RBP identification by mass spectrometry

h1. Worm - RBP samples

Desired amounts:

* 100 ug protein amount for digestion

* 8-10 ug peptide amount for LC-MS/MS analysis

"X" indicates that the substance was added, "NA" that no information is available.

The excess columns show how much sample material was not used for analysis and is in a -80deg freezer.

The "Protein concentration [ug/ul]" shows the protein concentration in the aliquot from the sample preparation (also RNA measurement would be done on them).

Concentrations were measured using 280nm abs assay of a  nanodrop instrument.

h2. N2

|*Sample name*|*Worm culture*|*Protein concentration before RNAse treatment [ug/ul]*|*prepared by*|*RBP isolation date*|*Biological replicate*|*Is negative control*|*RBP protein yield [ug]*|*RBP protein excess[ug]*|*RBP peptide yield [ug]*|*RBP peptide excess [ug]*|*MS samples*|*MS analysis date*|*Technical replicates*|*4SU*|*XL*|*DMSO*|*Identified proteins*|*Notes*|

|NA|850 T|NA|Zisong|07/2014|1|No|NA|NA|4.6|NA|140729Li_QX1_Chang_N2_1400ng_01.raw

140729Li_QX1_Chang_N2_1400ng_02.raw

140729Li_QX1_Chang_N2_1400ng_03.raw|30/07/2014|3|X|X|NA|2390  

2363  

2353||

|1a|500 T|2|Puneet|22/01/2015|1|No|2000|1700|32|20|NA|NA|NA|X|X||NA||

|1b|200 T|2|Puneet|22/01/2015|1|No|900|720|26|13|NA|NA|NA|X|X||NA||

|1c|100 T|1|Puneet|22/01/2015|1|No|300|180|16|6|NA|NA|NA|X|X||NA||

|1d|50 T|0.6|Puneet|22/01/2015|1|No|100|0|17|7|NA|NA|NA|X|X||NA||

|2|500 T|2|Puneet|22/01/2015|1|Yes|2000|1800|36|23|NA|NA|NA||X|X|NA||

|3|200 T|2|Puneet|22/01/2015|1|Yes|850|680|18|7|NA|NA|NA|X||NA|NA|vhl-1 mutant|

h2. P6662

|*Sample name*|*Worm culture*|*Protein concentration [ug/ul]*|*prepared by*|*RBP isolation date*|*Biological replicate*|*Is negative control*|*RBP protein yield [ug]*|*RBP protein excess[ug]*|*RBP peptide yield [ug]*|*RBP peptide excess [ug]*|*MS samples name*|*MS analysis date*|*Technical replicates*|*4SU*|*XL*|*DMSO*|*Identified proteins*|*Notes*|

|NA|650 T|NA|Zisong|07/2014|1|No|NA|NA|4.2|NA|140729Li_QX1_Chang_PS6662_1250ng_01.raw

140729Li_QX1_Chang_PS6662_1250ng_02.raw

140729Li_QX1_Chang_PS6662_1250ng_03.raw|31/07/2014|3|X|X|NA|2226 

2199 

2173||

*------------------------------------------------------------------------------------------- Analysis in June 2015 -----------------------------------------------------------------------------------------------------------------*

h2. N2

|*Sample name*|*Worm culture*|*prepared by*|*RBP isolation date*|*Biological replicate*|*Is negative control*|*RBP protein yield [ug]*|*RBP protein excess[ug]*|*RBP peptide yield [ug]*|*RBP peptide excess [ug]*|*MS samples*|*MS analysis date*|*Technical replicates*|*4SU*|*XL*|*DMSO*|*Identified proteins*|*Notes*|

|NA|500 T|NA|Rene, 

Puneet, 

Francesca|06/2015|1|Yes|NA|NA|2.5|0|150609Li_Dieterich_N2minusCL|10/06/2015|1|X|||872||

|NA|500 T|NA|Rene, 

Puneet, 

Francesca|06/2015|1|No|NA|NA|4.5|0|150609Li_Dieterich_N2PlusCL.raw|10/06/2015|1|X|X||1186||

|NA|500 T|NA|Rene, 

Puneet, 

Francesca|06/2015|2|Yes|NA|NA|2.5|0|||1|X|||||

|NA|500 T|NA|Rene, 

Puneet, 

Francesca|06/2015|2|No|NA|NA|4.5|0|||1|X|X||||

h2. IMCD

|*Sample name*|*Cell culture*|*prepared by*|*RBP isolation date*|*Biological replicate*|*Is negative control*|*RBP protein yield [ug]*|*RBP protein excess[ug]*|*RBP peptide yield [ug]*|*RBP peptide excess [ug]*|*MS samples*|*MS analysis date*|*Technical replicates*|*4SU*|*XL*|*DMSO*|*Identified proteins*|*Notes*|

|NA|NA|Rene,  

Francesca|06/2015|1|Yes|NA|NA|60.4|0|150610Li_Dieterich_IMCD_Norm_minusCL_4ul.raw|11/06/2015|1|X|||728|Normoxia, 40% input|

|NA|NA|Rene, 

Francesca|06/2015|1|No|NA|NA|55.3|0|150610Li_Dieterich_IMCD_Norm_PlusCL_4ul.raw|12/06/2015|1|X|X||759|Normoxia, 40% input|

|NA|NA|Rene, 

Francesca|06/2015|1|Yes|NA|NA|50|0|150610Li_Dieterich_IMCD_Hyp_minusCL_4ul.raw|12/06/2015|1|X|||728|Hypoxia, 40% input|

|NA|NA|Rene, 

Francesca|06/2015|1|No|NA|NA|54|0|150610Li_Dieterich_IMCD_Hyp_PlusCL_4ul.raw|12/06/2015|1|X|X||786|Hypoxia, 40% input|