><\/p>\n
\u00a0[RO1]<\/a>Does this comment refer to R3? Overall I would bet that it is the S-trap method that removes the bulk non-protein derived material, most other labs inject directly after S-trap processing, we do it as a polishing step, and I guess because we do not have a trap on our LC systems.<\/p>\n
\u00a0[RO2]<\/a>I would emphasis this aspect of sample submission.<\/p>\n
For this I would say that the samples on submission must meet the minimum criteria for acceptance, these include PPMS order number, samples dried down in vials, and a sample manifest number, with a manifest that makes sense. The organism from which the smaples are to be searched against, any consideration of run order, carry-over and so on.<\/p>\n
\u00a0<\/p>\n
\u00a0<\/p>\n
\u00a0[RO3]<\/a>Following on from this, we would then ensure that Upon arrival to the laboratory, the samples and their accompanying request form are checked to ensure they meet the minimum criteria for acceptance. Staff ensure\u00a0that the names on form and LCMS vials match and that the correct type of vial is received<\/p>\n
Tags: #workflows, s-trap<\/p>\n
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Contact the Facility Manager:<\/strong>
Dr David Knight
david.knight@manchester.ac.uk <\/a>
+44 (0) 161 275 1394<\/p>\nContact the whole facility:<\/strong>
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+44 (0) 161 275 6916<\/p>\n\u00a0<\/p>\n
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